Long Tests report for BioC 3.22 - CHECK results for biodbNcbi on merida1

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo2	Linux (Ubuntu 24.04.3 LTS)	x86_64	4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"	4888
merida1	macOS 12.7.6 Monterey	x86_64	4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"	4678
Click on any hostname to see more info about the system (e.g. compilers) () as reported by 'uname -p', except on Windows and Mac OS X*

CHECK results for biodbNcbi on merida1

To the developers/maintainers of the biodbNcbi package:
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results

Summary

Package: biodbNcbi

Version: 1.14.0

Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --test-dir=longtests --no-stop-on-test-error --no-codoc --no-examples --no-manual --ignore-vignettes --check-subdirs=no biodbNcbi_1.14.0.tar.gz

StartedAt: 2026-01-31 16:01:16 -0500 (Sat, 31 Jan 2026)

EndedAt: 2026-01-31 16:02:27 -0500 (Sat, 31 Jan 2026)

EllapsedTime: 71.0 seconds

RetCode: 1

Status: ERROR

CheckDir: biodbNcbi.Rcheck

Warnings: NA

Tests output

biodbNcbi.Rcheck/tests/testthat.Rout.fail


R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"
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Platform: x86_64-apple-darwin20

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> # Script needed to run testthat automatically from ‘R CMD check’. See
> # testthat::test_dir documentation.
> library(testthat)
> library(biodbNci)
Warning message:
In fun(libname, pkgname) :
  Package 'biodbNci' is deprecated and will be removed from Bioconductor
  version 3.23
> Sys.setenv(TESTTHAT_REPORTER="summary")
> Sys.setenv(BIODB_LOG_DST="console")
> test_check("biodbNcbi")
Loading required package: biodbNcbi
biodb.INFO [2026-01-31 16:02:14.038][biodb::testContext]
biodb.INFO [2026-01-31 16:02:14.042][biodb::testContext] ********************************************************************************
biodb.INFO [2026-01-31 16:02:14.043][biodb::testContext] Test context - CCDS long tests
biodb.INFO [2026-01-31 16:02:14.045][biodb::testContext] ********************************************************************************
biodb.INFO [2026-01-31 16:02:14.046][biodb::testContext]
biodb.INFO [2026-01-31 16:02:14.052][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.18.0.
biodb.DEBUG[2026-01-31 16:02:14.054][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2026-01-31 16:02:14.062][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2026-01-31 16:02:14.063][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2026-01-31 16:02:14.064][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2026-01-31 16:02:14.066][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:14.067][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:14.068][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:02:14.069][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2026-01-31 16:02:14.093][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2026-01-31 16:02:14.095][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:14.096][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:14.097][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:02:14.098][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2026-01-31 16:02:14.100][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2026-01-31 16:02:14.101][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:14.102][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:14.103][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:02:14.104][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2026-01-31 16:02:14.106][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2026-01-31 16:02:14.107][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2026-01-31 16:02:14.108][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:14.109][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:14.110][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:02:14.111][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2026-01-31 16:02:14.113][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2026-01-31 16:02:14.114][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2026-01-31 16:02:14.115][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:14.116][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:14.117][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:02:14.119][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2026-01-31 16:02:14.120][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2026-01-31 16:02:14.121][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:14.122][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:14.123][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:02:14.124][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2026-01-31 16:02:14.126][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2026-01-31 16:02:14.127][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2026-01-31 16:02:14.128][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:14.129][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:14.130][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:02:14.132][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2026-01-31 16:02:14.133][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2026-01-31 16:02:14.134][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:14.135][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:14.136][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:02:14.138][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2026-01-31 16:02:14.139][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2026-01-31 16:02:14.140][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2026-01-31 16:02:14.141][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:14.143][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:14.144][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:02:14.145][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2026-01-31 16:02:14.146][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2026-01-31 16:02:14.148][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2026-01-31 16:02:14.149][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2026-01-31 16:02:14.150][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2026-01-31 16:02:14.152][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2026-01-31 16:02:14.153][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:14.154][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:14.155][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:02:14.156][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2026-01-31 16:02:14.158][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2026-01-31 16:02:14.159][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:14.160][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:14.161][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:02:14.162][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2026-01-31 16:02:14.164][self$set] Set key entries.sep to "|".
biodb.DEBUG[2026-01-31 16:02:14.165][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:14.166][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:14.167][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:02:14.168][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2026-01-31 16:02:14.170][self$set] Set key offline to FALSE.
biodb.DEBUG[2026-01-31 16:02:14.171][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:14.172][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:14.173][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:02:14.174][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2026-01-31 16:02:14.176][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2026-01-31 16:02:14.177][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2026-01-31 16:02:14.178][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:14.179][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:14.180][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:02:14.182][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2026-01-31 16:02:14.183][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2026-01-31 16:02:14.194][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2026-01-31 16:02:14.195][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:14.196][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:14.197][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:02:14.199][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2026-01-31 16:02:14.200][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2026-01-31 16:02:14.201][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2026-01-31 16:02:14.202][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:14.204][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:14.205][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:02:14.209][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2026-01-31 16:02:14.259][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2026-01-31 16:02:14.281][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2026-01-31 16:02:14.282][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-01-31 16:02:14.283][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-01-31 16:02:14.285][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-01-31 16:02:14.286][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-01-31 16:02:14.287][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2026-01-31 16:02:14.288][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-01-31 16:02:14.290][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2026-01-31 16:02:14.291][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-01-31 16:02:14.292][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2026-01-31 16:02:14.293][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2026-01-31 16:02:14.295][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-01-31 16:02:14.296][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2026-01-31 16:02:14.297][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2026-01-31 16:02:14.298][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2026-01-31 16:02:14.298][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2026-01-31 16:02:14.298][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2026-01-31 16:02:14.298][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2026-01-31 16:02:14.298][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2026-01-31 16:02:14.300][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2026-01-31 16:02:14.301][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-01-31 16:02:14.302][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-01-31 16:02:14.303][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-01-31 16:02:14.305][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-01-31 16:02:14.306][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-01-31 16:02:14.307][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-01-31 16:02:14.308][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2026-01-31 16:02:14.309][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-01-31 16:02:14.311][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-01-31 16:02:14.312][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2026-01-31 16:02:14.313][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-01-31 16:02:14.315][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2026-01-31 16:02:14.317][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2026-01-31 16:02:14.318][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2026-01-31 16:02:14.319][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-01-31 16:02:14.321][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-01-31 16:02:14.322][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-01-31 16:02:14.323][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-01-31 16:02:14.324][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2026-01-31 16:02:14.326][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-01-31 16:02:14.327][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2026-01-31 16:02:14.328][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-01-31 16:02:14.329][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2026-01-31 16:02:14.331][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2026-01-31 16:02:14.332][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-01-31 16:02:14.333][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2026-01-31 16:02:14.334][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2026-01-31 16:02:14.336][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2026-01-31 16:02:14.336][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2026-01-31 16:02:14.336][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2026-01-31 16:02:14.336][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2026-01-31 16:02:14.336][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2026-01-31 16:02:14.337][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2026-01-31 16:02:14.338][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-01-31 16:02:14.339][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-01-31 16:02:14.341][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-01-31 16:02:14.342][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-01-31 16:02:14.343][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-01-31 16:02:14.344][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-01-31 16:02:14.346][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2026-01-31 16:02:14.347][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-01-31 16:02:14.348][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-01-31 16:02:14.349][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2026-01-31 16:02:14.350][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-01-31 16:02:14.352][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2026-01-31 16:02:14.354][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2026-01-31 16:02:14.355][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2026-01-31 16:02:14.357][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-01-31 16:02:14.358][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-01-31 16:02:14.359][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-01-31 16:02:14.360][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-01-31 16:02:14.362][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2026-01-31 16:02:14.363][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-01-31 16:02:14.364][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2026-01-31 16:02:14.366][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-01-31 16:02:14.367][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2026-01-31 16:02:14.368][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2026-01-31 16:02:14.370][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-01-31 16:02:14.371][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2026-01-31 16:02:14.372][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2026-01-31 16:02:14.373][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2026-01-31 16:02:14.375][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2026-01-31 16:02:14.376][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-01-31 16:02:14.377][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-01-31 16:02:14.378][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-01-31 16:02:14.379][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-01-31 16:02:14.380][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-01-31 16:02:14.382][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-01-31 16:02:14.383][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2026-01-31 16:02:14.384][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-01-31 16:02:14.385][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-01-31 16:02:14.387][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2026-01-31 16:02:14.388][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-01-31 16:02:14.389][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2026-01-31 16:02:14.392][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2026-01-31 16:02:14.393][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2026-01-31 16:02:14.394][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-01-31 16:02:14.396][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-01-31 16:02:14.397][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-01-31 16:02:14.398][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-01-31 16:02:14.399][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2026-01-31 16:02:14.401][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-01-31 16:02:14.402][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2026-01-31 16:02:14.403][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-01-31 16:02:14.404][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2026-01-31 16:02:14.406][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2026-01-31 16:02:14.407][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-01-31 16:02:14.408][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2026-01-31 16:02:14.409][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2026-01-31 16:02:14.411][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2026-01-31 16:02:14.412][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2026-01-31 16:02:14.413][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-01-31 16:02:14.414][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-01-31 16:02:14.416][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-01-31 16:02:14.417][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-01-31 16:02:14.418][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-01-31 16:02:14.419][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-01-31 16:02:14.421][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2026-01-31 16:02:14.422][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-01-31 16:02:14.423][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-01-31 16:02:14.424][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2026-01-31 16:02:14.425][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-01-31 16:02:14.429][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2026-01-31 16:02:14.431][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:14.432][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:02:14.433][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:14.434][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-31 16:02:14.436][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-31 16:02:14.437][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:14.438][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:02:14.439][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:14.440][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-31 16:02:14.441][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-31 16:02:14.442][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:14.444][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:02:14.445][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:14.446][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-31 16:02:14.447][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-31 16:02:14.448][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:14.449][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:02:14.450][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:14.452][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-31 16:02:14.453][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-31 16:02:14.454][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:14.455][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:02:14.456][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:14.457][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-31 16:02:14.458][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-31 16:02:14.460][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:14.461][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:02:14.462][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:14.463][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-31 16:02:14.464][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-31 16:02:14.465][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:14.467][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:02:14.468][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:14.469][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-31 16:02:14.470][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-31 16:02:14.471][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:14.472][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:02:14.473][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:14.475][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-31 16:02:14.476][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-31 16:02:14.477][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:14.478][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:02:14.479][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:14.481][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-31 16:02:14.482][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-31 16:02:14.483][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:14.484][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:02:14.485][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:14.486][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-31 16:02:14.487][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-31 16:02:14.488][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:14.489][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:02:14.491][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:14.492][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-31 16:02:14.493][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-31 16:02:14.494][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:14.495][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:02:14.496][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:14.497][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-31 16:02:14.498][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-31 16:02:14.499][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:14.501][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:02:14.502][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:14.503][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-31 16:02:14.504][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-31 16:02:14.505][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:14.506][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:02:14.507][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:14.508][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-31 16:02:14.509][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-31 16:02:14.510][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:14.512][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:02:14.513][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:14.518][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-31 16:02:14.519][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-31 16:02:14.520][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:14.522][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:02:14.523][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:14.524][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-31 16:02:14.525][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-31 16:02:14.526][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:14.527][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:02:14.528][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2026-01-31 16:02:14.533][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2026-01-31 16:02:14.535][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2026-01-31 16:02:14.536][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2026-01-31 16:02:14.538][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2026-01-31 16:02:14.540][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2026-01-31 16:02:14.542][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2026-01-31 16:02:14.543][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2026-01-31 16:02:14.545][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2026-01-31 16:02:14.547][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2026-01-31 16:02:14.548][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2026-01-31 16:02:14.550][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2026-01-31 16:02:14.552][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2026-01-31 16:02:14.553][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2026-01-31 16:02:14.555][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2026-01-31 16:02:14.557][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2026-01-31 16:02:14.559][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2026-01-31 16:02:14.560][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2026-01-31 16:02:14.562][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2026-01-31 16:02:14.564][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2026-01-31 16:02:14.566][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2026-01-31 16:02:14.567][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2026-01-31 16:02:14.569][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2026-01-31 16:02:14.571][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2026-01-31 16:02:14.572][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2026-01-31 16:02:14.574][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2026-01-31 16:02:14.576][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2026-01-31 16:02:14.578][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2026-01-31 16:02:14.579][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2026-01-31 16:02:14.581][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2026-01-31 16:02:14.583][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2026-01-31 16:02:14.585][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2026-01-31 16:02:14.586][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2026-01-31 16:02:14.588][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2026-01-31 16:02:14.590][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2026-01-31 16:02:14.591][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2026-01-31 16:02:14.593][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2026-01-31 16:02:14.595][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2026-01-31 16:02:14.597][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2026-01-31 16:02:14.598][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2026-01-31 16:02:14.600][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2026-01-31 16:02:14.602][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2026-01-31 16:02:14.603][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2026-01-31 16:02:14.605][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2026-01-31 16:02:14.607][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2026-01-31 16:02:14.609][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2026-01-31 16:02:14.610][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2026-01-31 16:02:14.612][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2026-01-31 16:02:14.614][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2026-01-31 16:02:14.615][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2026-01-31 16:02:14.617][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2026-01-31 16:02:14.619][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2026-01-31 16:02:14.620][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2026-01-31 16:02:14.622][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2026-01-31 16:02:14.624][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2026-01-31 16:02:14.626][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2026-01-31 16:02:14.627][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2026-01-31 16:02:14.629][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2026-01-31 16:02:14.631][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2026-01-31 16:02:14.633][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2026-01-31 16:02:14.634][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2026-01-31 16:02:14.636][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2026-01-31 16:02:14.638][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2026-01-31 16:02:14.640][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2026-01-31 16:02:14.641][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2026-01-31 16:02:14.643][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2026-01-31 16:02:14.645][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2026-01-31 16:02:14.646][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2026-01-31 16:02:14.648][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2026-01-31 16:02:14.650][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2026-01-31 16:02:14.652][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2026-01-31 16:02:14.653][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2026-01-31 16:02:14.655][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2026-01-31 16:02:14.657][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2026-01-31 16:02:14.658][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2026-01-31 16:02:14.660][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2026-01-31 16:02:14.662][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2026-01-31 16:02:14.664][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2026-01-31 16:02:14.665][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2026-01-31 16:02:14.667][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2026-01-31 16:02:14.669][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2026-01-31 16:02:14.670][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2026-01-31 16:02:14.672][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2026-01-31 16:02:14.680][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2026-01-31 16:02:14.682][initialize] This is biodb version 1.18.0.
biodb.DEBUG[2026-01-31 16:02:14.685][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2026-01-31 16:02:14.686][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2026-01-31 16:02:14.687][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-31 16:02:14.688][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:14.689][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:02:14.695][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:14.697][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-01-31 16:02:14.698][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-01-31 16:02:14.699][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-31 16:02:14.700][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-31 16:02:14.701][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:14.702][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:02:14.703][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:14.704][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-01-31 16:02:14.705][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-01-31 16:02:14.707][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-31 16:02:14.708][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-31 16:02:14.709][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:14.710][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:02:14.711][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:14.712][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-01-31 16:02:14.713][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-01-31 16:02:14.714][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-31 16:02:14.715][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-31 16:02:14.717][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:14.718][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:02:14.719][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:14.720][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-01-31 16:02:14.721][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-01-31 16:02:14.722][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-31 16:02:14.723][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-31 16:02:14.725][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:14.726][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:02:14.727][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:14.728][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-01-31 16:02:14.729][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-01-31 16:02:14.730][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-31 16:02:14.731][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-31 16:02:14.733][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:14.734][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:02:14.735][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:14.736][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-01-31 16:02:14.737][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-01-31 16:02:14.738][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-31 16:02:14.739][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-31 16:02:14.741][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:14.742][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:02:14.743][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:14.744][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-01-31 16:02:14.745][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-01-31 16:02:14.746][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-31 16:02:14.747][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-31 16:02:14.748][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:14.750][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:02:14.751][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:14.752][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-01-31 16:02:14.753][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-01-31 16:02:14.754][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-31 16:02:14.755][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-31 16:02:14.756][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:14.758][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:02:14.759][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:14.760][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-01-31 16:02:14.761][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-01-31 16:02:14.762][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-31 16:02:14.763][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-31 16:02:14.764][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:14.766][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:02:14.772][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:14.773][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-01-31 16:02:14.774][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-01-31 16:02:14.775][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-31 16:02:14.777][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-31 16:02:14.778][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:14.779][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:02:14.780][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:14.781][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-01-31 16:02:14.782][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-01-31 16:02:14.783][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-31 16:02:14.784][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-31 16:02:14.785][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:14.787][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:02:14.788][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:14.789][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-01-31 16:02:14.790][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-01-31 16:02:14.791][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-31 16:02:14.792][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-31 16:02:14.793][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:14.794][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:02:14.796][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:14.797][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-01-31 16:02:14.798][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-01-31 16:02:14.799][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-31 16:02:14.800][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-31 16:02:14.801][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:14.802][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:02:14.803][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:14.804][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-01-31 16:02:14.806][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-01-31 16:02:14.807][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-31 16:02:14.808][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-31 16:02:14.809][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:14.810][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:02:14.811][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:14.812][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-01-31 16:02:14.814][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-01-31 16:02:14.815][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-31 16:02:14.816][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-31 16:02:14.817][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:14.818][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:02:14.819][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:14.820][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-01-31 16:02:14.821][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-01-31 16:02:14.823][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-31 16:02:14.824][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-31 16:02:14.825][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:14.826][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:02:14.829][bdb$loadDefinitions] Load definitions from file "/Users/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNcbi.Rcheck/biodbNcbi/definitions.yml".
biodb.DEBUG[2026-01-31 16:02:14.842][self$getDbsInfo()$define] Define connector ncbi.ccds.
biodb.DEBUG[2026-01-31 16:02:14.845][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2026-01-31 16:02:14.846][self$setPropertyValue] Setting property "description" to "NCBI CCDS database.".
biodb.DEBUG[2026-01-31 16:02:14.848][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-01-31 16:02:14.849][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-01-31 16:02:14.850][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-01-31 16:02:14.852][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-01-31 16:02:14.853][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2026-01-31 16:02:14.854][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-01-31 16:02:14.856][self$setPropertyValue] Setting property "entry.content.type" to "html".
biodb.DEBUG[2026-01-31 16:02:14.857][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-01-31 16:02:14.858][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2026-01-31 16:02:14.860][self$setPropertyValue] Setting property "name" to "NCBI CCDS".
biodb.DEBUG[2026-01-31 16:02:14.861][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-01-31 16:02:14.862][self$setPropertyValue] Setting property "parsing.expr" to "list(attr = "value", path = "//input[@id='DATA']")".
biodb.DEBUG[2026-01-31 16:02:14.862][self$setPropertyValue] Setting property "parsing.expr" to "//b[starts-with(.,'Nucleotide Sequence')]/../tt".
biodb.DEBUG[2026-01-31 16:02:14.863][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2026-01-31 16:02:14.865][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2026-01-31 16:02:14.866][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2026-01-31 16:02:14.867][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-01-31 16:02:14.868][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-01-31 16:02:14.870][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-01-31 16:02:14.871][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-01-31 16:02:14.872][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-01-31 16:02:14.874][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-01-31 16:02:14.875][self$setPropertyValue] Setting property "urls" to "https://www.ncbi.nlm.nih.gov/CCDS/".
biodb.DEBUG[2026-01-31 16:02:14.875][self$setPropertyValue] Setting property "urls" to "https://eutils.ncbi.nlm.nih.gov/entrez/eutils".
biodb.DEBUG[2026-01-31 16:02:14.876][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-01-31 16:02:14.877][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-01-31 16:02:14.878][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2026-01-31 16:02:14.880][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-01-31 16:02:14.882][self$getDbsInfo()$define] Define connector ncbi.gene.
biodb.DEBUG[2026-01-31 16:02:14.884][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2026-01-31 16:02:14.886][self$setPropertyValue] Setting property "description" to "NCBI Gene database.".
biodb.DEBUG[2026-01-31 16:02:14.887][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-01-31 16:02:14.889][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-01-31 16:02:14.890][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-01-31 16:02:14.891][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-01-31 16:02:14.893][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2026-01-31 16:02:14.894][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-01-31 16:02:14.896][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2026-01-31 16:02:14.897][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-01-31 16:02:14.899][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2026-01-31 16:02:14.900][self$setPropertyValue] Setting property "name" to "NCBI Gene".
biodb.DEBUG[2026-01-31 16:02:14.901][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-01-31 16:02:14.903][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-track_geneid".
biodb.DEBUG[2026-01-31 16:02:14.903][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-ref_desc".
biodb.DEBUG[2026-01-31 16:02:14.903][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-ref_maploc".
biodb.DEBUG[2026-01-31 16:02:14.903][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-ref_locus".
biodb.DEBUG[2026-01-31 16:02:14.903][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-ref_syn_E".
biodb.DEBUG[2026-01-31 16:02:14.903][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-commentary_heading[text()='UniProtKB']/..//Dbtag_db[text()='UniProtKB/Swiss-Prot']/..//Object-id_str".
biodb.DEBUG[2026-01-31 16:02:14.904][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2026-01-31 16:02:14.905][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2026-01-31 16:02:14.907][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2026-01-31 16:02:14.908][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-01-31 16:02:14.909][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-01-31 16:02:14.910][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-01-31 16:02:14.911][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-01-31 16:02:14.912][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-01-31 16:02:14.914][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-01-31 16:02:14.915][self$setPropertyValue] Setting property "urls" to "https://www.ncbi.nlm.nih.gov/".
biodb.DEBUG[2026-01-31 16:02:14.915][self$setPropertyValue] Setting property "urls" to "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/".
biodb.DEBUG[2026-01-31 16:02:14.916][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-01-31 16:02:14.917][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-01-31 16:02:14.919][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2026-01-31 16:02:14.920][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-01-31 16:02:14.921][self$getDbsInfo()$define] Define connector ncbi.pubchem.comp.
biodb.DEBUG[2026-01-31 16:02:14.924][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2026-01-31 16:02:14.925][self$setPropertyValue] Setting property "description" to "PubChem Compound database.".
biodb.DEBUG[2026-01-31 16:02:14.926][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-01-31 16:02:14.928][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-01-31 16:02:14.929][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-01-31 16:02:14.930][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-01-31 16:02:14.931][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2026-01-31 16:02:14.933][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-01-31 16:02:14.934][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2026-01-31 16:02:14.935][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-01-31 16:02:14.936][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2026-01-31 16:02:14.938][self$setPropertyValue] Setting property "name" to "PubChem Compound".
biodb.DEBUG[2026-01-31 16:02:14.939][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-01-31 16:02:14.940][self$setPropertyValue] Setting property "parsing.expr" to "//PC-CompoundType_id_cid".
biodb.DEBUG[2026-01-31 16:02:14.940][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='Allowed']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-01-31 16:02:14.940][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='CAS-like Style']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-01-31 16:02:14.940][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='Preferred']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-01-31 16:02:14.940][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='Systematic']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-01-31 16:02:14.940][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='Traditional']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-01-31 16:02:14.940][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='Mass']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-01-31 16:02:14.940][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='Molecular Formula']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-01-31 16:02:14.940][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='InChI']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-01-31 16:02:14.940][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='InChIKey']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-01-31 16:02:14.940][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='Log P']/../../..//PC-InfoData_value_fval".
biodb.DEBUG[2026-01-31 16:02:14.940][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='Molecular Weight']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-01-31 16:02:14.940][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='SMILES']/../PC-Urn_name[text()='Canonical']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-01-31 16:02:14.940][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='SMILES']/../PC-Urn_name[text()='Isomeric']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-01-31 16:02:14.942][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2026-01-31 16:02:14.943][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2026-01-31 16:02:14.943][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2026-01-31 16:02:14.943][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2026-01-31 16:02:14.944][self$setPropertyValue] Setting property "scheduler.n" to "5".
biodb.DEBUG[2026-01-31 16:02:14.946][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-01-31 16:02:14.947][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-01-31 16:02:14.948][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-01-31 16:02:14.949][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-01-31 16:02:14.950][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-01-31 16:02:14.952][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-01-31 16:02:14.953][self$setPropertyValue] Setting property "urls" to "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2026-01-31 16:02:14.953][self$setPropertyValue] Setting property "urls" to "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/".
biodb.DEBUG[2026-01-31 16:02:14.953][self$setPropertyValue] Setting property "urls" to "https://pubchem.ncbi.nlm.nih.gov/rest/pug/".
biodb.DEBUG[2026-01-31 16:02:14.954][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-01-31 16:02:14.955][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-01-31 16:02:14.956][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2026-01-31 16:02:14.958][self$setPropertyValue] Setting property "xml.ns" to "http://www.ncbi.nlm.nih.gov".
biodb.DEBUG[2026-01-31 16:02:14.959][self$getDbsInfo()$define] Define connector ncbi.pubchem.subst.
biodb.DEBUG[2026-01-31 16:02:14.962][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2026-01-31 16:02:14.963][self$setPropertyValue] Setting property "description" to "PubChem Substance database.".
biodb.DEBUG[2026-01-31 16:02:14.964][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-01-31 16:02:14.966][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-01-31 16:02:14.967][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-01-31 16:02:14.968][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-01-31 16:02:14.969][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2026-01-31 16:02:14.971][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-01-31 16:02:14.972][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2026-01-31 16:02:14.973][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-01-31 16:02:14.974][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2026-01-31 16:02:14.976][self$setPropertyValue] Setting property "name" to "PubChem Substance".
biodb.DEBUG[2026-01-31 16:02:14.977][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-01-31 16:02:14.978][self$setPropertyValue] Setting property "parsing.expr" to "//PC-ID_id".
biodb.DEBUG[2026-01-31 16:02:14.978][self$setPropertyValue] Setting property "parsing.expr" to "//PC-CompoundType_id_cid".
biodb.DEBUG[2026-01-31 16:02:14.979][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2026-01-31 16:02:14.981][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2026-01-31 16:02:14.982][self$setPropertyValue] Setting property "scheduler.n" to "5".
biodb.DEBUG[2026-01-31 16:02:14.983][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-01-31 16:02:14.984][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-01-31 16:02:14.986][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-01-31 16:02:14.987][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-01-31 16:02:14.988][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-01-31 16:02:14.989][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-01-31 16:02:14.990][self$setPropertyValue] Setting property "urls" to "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2026-01-31 16:02:14.990][self$setPropertyValue] Setting property "urls" to "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/".
biodb.DEBUG[2026-01-31 16:02:14.990][self$setPropertyValue] Setting property "urls" to "https://pubchem.ncbi.nlm.nih.gov/rest/pug/".
biodb.DEBUG[2026-01-31 16:02:14.992][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-01-31 16:02:14.993][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-01-31 16:02:14.994][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2026-01-31 16:02:14.995][self$setPropertyValue] Setting property "xml.ns" to "http://www.ncbi.nlm.nih.gov".
biodb.DEBUG[2026-01-31 16:02:15.003][self$getEntryFields()$define] Define field ncbi.ccds.id.
biodb.DEBUG[2026-01-31 16:02:15.005][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2026-01-31 16:02:15.007][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2026-01-31 16:02:15.009][self$getEntryFields()$define] Define field ncbi.pubchem.subst.id.
biodb.DEBUG[2026-01-31 16:02:15.011][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2026-01-31 16:02:15.013][self$getEntryFields()$define] Define field uniprot.id.
biodb.DEBUG[2026-01-31 16:02:15.039][initialize] Initialize connector ncbi.ccds.
biodb.DEBUG[2026-01-31 16:02:15.053][bdb$getFactory()$createConn] Creating new connector ncbi.ccds for database class ncbi.ccds .
biodb.INFO [2026-01-31 16:02:15.063][biodb::testThat]
biodb.INFO [2026-01-31 16:02:15.065][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2026-01-31 16:02:15.066][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-01-31 16:02:15.067][biodb::testThat]
biodb.TRACE[2026-01-31 16:02:15.072][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNcbi.Rcheck/biodbNcbi/testref/entry-ncbi.ccds-CCDS12227.1-content.html".
biodb.DEBUG[2026-01-31 16:02:15.074][biodb$getFactory()$createEntryFromCo ...] Creating NCBI CCDS entries from 1 content(s).
biodb.DEBUG[2026-01-31 16:02:15.078][biodb$getFactory()$createEntryFromCo ...] Parsing 1 NCBI CCDS entries.
biodb.DEBUG[2026-01-31 16:02:15.086][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2026-01-31 16:02:15.088][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2026-01-31 16:02:15.089][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-01-31 16:02:15.104][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2026-01-31 16:02:15.106][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-31 16:02:15.107][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:15.108][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2026-01-31 16:02:15.145][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-31 16:02:15.146][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-31 16:02:15.147][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:15.149][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:15.150][ef$get] Asked field names are: sequence.
biodb.TRACE[2026-01-31 16:02:15.167][ef$get] Realnames of fields are: aa.seq.
biodb.TRACE[2026-01-31 16:02:15.168][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:15.170][ef$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:15.206][self$getBiodb()$getEntryFields()$get] Asked field names are: sequence.
biodb.TRACE[2026-01-31 16:02:15.208][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2026-01-31 16:02:15.209][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:15.210][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:15.212][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2026-01-31 16:02:15.213][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2026-01-31 16:02:15.214][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:15.216][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:15.217][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2026-01-31 16:02:15.218][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2026-01-31 16:02:15.219][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:15.221][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:15.222][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-31 16:02:15.223][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-31 16:02:15.225][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:15.226][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:15.227][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2026-01-31 16:02:15.228][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2026-01-31 16:02:15.230][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:15.231][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:15.232][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-31 16:02:15.234][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-31 16:02:15.235][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:15.236][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:15.237][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-31 16:02:15.239][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-31 16:02:15.240][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:15.241][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:15.243][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-31 16:02:15.244][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-31 16:02:15.245][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:15.247][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:15.304][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-31 16:02:15.305][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-31 16:02:15.307][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:15.308][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:15.309][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-31 16:02:15.310][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-31 16:02:15.312][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:15.313][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:15.314][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-31 16:02:15.315][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-31 16:02:15.317][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:15.318][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2026-01-31 16:02:15.319][biodb$getFactory()$createEntryFromCo ...] Accession numbers: CCDS12227.1.
biodb.TRACE[2026-01-31 16:02:15.322][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2026-01-31 16:02:15.323][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2026-01-31 16:02:15.325][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:15.326][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:15.327][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2026-01-31 16:02:15.328][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2026-01-31 16:02:15.330][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:15.331][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:15.363][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2026-01-31 16:02:15.365][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2026-01-31 16:02:15.366][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:15.367][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:15.368][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2026-01-31 16:02:15.370][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2026-01-31 16:02:15.371][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:15.372][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:15.373][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2026-01-31 16:02:15.375][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2026-01-31 16:02:15.376][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:15.377][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:15.378][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2026-01-31 16:02:15.380][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2026-01-31 16:02:15.381][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:15.382][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:15.385][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-31 16:02:15.386][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-31 16:02:15.387][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:15.388][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:15.406][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2026-01-31 16:02:15.407][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2026-01-31 16:02:15.409][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:15.410][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:15.416][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-31 16:02:15.418][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-31 16:02:15.419][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:15.420][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:15.422][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-31 16:02:15.423][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-31 16:02:15.424][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:15.425][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:15.427][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-31 16:02:15.428][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-31 16:02:15.429][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:15.430][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:15.434][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-31 16:02:15.435][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-31 16:02:15.437][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:15.438][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:15.439][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-31 16:02:15.440][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-31 16:02:15.442][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:15.443][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:15.444][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-31 16:02:15.445][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-31 16:02:15.447][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:15.448][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:15.449][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2026-01-31 16:02:15.451][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2026-01-31 16:02:15.452][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:15.453][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:15.454][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2026-01-31 16:02:15.456][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2026-01-31 16:02:15.457][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:15.458][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:15.459][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2026-01-31 16:02:15.461][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2026-01-31 16:02:15.462][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:15.463][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:15.473][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-31 16:02:15.474][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-31 16:02:15.475][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:15.476][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:15.478][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-31 16:02:15.479][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-31 16:02:15.480][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:15.481][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:15.483][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-31 16:02:15.484][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-31 16:02:15.485][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:15.487][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:15.488][ef$get] Asked field names are: accession.
biodb.TRACE[2026-01-31 16:02:15.489][ef$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-31 16:02:15.490][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:15.492][ef$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:15.493][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-31 16:02:15.494][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-31 16:02:15.495][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:15.497][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:15.513][self$getBiodb()$getEntryFields()$get] Asked field names are: sequence.
biodb.TRACE[2026-01-31 16:02:15.515][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2026-01-31 16:02:15.516][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:15.517][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:15.519][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2026-01-31 16:02:15.520][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2026-01-31 16:02:15.521][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:15.522][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:15.524][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2026-01-31 16:02:15.525][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2026-01-31 16:02:15.526][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:15.527][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:15.529][ef$get] Asked field names are: sequence.
biodb.TRACE[2026-01-31 16:02:15.530][ef$get] Realnames of fields are: aa.seq.
biodb.TRACE[2026-01-31 16:02:15.531][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:15.533][ef$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:15.534][self$getBiodb()$getEntryFields()$get] Asked field names are: sequence.
biodb.TRACE[2026-01-31 16:02:15.535][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2026-01-31 16:02:15.536][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:15.538][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:15.549][ef$get] Asked field names are: aa.seq.
biodb.TRACE[2026-01-31 16:02:15.551][ef$get] Realnames of fields are: aa.seq.
biodb.TRACE[2026-01-31 16:02:15.552][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:15.553][ef$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:15.559][ef$get] Asked field names are: accession.
biodb.TRACE[2026-01-31 16:02:15.561][ef$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-31 16:02:15.562][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:15.563][ef$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:15.586][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNcbi.Rcheck/biodbNcbi/testref/entry-ncbi.ccds-CCDS43240.1-content.html".
biodb.DEBUG[2026-01-31 16:02:15.634][biodb$getFactory()$createEntryFromCo ...] Creating NCBI CCDS entries from 1 content(s).
biodb.DEBUG[2026-01-31 16:02:15.636][biodb$getFactory()$createEntryFromCo ...] Parsing 1 NCBI CCDS entries.
biodb.DEBUG[2026-01-31 16:02:15.638][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2026-01-31 16:02:15.639][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2026-01-31 16:02:15.640][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-01-31 16:02:15.646][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2026-01-31 16:02:15.647][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-31 16:02:15.648][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:15.649][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2026-01-31 16:02:15.665][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-31 16:02:15.666][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-31 16:02:15.667][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:15.668][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:15.693][ef$get] Asked field names are: sequence.
biodb.TRACE[2026-01-31 16:02:15.694][ef$get] Realnames of fields are: aa.seq.
biodb.TRACE[2026-01-31 16:02:15.695][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:15.697][ef$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:15.698][self$getBiodb()$getEntryFields()$get] Asked field names are: sequence.
biodb.TRACE[2026-01-31 16:02:15.700][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2026-01-31 16:02:15.701][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:15.702][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:15.704][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2026-01-31 16:02:15.705][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2026-01-31 16:02:15.706][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:15.708][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:15.709][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2026-01-31 16:02:15.710][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2026-01-31 16:02:15.711][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:15.750][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:15.751][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-31 16:02:15.752][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-31 16:02:15.754][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:15.755][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:15.756][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2026-01-31 16:02:15.758][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2026-01-31 16:02:15.759][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:15.760][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:15.761][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-31 16:02:15.763][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-31 16:02:15.764][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:15.765][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:15.766][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-31 16:02:15.768][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-31 16:02:15.769][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:15.770][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:15.771][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-31 16:02:15.773][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-31 16:02:15.774][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:15.775][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:15.777][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-31 16:02:15.778][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-31 16:02:15.779][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:15.780][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:15.782][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-31 16:02:15.783][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-31 16:02:15.784][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:15.785][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:15.787][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-31 16:02:15.788][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-31 16:02:15.789][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:15.790][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2026-01-31 16:02:15.792][biodb$getFactory()$createEntryFromCo ...] Accession numbers: CCDS43240.1.
biodb.TRACE[2026-01-31 16:02:15.820][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2026-01-31 16:02:15.821][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2026-01-31 16:02:15.823][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:15.824][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:15.825][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2026-01-31 16:02:15.827][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2026-01-31 16:02:15.828][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:15.829][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:15.831][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2026-01-31 16:02:15.832][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2026-01-31 16:02:15.833][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:15.835][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:15.836][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2026-01-31 16:02:15.837][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2026-01-31 16:02:15.838][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:15.840][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:15.841][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2026-01-31 16:02:15.842][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2026-01-31 16:02:15.843][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:15.845][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:15.846][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2026-01-31 16:02:15.847][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2026-01-31 16:02:15.849][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:15.850][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:15.852][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-31 16:02:15.854][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-31 16:02:15.855][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:15.857][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:15.863][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2026-01-31 16:02:15.865][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2026-01-31 16:02:15.866][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:15.867][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:15.874][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-31 16:02:15.875][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-31 16:02:15.876][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:15.878][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:15.879][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-31 16:02:15.880][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-31 16:02:15.882][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:15.883][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:15.884][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-31 16:02:15.885][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-31 16:02:15.887][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:15.888][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:15.891][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-31 16:02:15.893][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-31 16:02:15.894][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:15.895][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:15.896][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-31 16:02:15.898][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-31 16:02:15.899][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:15.900][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:15.901][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-31 16:02:15.903][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-31 16:02:15.904][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:15.905][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:15.907][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2026-01-31 16:02:15.908][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2026-01-31 16:02:15.909][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:15.910][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:15.912][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2026-01-31 16:02:15.913][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2026-01-31 16:02:15.914][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:15.915][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:15.917][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2026-01-31 16:02:15.918][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2026-01-31 16:02:15.919][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:15.920][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:15.944][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-31 16:02:15.945][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-31 16:02:15.947][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:15.948][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:15.949][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-31 16:02:15.950][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-31 16:02:15.952][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:15.953][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:15.954][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-31 16:02:15.956][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-31 16:02:15.957][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:15.958][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:15.959][ef$get] Asked field names are: accession.
biodb.TRACE[2026-01-31 16:02:15.961][ef$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-31 16:02:15.966][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:15.968][ef$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:15.969][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-31 16:02:15.970][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-31 16:02:15.971][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:15.973][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:15.984][self$getBiodb()$getEntryFields()$get] Asked field names are: sequence.
biodb.TRACE[2026-01-31 16:02:15.986][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2026-01-31 16:02:15.987][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:15.988][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:15.990][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2026-01-31 16:02:15.991][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2026-01-31 16:02:15.992][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:15.993][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:15.995][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2026-01-31 16:02:15.996][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2026-01-31 16:02:15.997][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:15.998][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:16.000][ef$get] Asked field names are: sequence.
biodb.TRACE[2026-01-31 16:02:16.001][ef$get] Realnames of fields are: aa.seq.
biodb.TRACE[2026-01-31 16:02:16.002][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:16.003][ef$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:16.005][self$getBiodb()$getEntryFields()$get] Asked field names are: sequence.
biodb.TRACE[2026-01-31 16:02:16.006][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2026-01-31 16:02:16.007][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:16.008][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:16.020][ef$get] Asked field names are: aa.seq.
biodb.TRACE[2026-01-31 16:02:16.022][ef$get] Realnames of fields are: aa.seq.
biodb.TRACE[2026-01-31 16:02:16.023][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:16.024][ef$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:16.031][ef$get] Asked field names are: accession.
biodb.TRACE[2026-01-31 16:02:16.032][ef$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-31 16:02:16.033][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:16.035][ef$get] fields variable is a list.
biodb.INFO [2026-01-31 16:02:16.045][biodb::testThat]
biodb.INFO [2026-01-31 16:02:16.046][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2026-01-31 16:02:16.047][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-01-31 16:02:16.049][biodb::testThat]
biodb.DEBUG[2026-01-31 16:02:16.051][private$loadEntries] Creating entries from ids [2]: "CCDS12227.1, CCDS43240.1".
biodb.DEBUG[2026-01-31 16:02:16.055][conn$getEntryContent] Get NCBI CCDS entry content(s) for 2 id(s)...
fscache.INFO [2026-01-31 16:02:16.059][cch$loadContents] Load 2 contents, from /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/ncbi.ccds-c3bf0257a03be04fd46e362b99907704.
biodb.DEBUG[2026-01-31 16:02:16.062][conn$getEntryContent] 0 NCBI CCDS entry content(s) loaded from cache.
biodb.DEBUG[2026-01-31 16:02:16.063][conn$getEntryContent] 2 entry content(s) need to be fetched from NCBI CCDS database "https://www.ncbi.nlm.nih.gov/CCDS/".
biodb.DEBUG[2026-01-31 16:02:16.064][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2026-01-31 16:02:16.066][conn$getEntryContent] 1 chunk(s) to download.
Saving _problems/test_long_100_ccds-38.R
biodb.INFO [2026-01-31 16:02:16.245][biodb::testThat]
biodb.INFO [2026-01-31 16:02:16.246][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2026-01-31 16:02:16.247][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-01-31 16:02:16.249][biodb::testThat]
biodb.INFO [2026-01-31 16:02:16.257][biodb::testThat]
biodb.INFO [2026-01-31 16:02:16.258][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2026-01-31 16:02:16.259][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-01-31 16:02:16.261][biodb::testThat]
biodb.WARN [2026-01-31 16:02:16.283][self$searchForEntries] This database is not searchable by field "name".
biodb.WARN [2026-01-31 16:02:16.308][self$searchForEntries] This database is not searchable by field "name".
biodb.INFO [2026-01-31 16:02:16.319][biodb::testThat]
biodb.INFO [2026-01-31 16:02:16.321][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2026-01-31 16:02:16.322][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-01-31 16:02:16.323][biodb::testThat]
biodb.DEBUG[2026-01-31 16:02:16.347][private$loadEntries] Creating entries from ids [1]: "CCDS12227.1".
biodb.DEBUG[2026-01-31 16:02:16.418][conn$getEntryContent] Get NCBI CCDS entry content(s) for 1 id(s)...
fscache.INFO [2026-01-31 16:02:16.458][cch$loadContents] Load 1 contents, from /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/ncbi.ccds-c3bf0257a03be04fd46e362b99907704.
biodb.DEBUG[2026-01-31 16:02:16.460][conn$getEntryContent] 0 NCBI CCDS entry content(s) loaded from cache.
biodb.DEBUG[2026-01-31 16:02:16.461][conn$getEntryContent] 1 entry content(s) need to be fetched from NCBI CCDS database "https://www.ncbi.nlm.nih.gov/CCDS/".
biodb.DEBUG[2026-01-31 16:02:16.463][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2026-01-31 16:02:16.464][conn$getEntryContent] 1 chunk(s) to download.
Saving _problems/test_long_100_ccds-38.R
biodb.INFO [2026-01-31 16:02:16.560][biodb::testThat]
biodb.INFO [2026-01-31 16:02:16.561][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2026-01-31 16:02:16.563][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-01-31 16:02:16.564][biodb::testThat]
Saving _problems/test_long_100_ccds-38.R
biodb.INFO [2026-01-31 16:02:16.625][biodb::testThat]
biodb.INFO [2026-01-31 16:02:16.626][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2026-01-31 16:02:16.628][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-01-31 16:02:16.629][biodb::testThat]
biodb.INFO [2026-01-31 16:02:16.641][biodb::testThat]
biodb.INFO [2026-01-31 16:02:16.643][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2026-01-31 16:02:16.645][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-01-31 16:02:16.646][biodb::testThat]
Saving _problems/test_long_100_ccds-38.R
biodb.INFO [2026-01-31 16:02:16.739][biodb::testThat]
biodb.INFO [2026-01-31 16:02:16.740][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2026-01-31 16:02:16.741][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-01-31 16:02:16.743][biodb::testThat]
biodb.INFO [2026-01-31 16:02:16.752][bdb$terminate] Closing BiodbMain instance...
biodb.INFO [2026-01-31 16:02:16.753][self$deleteConn] Connector "ncbi.ccds" deleted.
biodb.DEBUG[2026-01-31 16:02:16.755][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2026-01-31 16:02:16.756][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-01-31 16:02:16.757][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-01-31 16:02:16.758][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-31 16:02:16.759][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-31 16:02:16.761][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:16.762][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2026-01-31 16:02:16.780][biodb::testContext]
biodb.INFO [2026-01-31 16:02:16.782][biodb::testContext] ********************************************************************************
biodb.INFO [2026-01-31 16:02:16.783][biodb::testContext] Test context - Gene long tests
biodb.INFO [2026-01-31 16:02:16.784][biodb::testContext] ********************************************************************************
biodb.INFO [2026-01-31 16:02:16.785][biodb::testContext]
biodb.INFO [2026-01-31 16:02:16.788][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.18.0.
biodb.DEBUG[2026-01-31 16:02:16.790][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2026-01-31 16:02:16.795][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2026-01-31 16:02:16.796][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2026-01-31 16:02:16.797][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2026-01-31 16:02:16.799][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:16.800][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:16.801][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:02:16.802][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2026-01-31 16:02:16.803][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2026-01-31 16:02:16.805][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:16.806][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:16.807][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:02:16.808][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2026-01-31 16:02:16.809][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2026-01-31 16:02:16.810][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:16.811][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:16.813][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:02:16.814][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2026-01-31 16:02:16.815][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2026-01-31 16:02:16.816][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2026-01-31 16:02:16.818][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:16.819][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:16.820][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:02:16.821][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2026-01-31 16:02:16.823][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2026-01-31 16:02:16.824][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2026-01-31 16:02:16.825][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:16.826][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:16.827][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:02:16.829][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2026-01-31 16:02:16.830][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2026-01-31 16:02:16.831][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:16.832][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:16.833][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:02:16.835][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2026-01-31 16:02:16.836][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2026-01-31 16:02:16.837][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2026-01-31 16:02:16.838][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:16.839][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:16.840][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:02:16.842][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2026-01-31 16:02:16.843][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2026-01-31 16:02:16.844][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:16.845][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:16.846][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:02:16.848][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2026-01-31 16:02:16.849][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2026-01-31 16:02:16.850][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2026-01-31 16:02:16.851][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:16.852][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:16.853][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:02:16.855][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2026-01-31 16:02:16.856][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2026-01-31 16:02:16.857][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2026-01-31 16:02:16.858][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2026-01-31 16:02:16.860][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2026-01-31 16:02:16.861][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2026-01-31 16:02:16.862][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:16.863][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:16.864][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:02:16.865][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2026-01-31 16:02:16.867][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2026-01-31 16:02:16.868][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:16.869][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:16.870][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:02:16.871][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2026-01-31 16:02:16.873][self$set] Set key entries.sep to "|".
biodb.DEBUG[2026-01-31 16:02:16.874][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:16.875][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:16.876][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:02:16.877][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2026-01-31 16:02:16.878][self$set] Set key offline to FALSE.
biodb.DEBUG[2026-01-31 16:02:16.880][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:16.881][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:16.882][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:02:16.883][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2026-01-31 16:02:16.884][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2026-01-31 16:02:16.886][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2026-01-31 16:02:16.887][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:16.888][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:16.889][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:02:16.890][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2026-01-31 16:02:16.891][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2026-01-31 16:02:16.902][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2026-01-31 16:02:16.903][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:16.904][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:16.905][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:02:16.906][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2026-01-31 16:02:16.908][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2026-01-31 16:02:16.909][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2026-01-31 16:02:16.910][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:16.911][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:16.912][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:02:16.914][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2026-01-31 16:02:16.916][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2026-01-31 16:02:16.917][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2026-01-31 16:02:16.918][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-01-31 16:02:16.919][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-01-31 16:02:16.921][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-01-31 16:02:16.922][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-01-31 16:02:16.923][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2026-01-31 16:02:16.924][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-01-31 16:02:16.926][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2026-01-31 16:02:16.927][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-01-31 16:02:16.928][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2026-01-31 16:02:16.929][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2026-01-31 16:02:16.931][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-01-31 16:02:16.932][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2026-01-31 16:02:16.933][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2026-01-31 16:02:16.934][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2026-01-31 16:02:16.934][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2026-01-31 16:02:16.934][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2026-01-31 16:02:16.934][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2026-01-31 16:02:16.934][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2026-01-31 16:02:16.936][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2026-01-31 16:02:16.937][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-01-31 16:02:16.938][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-01-31 16:02:16.939][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-01-31 16:02:16.940][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-01-31 16:02:16.941][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-01-31 16:02:16.943][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-01-31 16:02:16.944][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2026-01-31 16:02:16.945][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-01-31 16:02:16.946][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-01-31 16:02:16.947][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2026-01-31 16:02:16.949][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-01-31 16:02:16.950][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2026-01-31 16:02:16.952][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2026-01-31 16:02:16.954][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2026-01-31 16:02:16.955][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-01-31 16:02:16.956][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-01-31 16:02:16.957][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-01-31 16:02:16.959][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-01-31 16:02:16.960][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2026-01-31 16:02:16.961][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-01-31 16:02:16.962][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2026-01-31 16:02:16.964][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-01-31 16:02:16.965][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2026-01-31 16:02:16.966][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2026-01-31 16:02:16.967][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-01-31 16:02:16.969][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2026-01-31 16:02:16.970][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2026-01-31 16:02:16.976][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2026-01-31 16:02:16.976][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2026-01-31 16:02:16.976][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2026-01-31 16:02:16.976][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2026-01-31 16:02:16.976][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2026-01-31 16:02:16.977][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2026-01-31 16:02:16.979][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-01-31 16:02:16.980][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-01-31 16:02:16.981][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-01-31 16:02:16.982][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-01-31 16:02:16.983][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-01-31 16:02:16.985][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-01-31 16:02:16.986][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2026-01-31 16:02:16.987][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-01-31 16:02:16.988][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-01-31 16:02:16.990][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2026-01-31 16:02:16.991][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-01-31 16:02:16.992][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2026-01-31 16:02:16.995][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2026-01-31 16:02:16.996][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2026-01-31 16:02:16.997][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-01-31 16:02:16.999][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-01-31 16:02:17.000][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-01-31 16:02:17.001][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-01-31 16:02:17.002][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2026-01-31 16:02:17.004][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-01-31 16:02:17.005][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2026-01-31 16:02:17.006][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-01-31 16:02:17.007][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2026-01-31 16:02:17.009][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2026-01-31 16:02:17.010][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-01-31 16:02:17.011][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2026-01-31 16:02:17.013][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2026-01-31 16:02:17.014][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2026-01-31 16:02:17.015][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2026-01-31 16:02:17.016][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-01-31 16:02:17.018][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-01-31 16:02:17.019][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-01-31 16:02:17.020][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-01-31 16:02:17.021][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-01-31 16:02:17.022][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-01-31 16:02:17.024][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2026-01-31 16:02:17.025][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-01-31 16:02:17.026][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-01-31 16:02:17.027][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2026-01-31 16:02:17.029][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-01-31 16:02:17.030][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2026-01-31 16:02:17.032][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2026-01-31 16:02:17.034][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2026-01-31 16:02:17.035][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-01-31 16:02:17.036][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-01-31 16:02:17.038][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-01-31 16:02:17.039][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-01-31 16:02:17.040][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2026-01-31 16:02:17.042][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-01-31 16:02:17.043][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2026-01-31 16:02:17.044][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-01-31 16:02:17.046][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2026-01-31 16:02:17.047][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2026-01-31 16:02:17.048][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-01-31 16:02:17.050][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2026-01-31 16:02:17.051][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2026-01-31 16:02:17.052][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2026-01-31 16:02:17.054][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2026-01-31 16:02:17.055][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-01-31 16:02:17.056][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-01-31 16:02:17.058][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-01-31 16:02:17.059][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-01-31 16:02:17.060][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-01-31 16:02:17.061][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-01-31 16:02:17.062][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2026-01-31 16:02:17.064][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-01-31 16:02:17.065][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-01-31 16:02:17.066][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2026-01-31 16:02:17.067][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-01-31 16:02:17.069][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2026-01-31 16:02:17.070][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:17.071][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:02:17.072][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:17.073][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-31 16:02:17.074][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-31 16:02:17.076][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:17.077][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:02:17.078][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:17.079][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-31 16:02:17.080][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-31 16:02:17.081][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:17.082][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:02:17.083][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:17.084][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-31 16:02:17.086][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-31 16:02:17.087][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:17.088][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:02:17.089][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:17.090][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-31 16:02:17.091][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-31 16:02:17.092][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:17.093][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:02:17.095][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:17.096][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-31 16:02:17.097][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-31 16:02:17.098][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:17.099][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:02:17.100][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:17.101][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-31 16:02:17.102][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-31 16:02:17.103][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:17.105][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:02:17.106][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:17.107][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-31 16:02:17.108][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-31 16:02:17.109][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:17.110][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:02:17.111][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:17.112][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-31 16:02:17.113][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-31 16:02:17.115][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:17.116][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:02:17.117][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:17.118][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-31 16:02:17.119][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-31 16:02:17.120][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:17.121][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:02:17.122][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:17.123][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-31 16:02:17.125][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-31 16:02:17.126][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:17.127][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:02:17.128][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:17.129][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-31 16:02:17.130][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-31 16:02:17.131][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:17.132][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:02:17.133][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:17.135][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-31 16:02:17.136][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-31 16:02:17.137][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:17.138][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:02:17.139][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:17.140][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-31 16:02:17.141][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-31 16:02:17.142][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:17.143][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:02:17.144][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:17.146][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-31 16:02:17.147][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-31 16:02:17.148][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:17.149][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:02:17.150][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:17.151][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-31 16:02:17.152][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-31 16:02:17.153][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:17.155][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:02:17.156][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:17.157][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-31 16:02:17.158][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-31 16:02:17.159][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:17.160][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:02:17.161][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2026-01-31 16:02:17.163][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2026-01-31 16:02:17.165][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2026-01-31 16:02:17.167][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2026-01-31 16:02:17.173][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2026-01-31 16:02:17.174][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2026-01-31 16:02:17.176][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2026-01-31 16:02:17.178][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2026-01-31 16:02:17.179][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2026-01-31 16:02:17.181][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2026-01-31 16:02:17.183][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2026-01-31 16:02:17.184][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2026-01-31 16:02:17.186][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2026-01-31 16:02:17.188][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2026-01-31 16:02:17.190][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2026-01-31 16:02:17.191][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2026-01-31 16:02:17.193][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2026-01-31 16:02:17.195][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2026-01-31 16:02:17.196][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2026-01-31 16:02:17.198][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2026-01-31 16:02:17.200][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2026-01-31 16:02:17.202][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2026-01-31 16:02:17.203][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2026-01-31 16:02:17.205][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2026-01-31 16:02:17.207][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2026-01-31 16:02:17.208][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2026-01-31 16:02:17.210][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2026-01-31 16:02:17.212][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2026-01-31 16:02:17.214][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2026-01-31 16:02:17.215][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2026-01-31 16:02:17.217][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2026-01-31 16:02:17.219][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2026-01-31 16:02:17.220][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2026-01-31 16:02:17.222][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2026-01-31 16:02:17.224][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2026-01-31 16:02:17.226][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2026-01-31 16:02:17.227][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2026-01-31 16:02:17.229][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2026-01-31 16:02:17.231][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2026-01-31 16:02:17.233][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2026-01-31 16:02:17.234][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2026-01-31 16:02:17.236][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2026-01-31 16:02:17.238][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2026-01-31 16:02:17.240][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2026-01-31 16:02:17.241][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2026-01-31 16:02:17.243][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2026-01-31 16:02:17.245][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2026-01-31 16:02:17.246][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2026-01-31 16:02:17.248][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2026-01-31 16:02:17.250][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2026-01-31 16:02:17.252][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2026-01-31 16:02:17.254][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2026-01-31 16:02:17.256][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2026-01-31 16:02:17.257][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2026-01-31 16:02:17.259][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2026-01-31 16:02:17.261][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2026-01-31 16:02:17.263][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2026-01-31 16:02:17.264][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2026-01-31 16:02:17.266][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2026-01-31 16:02:17.268][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2026-01-31 16:02:17.270][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2026-01-31 16:02:17.271][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2026-01-31 16:02:17.273][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2026-01-31 16:02:17.275][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2026-01-31 16:02:17.276][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2026-01-31 16:02:17.278][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2026-01-31 16:02:17.280][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2026-01-31 16:02:17.281][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2026-01-31 16:02:17.283][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2026-01-31 16:02:17.285][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2026-01-31 16:02:17.287][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2026-01-31 16:02:17.289][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2026-01-31 16:02:17.291][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2026-01-31 16:02:17.292][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2026-01-31 16:02:17.294][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2026-01-31 16:02:17.296][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2026-01-31 16:02:17.298][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2026-01-31 16:02:17.300][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2026-01-31 16:02:17.302][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2026-01-31 16:02:17.304][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2026-01-31 16:02:17.306][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2026-01-31 16:02:17.308][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2026-01-31 16:02:17.309][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2026-01-31 16:02:17.311][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2026-01-31 16:02:17.314][initialize] This is biodb version 1.18.0.
biodb.DEBUG[2026-01-31 16:02:17.315][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2026-01-31 16:02:17.316][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2026-01-31 16:02:17.317][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-31 16:02:17.319][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:17.320][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:02:17.321][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:17.322][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-01-31 16:02:17.323][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-01-31 16:02:17.324][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-31 16:02:17.325][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-31 16:02:17.326][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:17.327][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:02:17.328][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:17.329][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-01-31 16:02:17.331][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-01-31 16:02:17.332][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-31 16:02:17.333][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-31 16:02:17.334][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:17.335][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:02:17.336][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:17.337][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-01-31 16:02:17.338][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-01-31 16:02:17.340][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-31 16:02:17.341][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-31 16:02:17.342][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:17.343][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:02:17.344][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:17.345][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-01-31 16:02:17.346][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-01-31 16:02:17.347][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-31 16:02:17.349][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-31 16:02:17.350][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:17.351][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:02:17.352][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:17.353][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-01-31 16:02:17.354][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-01-31 16:02:17.355][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-31 16:02:17.356][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-31 16:02:17.357][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:17.364][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:02:17.365][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:17.366][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-01-31 16:02:17.367][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-01-31 16:02:17.368][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-31 16:02:17.369][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-31 16:02:17.370][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:17.372][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:02:17.373][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:17.374][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-01-31 16:02:17.375][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-01-31 16:02:17.376][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-31 16:02:17.377][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-31 16:02:17.378][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:17.379][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:02:17.380][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:17.381][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-01-31 16:02:17.382][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-01-31 16:02:17.383][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-31 16:02:17.385][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-31 16:02:17.386][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:17.387][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:02:17.388][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:17.389][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-01-31 16:02:17.390][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-01-31 16:02:17.391][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-31 16:02:17.392][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-31 16:02:17.393][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:17.394][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:02:17.396][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:17.397][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-01-31 16:02:17.398][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-01-31 16:02:17.399][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-31 16:02:17.400][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-31 16:02:17.401][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:17.402][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:02:17.403][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:17.404][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-01-31 16:02:17.405][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-01-31 16:02:17.406][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-31 16:02:17.408][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-31 16:02:17.409][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:17.410][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:02:17.411][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:17.412][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-01-31 16:02:17.413][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-01-31 16:02:17.414][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-31 16:02:17.415][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-31 16:02:17.416][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:17.417][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:02:17.419][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:17.420][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-01-31 16:02:17.421][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-01-31 16:02:17.422][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-31 16:02:17.423][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-31 16:02:17.424][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:17.425][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:02:17.426][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:17.427][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-01-31 16:02:17.428][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-01-31 16:02:17.430][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-31 16:02:17.431][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-31 16:02:17.432][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:17.433][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:02:17.434][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:17.435][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-01-31 16:02:17.436][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-01-31 16:02:17.437][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-31 16:02:17.438][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-31 16:02:17.439][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:17.441][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:02:17.442][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:17.443][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-01-31 16:02:17.444][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-01-31 16:02:17.445][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-31 16:02:17.446][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-31 16:02:17.447][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:17.448][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:02:17.451][biodb$loadDefinitions] Load definitions from file "/Users/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNcbi.Rcheck/biodbNcbi/definitions.yml".
biodb.DEBUG[2026-01-31 16:02:17.453][self$getDbsInfo()$define] Define connector ncbi.ccds.
biodb.DEBUG[2026-01-31 16:02:17.456][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2026-01-31 16:02:17.457][self$setPropertyValue] Setting property "description" to "NCBI CCDS database.".
biodb.DEBUG[2026-01-31 16:02:17.458][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-01-31 16:02:17.459][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-01-31 16:02:17.461][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-01-31 16:02:17.462][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-01-31 16:02:17.463][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2026-01-31 16:02:17.464][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-01-31 16:02:17.466][self$setPropertyValue] Setting property "entry.content.type" to "html".
biodb.DEBUG[2026-01-31 16:02:17.467][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-01-31 16:02:17.468][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2026-01-31 16:02:17.469][self$setPropertyValue] Setting property "name" to "NCBI CCDS".
biodb.DEBUG[2026-01-31 16:02:17.471][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-01-31 16:02:17.472][self$setPropertyValue] Setting property "parsing.expr" to "list(attr = "value", path = "//input[@id='DATA']")".
biodb.DEBUG[2026-01-31 16:02:17.472][self$setPropertyValue] Setting property "parsing.expr" to "//b[starts-with(.,'Nucleotide Sequence')]/../tt".
biodb.DEBUG[2026-01-31 16:02:17.473][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2026-01-31 16:02:17.474][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2026-01-31 16:02:17.476][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2026-01-31 16:02:17.477][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-01-31 16:02:17.478][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-01-31 16:02:17.479][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-01-31 16:02:17.480][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-01-31 16:02:17.481][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-01-31 16:02:17.483][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-01-31 16:02:17.484][self$setPropertyValue] Setting property "urls" to "https://www.ncbi.nlm.nih.gov/CCDS/".
biodb.DEBUG[2026-01-31 16:02:17.484][self$setPropertyValue] Setting property "urls" to "https://eutils.ncbi.nlm.nih.gov/entrez/eutils".
biodb.DEBUG[2026-01-31 16:02:17.485][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-01-31 16:02:17.486][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-01-31 16:02:17.487][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2026-01-31 16:02:17.489][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-01-31 16:02:17.490][self$getDbsInfo()$define] Define connector ncbi.gene.
biodb.DEBUG[2026-01-31 16:02:17.492][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2026-01-31 16:02:17.494][self$setPropertyValue] Setting property "description" to "NCBI Gene database.".
biodb.DEBUG[2026-01-31 16:02:17.495][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-01-31 16:02:17.496][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-01-31 16:02:17.497][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-01-31 16:02:17.498][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-01-31 16:02:17.500][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2026-01-31 16:02:17.501][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-01-31 16:02:17.502][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2026-01-31 16:02:17.503][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-01-31 16:02:17.505][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2026-01-31 16:02:17.506][self$setPropertyValue] Setting property "name" to "NCBI Gene".
biodb.DEBUG[2026-01-31 16:02:17.507][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-01-31 16:02:17.508][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-track_geneid".
biodb.DEBUG[2026-01-31 16:02:17.508][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-ref_desc".
biodb.DEBUG[2026-01-31 16:02:17.508][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-ref_maploc".
biodb.DEBUG[2026-01-31 16:02:17.508][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-ref_locus".
biodb.DEBUG[2026-01-31 16:02:17.508][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-ref_syn_E".
biodb.DEBUG[2026-01-31 16:02:17.508][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-commentary_heading[text()='UniProtKB']/..//Dbtag_db[text()='UniProtKB/Swiss-Prot']/..//Object-id_str".
biodb.DEBUG[2026-01-31 16:02:17.510][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2026-01-31 16:02:17.511][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2026-01-31 16:02:17.512][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2026-01-31 16:02:17.513][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-01-31 16:02:17.514][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-01-31 16:02:17.516][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-01-31 16:02:17.517][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-01-31 16:02:17.518][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-01-31 16:02:17.519][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-01-31 16:02:17.520][self$setPropertyValue] Setting property "urls" to "https://www.ncbi.nlm.nih.gov/".
biodb.DEBUG[2026-01-31 16:02:17.520][self$setPropertyValue] Setting property "urls" to "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/".
biodb.DEBUG[2026-01-31 16:02:17.522][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-01-31 16:02:17.523][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-01-31 16:02:17.524][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2026-01-31 16:02:17.525][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-01-31 16:02:17.527][self$getDbsInfo()$define] Define connector ncbi.pubchem.comp.
biodb.DEBUG[2026-01-31 16:02:17.529][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2026-01-31 16:02:17.530][self$setPropertyValue] Setting property "description" to "PubChem Compound database.".
biodb.DEBUG[2026-01-31 16:02:17.531][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-01-31 16:02:17.533][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-01-31 16:02:17.534][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-01-31 16:02:17.535][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-01-31 16:02:17.536][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2026-01-31 16:02:17.538][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-01-31 16:02:17.539][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2026-01-31 16:02:17.540][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-01-31 16:02:17.542][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2026-01-31 16:02:17.543][self$setPropertyValue] Setting property "name" to "PubChem Compound".
biodb.DEBUG[2026-01-31 16:02:17.544][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-01-31 16:02:17.545][self$setPropertyValue] Setting property "parsing.expr" to "//PC-CompoundType_id_cid".
biodb.DEBUG[2026-01-31 16:02:17.545][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='Allowed']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-01-31 16:02:17.545][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='CAS-like Style']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-01-31 16:02:17.545][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='Preferred']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-01-31 16:02:17.545][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='Systematic']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-01-31 16:02:17.545][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='Traditional']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-01-31 16:02:17.545][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='Mass']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-01-31 16:02:17.545][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='Molecular Formula']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-01-31 16:02:17.545][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='InChI']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-01-31 16:02:17.545][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='InChIKey']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-01-31 16:02:17.545][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='Log P']/../../..//PC-InfoData_value_fval".
biodb.DEBUG[2026-01-31 16:02:17.545][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='Molecular Weight']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-01-31 16:02:17.545][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='SMILES']/../PC-Urn_name[text()='Canonical']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-01-31 16:02:17.545][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='SMILES']/../PC-Urn_name[text()='Isomeric']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-01-31 16:02:17.547][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2026-01-31 16:02:17.549][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2026-01-31 16:02:17.549][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2026-01-31 16:02:17.549][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2026-01-31 16:02:17.554][self$setPropertyValue] Setting property "scheduler.n" to "5".
biodb.DEBUG[2026-01-31 16:02:17.555][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-01-31 16:02:17.556][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-01-31 16:02:17.557][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-01-31 16:02:17.559][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-01-31 16:02:17.560][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-01-31 16:02:17.561][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-01-31 16:02:17.562][self$setPropertyValue] Setting property "urls" to "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2026-01-31 16:02:17.562][self$setPropertyValue] Setting property "urls" to "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/".
biodb.DEBUG[2026-01-31 16:02:17.562][self$setPropertyValue] Setting property "urls" to "https://pubchem.ncbi.nlm.nih.gov/rest/pug/".
biodb.DEBUG[2026-01-31 16:02:17.564][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-01-31 16:02:17.565][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-01-31 16:02:17.566][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2026-01-31 16:02:17.567][self$setPropertyValue] Setting property "xml.ns" to "http://www.ncbi.nlm.nih.gov".
biodb.DEBUG[2026-01-31 16:02:17.569][self$getDbsInfo()$define] Define connector ncbi.pubchem.subst.
biodb.DEBUG[2026-01-31 16:02:17.571][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2026-01-31 16:02:17.573][self$setPropertyValue] Setting property "description" to "PubChem Substance database.".
biodb.DEBUG[2026-01-31 16:02:17.574][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-01-31 16:02:17.575][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-01-31 16:02:17.577][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-01-31 16:02:17.578][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-01-31 16:02:17.579][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2026-01-31 16:02:17.580][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-01-31 16:02:17.582][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2026-01-31 16:02:17.583][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-01-31 16:02:17.584][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2026-01-31 16:02:17.586][self$setPropertyValue] Setting property "name" to "PubChem Substance".
biodb.DEBUG[2026-01-31 16:02:17.587][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-01-31 16:02:17.588][self$setPropertyValue] Setting property "parsing.expr" to "//PC-ID_id".
biodb.DEBUG[2026-01-31 16:02:17.588][self$setPropertyValue] Setting property "parsing.expr" to "//PC-CompoundType_id_cid".
biodb.DEBUG[2026-01-31 16:02:17.589][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2026-01-31 16:02:17.591][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2026-01-31 16:02:17.592][self$setPropertyValue] Setting property "scheduler.n" to "5".
biodb.DEBUG[2026-01-31 16:02:17.593][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-01-31 16:02:17.594][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-01-31 16:02:17.595][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-01-31 16:02:17.597][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-01-31 16:02:17.598][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-01-31 16:02:17.599][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-01-31 16:02:17.601][self$setPropertyValue] Setting property "urls" to "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2026-01-31 16:02:17.601][self$setPropertyValue] Setting property "urls" to "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/".
biodb.DEBUG[2026-01-31 16:02:17.601][self$setPropertyValue] Setting property "urls" to "https://pubchem.ncbi.nlm.nih.gov/rest/pug/".
biodb.DEBUG[2026-01-31 16:02:17.602][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-01-31 16:02:17.603][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-01-31 16:02:17.604][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2026-01-31 16:02:17.605][self$setPropertyValue] Setting property "xml.ns" to "http://www.ncbi.nlm.nih.gov".
biodb.DEBUG[2026-01-31 16:02:17.607][self$getEntryFields()$define] Define field ncbi.ccds.id.
biodb.DEBUG[2026-01-31 16:02:17.609][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2026-01-31 16:02:17.611][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2026-01-31 16:02:17.613][self$getEntryFields()$define] Define field ncbi.pubchem.subst.id.
biodb.DEBUG[2026-01-31 16:02:17.615][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2026-01-31 16:02:17.617][self$getEntryFields()$define] Define field uniprot.id.
biodb.DEBUG[2026-01-31 16:02:17.626][super$initialize] Initialize connector ncbi.gene.
biodb.DEBUG[2026-01-31 16:02:17.665][biodb$getFactory()$createConn] Creating new connector ncbi.gene for database class ncbi.gene .
biodb.INFO [2026-01-31 16:02:17.672][biodb::testThat]
biodb.INFO [2026-01-31 16:02:17.674][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2026-01-31 16:02:17.675][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-01-31 16:02:17.676][biodb::testThat]
biodb.TRACE[2026-01-31 16:02:17.684][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNcbi.Rcheck/biodbNcbi/testref/entry-ncbi.gene-2833-content.xml".
biodb.DEBUG[2026-01-31 16:02:17.686][biodb$getFactory()$createEntryFromCo ...] Creating NCBI Gene entries from 1 content(s).
biodb.DEBUG[2026-01-31 16:02:17.690][biodb$getFactory()$createEntryFromCo ...] Parsing 1 NCBI Gene entries.
biodb.DEBUG[2026-01-31 16:02:17.693][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2026-01-31 16:02:17.695][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2026-01-31 16:02:17.697][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-01-31 16:02:17.706][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2026-01-31 16:02:17.708][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-31 16:02:17.710][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:17.712][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2026-01-31 16:02:17.730][ef$get] Asked field names are: accession.
biodb.TRACE[2026-01-31 16:02:17.732][ef$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-31 16:02:17.734][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:17.736][ef$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:17.739][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-31 16:02:17.742][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-31 16:02:17.744][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:17.746][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:17.747][ef$get] Asked field names are: description.
biodb.TRACE[2026-01-31 16:02:17.748][ef$get] Realnames of fields are: description.
biodb.TRACE[2026-01-31 16:02:17.750][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:17.751][ef$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:17.753][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2026-01-31 16:02:17.755][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2026-01-31 16:02:17.757][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:17.758][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:17.760][ef$get] Asked field names are: location.
biodb.TRACE[2026-01-31 16:02:17.761][ef$get] Realnames of fields are: aa.seq.location.
biodb.TRACE[2026-01-31 16:02:17.762][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:17.763][ef$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:17.765][self$getBiodb()$getEntryFields()$get] Asked field names are: location.
biodb.TRACE[2026-01-31 16:02:17.767][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.location.
biodb.TRACE[2026-01-31 16:02:17.768][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:17.769][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:17.771][ef$get] Asked field names are: symbol.
biodb.TRACE[2026-01-31 16:02:17.772][ef$get] Realnames of fields are: gene.symbol.
biodb.TRACE[2026-01-31 16:02:17.773][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:17.774][ef$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:17.776][self$getBiodb()$getEntryFields()$get] Asked field names are: symbol.
biodb.TRACE[2026-01-31 16:02:17.778][self$getBiodb()$getEntryFields()$get] Realnames of fields are: gene.symbol.
biodb.TRACE[2026-01-31 16:02:17.779][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:17.780][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:17.782][ef$get] Asked field names are: synonyms.
biodb.TRACE[2026-01-31 16:02:17.783][ef$get] Realnames of fields are: name.
biodb.TRACE[2026-01-31 16:02:17.790][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:17.792][ef$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:17.794][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2026-01-31 16:02:17.796][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-01-31 16:02:17.797][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:17.798][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:17.800][ef$get] Asked field names are: uniprot.id.
biodb.TRACE[2026-01-31 16:02:17.801][ef$get] Realnames of fields are: uniprot.id.
biodb.TRACE[2026-01-31 16:02:17.802][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:17.803][ef$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:17.807][self$getBiodb()$getEntryFields()$get] Asked field names are: uniprot.id.
biodb.TRACE[2026-01-31 16:02:17.808][self$getBiodb()$getEntryFields()$get] Realnames of fields are: uniprot.id.
biodb.TRACE[2026-01-31 16:02:17.809][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:17.811][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:17.817][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2026-01-31 16:02:17.819][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2026-01-31 16:02:17.820][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:17.821][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:17.822][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.gene.id.
biodb.TRACE[2026-01-31 16:02:17.824][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.gene.id.
biodb.TRACE[2026-01-31 16:02:17.825][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:17.826][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:17.828][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.gene.id.
biodb.TRACE[2026-01-31 16:02:17.829][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.gene.id.
biodb.TRACE[2026-01-31 16:02:17.830][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:17.831][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:17.833][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-31 16:02:17.834][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-31 16:02:17.835][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:17.837][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:17.838][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.gene.id.
biodb.TRACE[2026-01-31 16:02:17.839][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.gene.id.
biodb.TRACE[2026-01-31 16:02:17.841][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:17.842][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:17.843][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-31 16:02:17.845][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-31 16:02:17.846][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:17.847][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:17.848][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-31 16:02:17.850][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-31 16:02:17.851][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:17.852][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:17.854][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-31 16:02:17.855][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-31 16:02:17.856][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:17.857][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:17.859][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-31 16:02:17.860][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-31 16:02:17.861][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:17.863][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:17.864][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-31 16:02:17.865][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-31 16:02:17.867][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:17.868][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:17.869][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-31 16:02:17.870][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-31 16:02:17.872][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:17.873][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2026-01-31 16:02:17.874][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 2833.
biodb.TRACE[2026-01-31 16:02:17.877][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2026-01-31 16:02:17.879][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2026-01-31 16:02:17.880][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:17.882][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:17.884][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2026-01-31 16:02:17.886][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2026-01-31 16:02:17.887][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:17.889][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:17.891][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2026-01-31 16:02:17.892][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2026-01-31 16:02:17.894][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:17.896][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:17.898][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2026-01-31 16:02:17.899][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2026-01-31 16:02:17.900][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:17.902][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:17.903][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2026-01-31 16:02:17.904][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2026-01-31 16:02:17.906][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:17.907][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2026-01-31 16:02:17.908][private$computeField] Compute value for field "aa.seq".
biodb.DEBUG[2026-01-31 16:02:17.949][initialize] Initialize connector ncbi.ccds.
biodb.DEBUG[2026-01-31 16:02:17.969][self$createConn] Creating new connector ncbi.ccds for database class ncbi.ccds .
biodb.DEBUG[2026-01-31 16:02:17.971][private$loadEntries] Creating entries from ids [1]: "CCDS14416.1".
biodb.DEBUG[2026-01-31 16:02:17.975][conn$getEntryContent] Get NCBI CCDS entry content(s) for 1 id(s)...
fscache.INFO [2026-01-31 16:02:17.977][cch$loadContents] Load 1 contents, from /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/ncbi.ccds-c3bf0257a03be04fd46e362b99907704.
biodb.DEBUG[2026-01-31 16:02:17.979][conn$getEntryContent] 0 NCBI CCDS entry content(s) loaded from cache.
biodb.DEBUG[2026-01-31 16:02:17.985][conn$getEntryContent] 1 entry content(s) need to be fetched from NCBI CCDS database "https://www.ncbi.nlm.nih.gov/CCDS/".
biodb.DEBUG[2026-01-31 16:02:17.986][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2026-01-31 16:02:17.987][conn$getEntryContent] 1 chunk(s) to download.
Saving _problems/test_long_200_gene-38.R
biodb.INFO [2026-01-31 16:02:18.047][biodb::testThat]
biodb.INFO [2026-01-31 16:02:18.049][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2026-01-31 16:02:18.050][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-01-31 16:02:18.051][biodb::testThat]
biodb.DEBUG[2026-01-31 16:02:18.054][private$loadEntries] Creating entries from ids [8]: "2833, 3002, 3627, 4316, 50943, 5551, 916, 9606".
biodb.DEBUG[2026-01-31 16:02:18.056][conn$getEntryContent] Get NCBI Gene entry content(s) for 8 id(s)...
fscache.INFO [2026-01-31 16:02:18.058][cch$loadContents] Load 8 contents, from /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/ncbi.gene-b6d7417e507eb4f1a2e0047bde5295e8.
biodb.DEBUG[2026-01-31 16:02:18.060][conn$getEntryContent] 0 NCBI Gene entry content(s) loaded from cache.
biodb.DEBUG[2026-01-31 16:02:18.061][conn$getEntryContent] 8 entry content(s) need to be fetched from NCBI Gene database "https://www.ncbi.nlm.nih.gov/".
biodb.DEBUG[2026-01-31 16:02:18.063][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2026-01-31 16:02:18.064][conn$getEntryContent] 1 chunk(s) to download.
biodb.INFO [2026-01-31 16:02:18.065][private$retrieveContents] Get entry content(s) for 8 id(s)...
Saving _problems/test_long_200_gene-38.R
biodb.INFO [2026-01-31 16:02:18.133][biodb::testThat]
biodb.INFO [2026-01-31 16:02:18.134][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2026-01-31 16:02:18.136][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-01-31 16:02:18.137][biodb::testThat]
biodb.TRACE[2026-01-31 16:02:18.141][ef$get] Asked field names are: name.
biodb.TRACE[2026-01-31 16:02:18.143][ef$get] Realnames of fields are: name.
biodb.TRACE[2026-01-31 16:02:18.144][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:18.145][ef$get] fields variable is a list.
biodb.DEBUG[2026-01-31 16:02:18.147][function(conn, opt)] Testing searchForEntries() with entry "2833" and field "name".
biodb.DEBUG[2026-01-31 16:02:18.159][private$loadEntries] Creating entries from ids [1]: "2833".
biodb.DEBUG[2026-01-31 16:02:18.161][conn$getEntryContent] Get NCBI Gene entry content(s) for 1 id(s)...
fscache.INFO [2026-01-31 16:02:18.163][cch$loadContents] Load 1 contents, from /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/ncbi.gene-b6d7417e507eb4f1a2e0047bde5295e8.
biodb.DEBUG[2026-01-31 16:02:18.164][conn$getEntryContent] 0 NCBI Gene entry content(s) loaded from cache.
biodb.DEBUG[2026-01-31 16:02:18.171][conn$getEntryContent] 1 entry content(s) need to be fetched from NCBI Gene database "https://www.ncbi.nlm.nih.gov/".
biodb.DEBUG[2026-01-31 16:02:18.172][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2026-01-31 16:02:18.174][conn$getEntryContent] 1 chunk(s) to download.
biodb.INFO [2026-01-31 16:02:18.197][private$retrieveContents] Get entry content(s) for 1 id(s)...
Saving _problems/test_long_200_gene-38.R
biodb.INFO [2026-01-31 16:02:18.275][biodb::testThat]
biodb.INFO [2026-01-31 16:02:18.276][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2026-01-31 16:02:18.277][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-01-31 16:02:18.278][biodb::testThat]
biodb.DEBUG[2026-01-31 16:02:18.288][private$loadEntries] Creating entries from ids [1]: "2833".
biodb.DEBUG[2026-01-31 16:02:18.290][conn$getEntryContent] Get NCBI Gene entry content(s) for 1 id(s)...
fscache.INFO [2026-01-31 16:02:18.292][cch$loadContents] Load 1 contents, from /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/ncbi.gene-b6d7417e507eb4f1a2e0047bde5295e8.
biodb.DEBUG[2026-01-31 16:02:18.293][conn$getEntryContent] 0 NCBI Gene entry content(s) loaded from cache.
biodb.DEBUG[2026-01-31 16:02:18.294][conn$getEntryContent] 1 entry content(s) need to be fetched from NCBI Gene database "https://www.ncbi.nlm.nih.gov/".
biodb.DEBUG[2026-01-31 16:02:18.296][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2026-01-31 16:02:18.297][conn$getEntryContent] 1 chunk(s) to download.
biodb.INFO [2026-01-31 16:02:18.298][private$retrieveContents] Get entry content(s) for 1 id(s)...
Saving _problems/test_long_200_gene-38.R
biodb.INFO [2026-01-31 16:02:18.361][biodb::testThat]
biodb.INFO [2026-01-31 16:02:18.362][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2026-01-31 16:02:18.363][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-01-31 16:02:18.364][biodb::testThat]
biodb.DEBUG[2026-01-31 16:02:18.370][private$loadEntries] Creating entries from ids [1]: "2833".
biodb.DEBUG[2026-01-31 16:02:18.371][conn$getEntryContent] Get NCBI Gene entry content(s) for 1 id(s)...
fscache.INFO [2026-01-31 16:02:18.373][cch$loadContents] Load 1 contents, from /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/ncbi.gene-b6d7417e507eb4f1a2e0047bde5295e8.
biodb.DEBUG[2026-01-31 16:02:18.374][conn$getEntryContent] 0 NCBI Gene entry content(s) loaded from cache.
biodb.DEBUG[2026-01-31 16:02:18.376][conn$getEntryContent] 1 entry content(s) need to be fetched from NCBI Gene database "https://www.ncbi.nlm.nih.gov/".
biodb.DEBUG[2026-01-31 16:02:18.377][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2026-01-31 16:02:18.378][conn$getEntryContent] 1 chunk(s) to download.
biodb.INFO [2026-01-31 16:02:18.379][private$retrieveContents] Get entry content(s) for 1 id(s)...
Saving _problems/test_long_200_gene-38.R
biodb.INFO [2026-01-31 16:02:18.438][biodb::testThat]
biodb.INFO [2026-01-31 16:02:18.440][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2026-01-31 16:02:18.441][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-01-31 16:02:18.442][biodb::testThat]
Saving _problems/test_long_200_gene-38.R
biodb.INFO [2026-01-31 16:02:18.506][biodb::testThat]
biodb.INFO [2026-01-31 16:02:18.507][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2026-01-31 16:02:18.508][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-01-31 16:02:18.509][biodb::testThat]
biodb.INFO [2026-01-31 16:02:18.520][biodb::testThat]
biodb.INFO [2026-01-31 16:02:18.521][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2026-01-31 16:02:18.522][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-01-31 16:02:18.523][biodb::testThat]
Saving _problems/test_long_200_gene-38.R
biodb.INFO [2026-01-31 16:02:18.582][biodb::testThat]
biodb.INFO [2026-01-31 16:02:18.583][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2026-01-31 16:02:18.584][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-01-31 16:02:18.585][biodb::testThat]
biodb.INFO [2026-01-31 16:02:18.595][biodb$terminate] Closing BiodbMain instance...
biodb.INFO [2026-01-31 16:02:18.596][self$deleteConn] Connector "ncbi.gene" deleted.
biodb.INFO [2026-01-31 16:02:18.597][self$deleteConn] Connector "ncbi.ccds" deleted.
biodb.DEBUG[2026-01-31 16:02:18.598][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2026-01-31 16:02:18.600][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-01-31 16:02:18.601][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-01-31 16:02:18.602][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-31 16:02:18.603][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-31 16:02:18.604][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:18.605][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2026-01-31 16:02:18.610][biodb::testContext]
biodb.INFO [2026-01-31 16:02:18.611][biodb::testContext] ********************************************************************************
biodb.INFO [2026-01-31 16:02:18.613][biodb::testContext] Test context - Pubchem comp long tests
biodb.INFO [2026-01-31 16:02:18.614][biodb::testContext] ********************************************************************************
biodb.INFO [2026-01-31 16:02:18.615][biodb::testContext]
biodb.INFO [2026-01-31 16:02:18.617][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.18.0.
biodb.DEBUG[2026-01-31 16:02:18.619][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2026-01-31 16:02:18.624][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2026-01-31 16:02:18.625][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2026-01-31 16:02:18.626][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2026-01-31 16:02:18.628][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:18.629][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:18.630][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:02:18.631][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2026-01-31 16:02:18.632][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2026-01-31 16:02:18.633][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:18.635][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:18.636][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:02:18.637][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2026-01-31 16:02:18.638][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2026-01-31 16:02:18.639][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:18.640][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:18.641][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:02:18.643][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2026-01-31 16:02:18.644][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2026-01-31 16:02:18.645][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2026-01-31 16:02:18.646][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:18.647][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:18.649][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:02:18.650][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2026-01-31 16:02:18.651][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2026-01-31 16:02:18.652][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2026-01-31 16:02:18.653][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:18.654][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:18.656][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:02:18.658][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2026-01-31 16:02:18.660][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2026-01-31 16:02:18.662][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:18.664][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:18.667][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:02:18.669][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2026-01-31 16:02:18.670][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2026-01-31 16:02:18.672][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2026-01-31 16:02:18.673][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:18.674][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:18.675][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:02:18.677][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2026-01-31 16:02:18.680][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2026-01-31 16:02:18.682][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:18.684][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:18.685][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:02:18.686][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2026-01-31 16:02:18.688][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2026-01-31 16:02:18.690][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2026-01-31 16:02:18.691][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:18.697][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:18.698][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:02:18.699][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2026-01-31 16:02:18.700][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2026-01-31 16:02:18.702][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2026-01-31 16:02:18.703][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2026-01-31 16:02:18.704][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2026-01-31 16:02:18.706][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2026-01-31 16:02:18.707][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:18.708][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:18.709][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:02:18.710][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2026-01-31 16:02:18.711][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2026-01-31 16:02:18.712][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:18.714][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:18.715][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:02:18.716][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2026-01-31 16:02:18.717][self$set] Set key entries.sep to "|".
biodb.DEBUG[2026-01-31 16:02:18.718][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:18.719][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:18.721][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:02:18.722][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2026-01-31 16:02:18.723][self$set] Set key offline to FALSE.
biodb.DEBUG[2026-01-31 16:02:18.724][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:18.725][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:18.726][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:02:18.728][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2026-01-31 16:02:18.729][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2026-01-31 16:02:18.730][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2026-01-31 16:02:18.731][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:18.732][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:18.733][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:02:18.735][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2026-01-31 16:02:18.736][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2026-01-31 16:02:18.746][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2026-01-31 16:02:18.747][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:18.748][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:18.749][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:02:18.751][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2026-01-31 16:02:18.752][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2026-01-31 16:02:18.753][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2026-01-31 16:02:18.754][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:18.755][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:18.757][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:02:18.758][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2026-01-31 16:02:18.760][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2026-01-31 16:02:18.761][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2026-01-31 16:02:18.763][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-01-31 16:02:18.764][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-01-31 16:02:18.765][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-01-31 16:02:18.766][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-01-31 16:02:18.768][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2026-01-31 16:02:18.769][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-01-31 16:02:18.770][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2026-01-31 16:02:18.771][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-01-31 16:02:18.773][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2026-01-31 16:02:18.774][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2026-01-31 16:02:18.775][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-01-31 16:02:18.777][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2026-01-31 16:02:18.778][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2026-01-31 16:02:18.779][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2026-01-31 16:02:18.779][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2026-01-31 16:02:18.779][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2026-01-31 16:02:18.779][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2026-01-31 16:02:18.779][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2026-01-31 16:02:18.780][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2026-01-31 16:02:18.782][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-01-31 16:02:18.783][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-01-31 16:02:18.784][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-01-31 16:02:18.785][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-01-31 16:02:18.786][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-01-31 16:02:18.788][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-01-31 16:02:18.789][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2026-01-31 16:02:18.790][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-01-31 16:02:18.791][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-01-31 16:02:18.792][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2026-01-31 16:02:18.794][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-01-31 16:02:18.795][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2026-01-31 16:02:18.797][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2026-01-31 16:02:18.799][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2026-01-31 16:02:18.800][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-01-31 16:02:18.801][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-01-31 16:02:18.803][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-01-31 16:02:18.804][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-01-31 16:02:18.805][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2026-01-31 16:02:18.807][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-01-31 16:02:18.809][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2026-01-31 16:02:18.810][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-01-31 16:02:18.812][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2026-01-31 16:02:18.814][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2026-01-31 16:02:18.816][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-01-31 16:02:18.818][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2026-01-31 16:02:18.821][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2026-01-31 16:02:18.824][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2026-01-31 16:02:18.824][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2026-01-31 16:02:18.824][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2026-01-31 16:02:18.824][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2026-01-31 16:02:18.824][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2026-01-31 16:02:18.826][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2026-01-31 16:02:18.828][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-01-31 16:02:18.830][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-01-31 16:02:18.832][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-01-31 16:02:18.835][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-01-31 16:02:18.837][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-01-31 16:02:18.839][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-01-31 16:02:18.842][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2026-01-31 16:02:18.844][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-01-31 16:02:18.846][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-01-31 16:02:18.849][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2026-01-31 16:02:18.851][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-01-31 16:02:18.853][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2026-01-31 16:02:18.856][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2026-01-31 16:02:18.859][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2026-01-31 16:02:18.861][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-01-31 16:02:18.863][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-01-31 16:02:18.866][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-01-31 16:02:18.868][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-01-31 16:02:18.871][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2026-01-31 16:02:18.873][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-01-31 16:02:18.876][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2026-01-31 16:02:18.879][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-01-31 16:02:18.882][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2026-01-31 16:02:18.884][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2026-01-31 16:02:18.886][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-01-31 16:02:18.889][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2026-01-31 16:02:18.891][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2026-01-31 16:02:18.894][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2026-01-31 16:02:18.896][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2026-01-31 16:02:18.898][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-01-31 16:02:18.900][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-01-31 16:02:18.902][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-01-31 16:02:18.904][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-01-31 16:02:18.906][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-01-31 16:02:18.908][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-01-31 16:02:18.911][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2026-01-31 16:02:18.913][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-01-31 16:02:18.916][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-01-31 16:02:18.918][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2026-01-31 16:02:18.920][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-01-31 16:02:18.923][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2026-01-31 16:02:18.926][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2026-01-31 16:02:18.928][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2026-01-31 16:02:18.931][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-01-31 16:02:18.934][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-01-31 16:02:18.936][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-01-31 16:02:18.939][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-01-31 16:02:18.941][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2026-01-31 16:02:18.943][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-01-31 16:02:18.944][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2026-01-31 16:02:18.952][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-01-31 16:02:18.954][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2026-01-31 16:02:18.957][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2026-01-31 16:02:18.959][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-01-31 16:02:18.960][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2026-01-31 16:02:18.961][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2026-01-31 16:02:18.963][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2026-01-31 16:02:18.964][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2026-01-31 16:02:18.965][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-01-31 16:02:18.966][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-01-31 16:02:18.968][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-01-31 16:02:18.969][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-01-31 16:02:18.970][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-01-31 16:02:18.971][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-01-31 16:02:18.972][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2026-01-31 16:02:18.974][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-01-31 16:02:18.975][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-01-31 16:02:18.976][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2026-01-31 16:02:18.977][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-01-31 16:02:18.979][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2026-01-31 16:02:18.980][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:18.981][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:02:18.982][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:18.984][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-31 16:02:18.985][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-31 16:02:18.986][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:18.987][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:02:18.988][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:18.989][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-31 16:02:18.991][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-31 16:02:18.992][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:18.993][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:02:18.994][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:18.995][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-31 16:02:18.996][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-31 16:02:18.997][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:18.999][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:02:19.000][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:19.001][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-31 16:02:19.002][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-31 16:02:19.003][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:19.004][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:02:19.006][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:19.007][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-31 16:02:19.008][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-31 16:02:19.009][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:19.010][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:02:19.011][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:19.012][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-31 16:02:19.014][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-31 16:02:19.015][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:19.016][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:02:19.017][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:19.018][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-31 16:02:19.019][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-31 16:02:19.020][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:19.022][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:02:19.023][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:19.024][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-31 16:02:19.025][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-31 16:02:19.026][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:19.027][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:02:19.028][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:19.030][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-31 16:02:19.031][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-31 16:02:19.032][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:19.033][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:02:19.034][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:19.035][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-31 16:02:19.036][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-31 16:02:19.038][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:19.039][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:02:19.040][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:19.041][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-31 16:02:19.042][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-31 16:02:19.043][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:19.045][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:02:19.046][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:19.047][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-31 16:02:19.048][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-31 16:02:19.049][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:19.050][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:02:19.052][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:19.053][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-31 16:02:19.054][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-31 16:02:19.055][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:19.056][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:02:19.057][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:19.058][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-31 16:02:19.060][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-31 16:02:19.061][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:19.062][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:02:19.063][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:19.064][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-31 16:02:19.065][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-31 16:02:19.066][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:19.068][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:02:19.069][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:19.070][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-31 16:02:19.071][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-31 16:02:19.072][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:19.073][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:02:19.074][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2026-01-31 16:02:19.076][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2026-01-31 16:02:19.078][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2026-01-31 16:02:19.080][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2026-01-31 16:02:19.081][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2026-01-31 16:02:19.083][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2026-01-31 16:02:19.085][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2026-01-31 16:02:19.087][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2026-01-31 16:02:19.088][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2026-01-31 16:02:19.090][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2026-01-31 16:02:19.092][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2026-01-31 16:02:19.094][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2026-01-31 16:02:19.095][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2026-01-31 16:02:19.097][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2026-01-31 16:02:19.099][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2026-01-31 16:02:19.101][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2026-01-31 16:02:19.103][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2026-01-31 16:02:19.105][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2026-01-31 16:02:19.107][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2026-01-31 16:02:19.108][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2026-01-31 16:02:19.110][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2026-01-31 16:02:19.112][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2026-01-31 16:02:19.114][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2026-01-31 16:02:19.116][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2026-01-31 16:02:19.117][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2026-01-31 16:02:19.119][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2026-01-31 16:02:19.121][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2026-01-31 16:02:19.123][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2026-01-31 16:02:19.124][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2026-01-31 16:02:19.126][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2026-01-31 16:02:19.128][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2026-01-31 16:02:19.130][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2026-01-31 16:02:19.136][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2026-01-31 16:02:19.137][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2026-01-31 16:02:19.139][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2026-01-31 16:02:19.141][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2026-01-31 16:02:19.142][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2026-01-31 16:02:19.144][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2026-01-31 16:02:19.146][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2026-01-31 16:02:19.147][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2026-01-31 16:02:19.149][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2026-01-31 16:02:19.151][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2026-01-31 16:02:19.152][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2026-01-31 16:02:19.154][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2026-01-31 16:02:19.156][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2026-01-31 16:02:19.158][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2026-01-31 16:02:19.159][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2026-01-31 16:02:19.161][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2026-01-31 16:02:19.163][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2026-01-31 16:02:19.165][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2026-01-31 16:02:19.166][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2026-01-31 16:02:19.168][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2026-01-31 16:02:19.170][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2026-01-31 16:02:19.171][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2026-01-31 16:02:19.173][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2026-01-31 16:02:19.175][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2026-01-31 16:02:19.177][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2026-01-31 16:02:19.178][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2026-01-31 16:02:19.180][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2026-01-31 16:02:19.182][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2026-01-31 16:02:19.183][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2026-01-31 16:02:19.185][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2026-01-31 16:02:19.187][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2026-01-31 16:02:19.189][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2026-01-31 16:02:19.190][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2026-01-31 16:02:19.192][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2026-01-31 16:02:19.194][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2026-01-31 16:02:19.195][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2026-01-31 16:02:19.197][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2026-01-31 16:02:19.199][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2026-01-31 16:02:19.201][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2026-01-31 16:02:19.202][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2026-01-31 16:02:19.204][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2026-01-31 16:02:19.206][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2026-01-31 16:02:19.207][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2026-01-31 16:02:19.209][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2026-01-31 16:02:19.211][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2026-01-31 16:02:19.213][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2026-01-31 16:02:19.215][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2026-01-31 16:02:19.216][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2026-01-31 16:02:19.218][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2026-01-31 16:02:19.220][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2026-01-31 16:02:19.222][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2026-01-31 16:02:19.224][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2026-01-31 16:02:19.226][initialize] This is biodb version 1.18.0.
biodb.DEBUG[2026-01-31 16:02:19.227][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2026-01-31 16:02:19.228][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2026-01-31 16:02:19.229][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-31 16:02:19.230][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:19.231][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:02:19.232][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:19.234][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-01-31 16:02:19.235][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-01-31 16:02:19.236][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-31 16:02:19.237][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-31 16:02:19.238][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:19.239][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:02:19.240][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:19.241][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-01-31 16:02:19.243][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-01-31 16:02:19.244][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-31 16:02:19.245][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-31 16:02:19.246][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:19.247][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:02:19.248][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:19.249][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-01-31 16:02:19.250][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-01-31 16:02:19.251][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-31 16:02:19.253][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-31 16:02:19.254][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:19.255][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:02:19.256][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:19.257][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-01-31 16:02:19.258][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-01-31 16:02:19.259][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-31 16:02:19.260][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-31 16:02:19.261][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:19.262][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:02:19.264][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:19.265][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-01-31 16:02:19.266][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-01-31 16:02:19.267][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-31 16:02:19.268][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-31 16:02:19.269][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:19.270][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:02:19.271][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:19.273][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-01-31 16:02:19.274][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-01-31 16:02:19.275][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-31 16:02:19.276][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-31 16:02:19.277][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:19.278][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:02:19.279][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:19.281][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-01-31 16:02:19.282][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-01-31 16:02:19.283][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-31 16:02:19.284][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-31 16:02:19.285][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:19.286][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:02:19.287][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:19.288][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-01-31 16:02:19.290][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-01-31 16:02:19.291][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-31 16:02:19.292][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-31 16:02:19.293][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:19.294][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:02:19.295][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:19.296][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-01-31 16:02:19.298][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-01-31 16:02:19.299][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-31 16:02:19.300][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-31 16:02:19.301][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:19.302][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:02:19.303][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:19.304][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-01-31 16:02:19.305][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-01-31 16:02:19.311][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-31 16:02:19.312][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-31 16:02:19.313][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:19.314][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:02:19.316][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:19.317][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-01-31 16:02:19.318][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-01-31 16:02:19.319][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-31 16:02:19.320][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-31 16:02:19.321][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:19.322][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:02:19.323][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:19.324][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-01-31 16:02:19.325][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-01-31 16:02:19.327][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-31 16:02:19.328][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-31 16:02:19.330][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:19.332][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:02:19.334][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:19.335][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-01-31 16:02:19.337][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-01-31 16:02:19.339][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-31 16:02:19.340][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-31 16:02:19.341][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:19.343][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:02:19.344][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:19.346][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-01-31 16:02:19.347][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-01-31 16:02:19.350][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-31 16:02:19.352][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-31 16:02:19.354][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:19.356][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:02:19.358][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:19.360][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-01-31 16:02:19.361][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-01-31 16:02:19.363][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-31 16:02:19.364][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-31 16:02:19.366][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:19.368][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:02:19.371][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:19.373][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-01-31 16:02:19.375][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-01-31 16:02:19.377][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-31 16:02:19.379][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-31 16:02:19.381][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:19.384][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:02:19.388][biodb$loadDefinitions] Load definitions from file "/Users/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNcbi.Rcheck/biodbNcbi/definitions.yml".
biodb.DEBUG[2026-01-31 16:02:19.391][self$getDbsInfo()$define] Define connector ncbi.ccds.
biodb.DEBUG[2026-01-31 16:02:19.395][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2026-01-31 16:02:19.396][self$setPropertyValue] Setting property "description" to "NCBI CCDS database.".
biodb.DEBUG[2026-01-31 16:02:19.397][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-01-31 16:02:19.398][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-01-31 16:02:19.400][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-01-31 16:02:19.401][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-01-31 16:02:19.402][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2026-01-31 16:02:19.403][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-01-31 16:02:19.405][self$setPropertyValue] Setting property "entry.content.type" to "html".
biodb.DEBUG[2026-01-31 16:02:19.406][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-01-31 16:02:19.408][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2026-01-31 16:02:19.410][self$setPropertyValue] Setting property "name" to "NCBI CCDS".
biodb.DEBUG[2026-01-31 16:02:19.411][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-01-31 16:02:19.413][self$setPropertyValue] Setting property "parsing.expr" to "list(attr = "value", path = "//input[@id='DATA']")".
biodb.DEBUG[2026-01-31 16:02:19.413][self$setPropertyValue] Setting property "parsing.expr" to "//b[starts-with(.,'Nucleotide Sequence')]/../tt".
biodb.DEBUG[2026-01-31 16:02:19.414][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2026-01-31 16:02:19.415][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2026-01-31 16:02:19.416][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2026-01-31 16:02:19.418][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-01-31 16:02:19.419][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-01-31 16:02:19.421][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-01-31 16:02:19.423][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-01-31 16:02:19.425][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-01-31 16:02:19.426][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-01-31 16:02:19.427][self$setPropertyValue] Setting property "urls" to "https://www.ncbi.nlm.nih.gov/CCDS/".
biodb.DEBUG[2026-01-31 16:02:19.427][self$setPropertyValue] Setting property "urls" to "https://eutils.ncbi.nlm.nih.gov/entrez/eutils".
biodb.DEBUG[2026-01-31 16:02:19.428][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-01-31 16:02:19.429][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-01-31 16:02:19.431][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2026-01-31 16:02:19.432][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-01-31 16:02:19.433][self$getDbsInfo()$define] Define connector ncbi.gene.
biodb.DEBUG[2026-01-31 16:02:19.436][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2026-01-31 16:02:19.437][self$setPropertyValue] Setting property "description" to "NCBI Gene database.".
biodb.DEBUG[2026-01-31 16:02:19.438][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-01-31 16:02:19.439][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-01-31 16:02:19.441][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-01-31 16:02:19.442][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-01-31 16:02:19.443][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2026-01-31 16:02:19.444][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-01-31 16:02:19.445][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2026-01-31 16:02:19.447][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-01-31 16:02:19.448][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2026-01-31 16:02:19.449][self$setPropertyValue] Setting property "name" to "NCBI Gene".
biodb.DEBUG[2026-01-31 16:02:19.450][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-01-31 16:02:19.452][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-track_geneid".
biodb.DEBUG[2026-01-31 16:02:19.452][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-ref_desc".
biodb.DEBUG[2026-01-31 16:02:19.452][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-ref_maploc".
biodb.DEBUG[2026-01-31 16:02:19.452][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-ref_locus".
biodb.DEBUG[2026-01-31 16:02:19.452][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-ref_syn_E".
biodb.DEBUG[2026-01-31 16:02:19.452][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-commentary_heading[text()='UniProtKB']/..//Dbtag_db[text()='UniProtKB/Swiss-Prot']/..//Object-id_str".
biodb.DEBUG[2026-01-31 16:02:19.453][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2026-01-31 16:02:19.454][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2026-01-31 16:02:19.456][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2026-01-31 16:02:19.457][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-01-31 16:02:19.458][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-01-31 16:02:19.459][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-01-31 16:02:19.460][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-01-31 16:02:19.461][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-01-31 16:02:19.463][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-01-31 16:02:19.464][self$setPropertyValue] Setting property "urls" to "https://www.ncbi.nlm.nih.gov/".
biodb.DEBUG[2026-01-31 16:02:19.464][self$setPropertyValue] Setting property "urls" to "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/".
biodb.DEBUG[2026-01-31 16:02:19.465][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-01-31 16:02:19.466][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-01-31 16:02:19.467][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2026-01-31 16:02:19.469][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-01-31 16:02:19.470][self$getDbsInfo()$define] Define connector ncbi.pubchem.comp.
biodb.DEBUG[2026-01-31 16:02:19.472][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2026-01-31 16:02:19.474][self$setPropertyValue] Setting property "description" to "PubChem Compound database.".
biodb.DEBUG[2026-01-31 16:02:19.475][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-01-31 16:02:19.476][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-01-31 16:02:19.477][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-01-31 16:02:19.479][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-01-31 16:02:19.480][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2026-01-31 16:02:19.481][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-01-31 16:02:19.482][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2026-01-31 16:02:19.484][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-01-31 16:02:19.485][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2026-01-31 16:02:19.486][self$setPropertyValue] Setting property "name" to "PubChem Compound".
biodb.DEBUG[2026-01-31 16:02:19.487][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-01-31 16:02:19.489][self$setPropertyValue] Setting property "parsing.expr" to "//PC-CompoundType_id_cid".
biodb.DEBUG[2026-01-31 16:02:19.489][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='Allowed']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-01-31 16:02:19.489][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='CAS-like Style']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-01-31 16:02:19.489][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='Preferred']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-01-31 16:02:19.489][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='Systematic']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-01-31 16:02:19.489][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='Traditional']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-01-31 16:02:19.489][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='Mass']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-01-31 16:02:19.489][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='Molecular Formula']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-01-31 16:02:19.489][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='InChI']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-01-31 16:02:19.489][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='InChIKey']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-01-31 16:02:19.489][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='Log P']/../../..//PC-InfoData_value_fval".
biodb.DEBUG[2026-01-31 16:02:19.489][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='Molecular Weight']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-01-31 16:02:19.489][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='SMILES']/../PC-Urn_name[text()='Canonical']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-01-31 16:02:19.489][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='SMILES']/../PC-Urn_name[text()='Isomeric']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-01-31 16:02:19.490][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2026-01-31 16:02:19.491][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2026-01-31 16:02:19.491][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2026-01-31 16:02:19.491][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2026-01-31 16:02:19.493][self$setPropertyValue] Setting property "scheduler.n" to "5".
biodb.DEBUG[2026-01-31 16:02:19.494][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-01-31 16:02:19.495][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-01-31 16:02:19.496][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-01-31 16:02:19.498][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-01-31 16:02:19.499][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-01-31 16:02:19.500][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-01-31 16:02:19.501][self$setPropertyValue] Setting property "urls" to "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2026-01-31 16:02:19.501][self$setPropertyValue] Setting property "urls" to "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/".
biodb.DEBUG[2026-01-31 16:02:19.501][self$setPropertyValue] Setting property "urls" to "https://pubchem.ncbi.nlm.nih.gov/rest/pug/".
biodb.DEBUG[2026-01-31 16:02:19.503][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-01-31 16:02:19.504][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-01-31 16:02:19.505][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2026-01-31 16:02:19.506][self$setPropertyValue] Setting property "xml.ns" to "http://www.ncbi.nlm.nih.gov".
biodb.DEBUG[2026-01-31 16:02:19.508][self$getDbsInfo()$define] Define connector ncbi.pubchem.subst.
biodb.DEBUG[2026-01-31 16:02:19.510][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2026-01-31 16:02:19.512][self$setPropertyValue] Setting property "description" to "PubChem Substance database.".
biodb.DEBUG[2026-01-31 16:02:19.513][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-01-31 16:02:19.514][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-01-31 16:02:19.520][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-01-31 16:02:19.522][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-01-31 16:02:19.523][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2026-01-31 16:02:19.525][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-01-31 16:02:19.526][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2026-01-31 16:02:19.527][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-01-31 16:02:19.529][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2026-01-31 16:02:19.530][self$setPropertyValue] Setting property "name" to "PubChem Substance".
biodb.DEBUG[2026-01-31 16:02:19.531][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-01-31 16:02:19.532][self$setPropertyValue] Setting property "parsing.expr" to "//PC-ID_id".
biodb.DEBUG[2026-01-31 16:02:19.532][self$setPropertyValue] Setting property "parsing.expr" to "//PC-CompoundType_id_cid".
biodb.DEBUG[2026-01-31 16:02:19.534][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2026-01-31 16:02:19.535][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2026-01-31 16:02:19.536][self$setPropertyValue] Setting property "scheduler.n" to "5".
biodb.DEBUG[2026-01-31 16:02:19.537][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-01-31 16:02:19.538][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-01-31 16:02:19.540][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-01-31 16:02:19.541][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-01-31 16:02:19.542][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-01-31 16:02:19.543][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-01-31 16:02:19.544][self$setPropertyValue] Setting property "urls" to "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2026-01-31 16:02:19.544][self$setPropertyValue] Setting property "urls" to "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/".
biodb.DEBUG[2026-01-31 16:02:19.544][self$setPropertyValue] Setting property "urls" to "https://pubchem.ncbi.nlm.nih.gov/rest/pug/".
biodb.DEBUG[2026-01-31 16:02:19.546][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-01-31 16:02:19.547][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-01-31 16:02:19.548][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2026-01-31 16:02:19.549][self$setPropertyValue] Setting property "xml.ns" to "http://www.ncbi.nlm.nih.gov".
biodb.DEBUG[2026-01-31 16:02:19.551][self$getEntryFields()$define] Define field ncbi.ccds.id.
biodb.DEBUG[2026-01-31 16:02:19.554][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2026-01-31 16:02:19.558][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2026-01-31 16:02:19.562][self$getEntryFields()$define] Define field ncbi.pubchem.subst.id.
biodb.DEBUG[2026-01-31 16:02:19.565][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2026-01-31 16:02:19.570][self$getEntryFields()$define] Define field uniprot.id.
biodb.DEBUG[2026-01-31 16:02:19.589][super$initialize] Initialize connector ncbi.pubchem.comp.
biodb.DEBUG[2026-01-31 16:02:19.600][biodb$getFactory()$createConn] Creating new connector ncbi.pubchem.comp for database class ncbi.pubchem.comp .
biodb.INFO [2026-01-31 16:02:19.609][biodb::testThat]
biodb.INFO [2026-01-31 16:02:19.612][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2026-01-31 16:02:19.614][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-01-31 16:02:19.616][biodb::testThat]
biodb.TRACE[2026-01-31 16:02:19.622][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNcbi.Rcheck/biodbNcbi/testref/entry-ncbi.pubchem.comp-2-content.xml".
biodb.DEBUG[2026-01-31 16:02:19.625][biodb$getFactory()$createEntryFromCo ...] Creating PubChem Compound entries from 1 content(s).
biodb.DEBUG[2026-01-31 16:02:19.632][biodb$getFactory()$createEntryFromCo ...] Parsing 1 PubChem Compound entries.
biodb.DEBUG[2026-01-31 16:02:19.635][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2026-01-31 16:02:19.637][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2026-01-31 16:02:19.639][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-01-31 16:02:19.651][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2026-01-31 16:02:19.653][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-31 16:02:19.654][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:19.656][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2026-01-31 16:02:19.666][ef$get] Asked field names are: accession.
biodb.TRACE[2026-01-31 16:02:19.669][ef$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-31 16:02:19.671][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:19.673][ef$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:19.675][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-31 16:02:19.678][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-31 16:02:19.680][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:19.682][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:19.684][ef$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2026-01-31 16:02:19.687][ef$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2026-01-31 16:02:19.689][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:19.692][ef$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:19.694][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2026-01-31 16:02:19.697][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2026-01-31 16:02:19.699][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:19.701][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:19.704][ef$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2026-01-31 16:02:19.706][ef$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2026-01-31 16:02:19.709][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:19.711][ef$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:19.714][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2026-01-31 16:02:19.717][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2026-01-31 16:02:19.719][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:19.721][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:19.724][ef$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2026-01-31 16:02:19.726][ef$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2026-01-31 16:02:19.728][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:19.730][ef$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:19.733][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2026-01-31 16:02:19.735][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2026-01-31 16:02:19.738][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:19.740][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:19.743][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2026-01-31 16:02:19.746][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2026-01-31 16:02:19.748][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:19.750][ef$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:19.753][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2026-01-31 16:02:19.756][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2026-01-31 16:02:19.758][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:19.760][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:19.763][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2026-01-31 16:02:19.766][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2026-01-31 16:02:19.768][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:19.770][ef$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:19.773][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2026-01-31 16:02:19.776][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2026-01-31 16:02:19.778][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:19.780][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:19.783][ef$get] Asked field names are: exact.mass.
biodb.TRACE[2026-01-31 16:02:19.786][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2026-01-31 16:02:19.788][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:19.791][ef$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:19.794][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2026-01-31 16:02:19.797][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2026-01-31 16:02:19.799][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:19.802][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:19.804][ef$get] Asked field names are: formula.
biodb.TRACE[2026-01-31 16:02:19.807][ef$get] Realnames of fields are: formula.
biodb.TRACE[2026-01-31 16:02:19.809][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:19.811][ef$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:19.815][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2026-01-31 16:02:19.818][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2026-01-31 16:02:19.820][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:19.822][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:19.825][ef$get] Asked field names are: inchi.
biodb.TRACE[2026-01-31 16:02:19.827][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2026-01-31 16:02:19.830][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:19.832][ef$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:19.835][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2026-01-31 16:02:19.837][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2026-01-31 16:02:19.849][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:19.852][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:19.855][ef$get] Asked field names are: inchikey.
biodb.TRACE[2026-01-31 16:02:19.858][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-01-31 16:02:19.860][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:19.862][ef$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:19.865][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-01-31 16:02:19.867][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-01-31 16:02:19.870][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:19.872][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:19.875][ef$get] Asked field names are: logp.
biodb.TRACE[2026-01-31 16:02:19.877][ef$get] Realnames of fields are: logp.
biodb.TRACE[2026-01-31 16:02:19.878][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:19.880][ef$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:19.882][self$getBiodb()$getEntryFields()$get] Asked field names are: logp.
biodb.TRACE[2026-01-31 16:02:19.884][self$getBiodb()$getEntryFields()$get] Realnames of fields are: logp.
biodb.TRACE[2026-01-31 16:02:19.886][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:19.888][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:19.889][ef$get] Asked field names are: molecular.weight.
biodb.TRACE[2026-01-31 16:02:19.891][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2026-01-31 16:02:19.892][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:19.894][ef$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:19.896][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.weight.
biodb.TRACE[2026-01-31 16:02:19.898][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2026-01-31 16:02:19.900][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:19.902][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:19.904][ef$get] Asked field names are: smiles.canonical.
biodb.TRACE[2026-01-31 16:02:19.906][ef$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2026-01-31 16:02:19.908][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:19.909][ef$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:19.911][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.canonical.
biodb.TRACE[2026-01-31 16:02:19.912][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2026-01-31 16:02:19.913][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:19.915][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:19.916][ef$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2026-01-31 16:02:19.917][ef$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2026-01-31 16:02:19.918][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:19.920][ef$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:19.921][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2026-01-31 16:02:19.922][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2026-01-31 16:02:19.924][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:19.925][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:19.926][self$getBiodb()$getEntryFields()$get] Asked field names are: COMP.IUPAC.NAME.PREF.
biodb.TRACE[2026-01-31 16:02:19.928][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2026-01-31 16:02:19.929][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:19.930][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:19.931][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2026-01-31 16:02:19.933][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2026-01-31 16:02:19.934][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:19.935][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:19.936][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2026-01-31 16:02:19.937][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2026-01-31 16:02:19.939][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:19.940][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:19.941][self$getBiodb()$getEntryFields()$get] Asked field names are: COMP.IUPAC.NAME.ALLOWED.
biodb.TRACE[2026-01-31 16:02:19.942][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2026-01-31 16:02:19.944][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:19.945][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:19.946][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2026-01-31 16:02:19.947][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2026-01-31 16:02:19.949][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:19.950][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:19.951][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2026-01-31 16:02:19.952][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2026-01-31 16:02:19.953][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:19.955][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:19.956][self$getBiodb()$getEntryFields()$get] Asked field names are: COMP.IUPAC.NAME.TRAD.
biodb.TRACE[2026-01-31 16:02:19.957][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2026-01-31 16:02:19.958][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:19.960][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:19.961][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2026-01-31 16:02:19.962][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2026-01-31 16:02:19.963][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:19.965][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:19.966][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2026-01-31 16:02:19.967][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2026-01-31 16:02:19.968][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:19.969][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:19.971][self$getBiodb()$getEntryFields()$get] Asked field names are: COMP.IUPAC.NAME.SYST.
biodb.TRACE[2026-01-31 16:02:19.972][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2026-01-31 16:02:19.973][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:19.974][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:19.976][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2026-01-31 16:02:19.977][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2026-01-31 16:02:19.978][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:19.979][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:19.981][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2026-01-31 16:02:19.982][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2026-01-31 16:02:19.983][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:19.984][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:19.986][self$getBiodb()$getEntryFields()$get] Asked field names are: COMP.IUPAC.NAME.CAS.
biodb.TRACE[2026-01-31 16:02:19.987][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2026-01-31 16:02:19.988][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:19.989][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:19.991][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2026-01-31 16:02:19.992][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2026-01-31 16:02:19.993][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:19.994][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:19.995][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2026-01-31 16:02:19.997][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2026-01-31 16:02:19.998][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:19.999][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:20.000][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-01-31 16:02:20.002][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-01-31 16:02:20.003][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:20.004][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:20.005][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-01-31 16:02:20.007][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-01-31 16:02:20.008][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:20.009][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:20.010][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-01-31 16:02:20.012][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-01-31 16:02:20.013][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:20.014][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:20.015][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-31 16:02:20.017][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-31 16:02:20.018][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:20.019][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:20.020][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-01-31 16:02:20.022][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-01-31 16:02:20.023][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:20.024][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:20.025][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-31 16:02:20.027][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-31 16:02:20.028][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:20.029][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:20.030][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-31 16:02:20.032][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-31 16:02:20.033][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:20.034][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:20.035][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-31 16:02:20.037][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-31 16:02:20.038][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:20.062][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:20.064][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-31 16:02:20.065][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-31 16:02:20.066][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:20.068][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:20.069][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-31 16:02:20.070][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-31 16:02:20.071][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:20.073][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:20.074][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-31 16:02:20.075][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-31 16:02:20.076][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:20.078][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2026-01-31 16:02:20.079][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 2.
biodb.TRACE[2026-01-31 16:02:20.081][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2026-01-31 16:02:20.083][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2026-01-31 16:02:20.084][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:20.085][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:20.086][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2026-01-31 16:02:20.088][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2026-01-31 16:02:20.089][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:20.090][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:20.091][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2026-01-31 16:02:20.093][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2026-01-31 16:02:20.094][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:20.095][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:20.096][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2026-01-31 16:02:20.098][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2026-01-31 16:02:20.099][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:20.100][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:20.101][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2026-01-31 16:02:20.103][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2026-01-31 16:02:20.104][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:20.105][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:20.106][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2026-01-31 16:02:20.108][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2026-01-31 16:02:20.109][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:20.110][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:20.111][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2026-01-31 16:02:20.113][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2026-01-31 16:02:20.114][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:20.115][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:20.118][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-31 16:02:20.119][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-31 16:02:20.120][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:20.122][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:20.128][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-01-31 16:02:20.129][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-01-31 16:02:20.131][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:20.132][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:20.138][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-31 16:02:20.140][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-31 16:02:20.141][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:20.142][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:20.144][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-31 16:02:20.145][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-31 16:02:20.146][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:20.147][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:20.149][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-31 16:02:20.150][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-31 16:02:20.151][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:20.152][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:20.155][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-31 16:02:20.157][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-31 16:02:20.158][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:20.159][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:20.160][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-31 16:02:20.162][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-31 16:02:20.163][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:20.164][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:20.165][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-31 16:02:20.167][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-31 16:02:20.168][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:20.169][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:20.171][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-01-31 16:02:20.172][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-01-31 16:02:20.173][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:20.174][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:20.176][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-01-31 16:02:20.177][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-01-31 16:02:20.178][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:20.179][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:20.181][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-01-31 16:02:20.182][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-01-31 16:02:20.183][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:20.184][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:20.193][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-31 16:02:20.195][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-31 16:02:20.196][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:20.197][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:20.199][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-31 16:02:20.200][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-31 16:02:20.201][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:20.202][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:20.204][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-31 16:02:20.205][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-31 16:02:20.206][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:20.207][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:20.209][ef$get] Asked field names are: accession.
biodb.TRACE[2026-01-31 16:02:20.210][ef$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-31 16:02:20.211][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:20.212][ef$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:20.214][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-31 16:02:20.215][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-31 16:02:20.216][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:20.217][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:20.229][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2026-01-31 16:02:20.230][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2026-01-31 16:02:20.231][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:20.233][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:20.234][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2026-01-31 16:02:20.235][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2026-01-31 16:02:20.236][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:20.242][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:20.244][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2026-01-31 16:02:20.245][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2026-01-31 16:02:20.247][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:20.248][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:20.249][ef$get] Asked field names are: exact.mass.
biodb.TRACE[2026-01-31 16:02:20.250][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2026-01-31 16:02:20.252][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:20.253][ef$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:20.254][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2026-01-31 16:02:20.255][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2026-01-31 16:02:20.256][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:20.258][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:20.269][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.weight.
biodb.TRACE[2026-01-31 16:02:20.271][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2026-01-31 16:02:20.272][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:20.273][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:20.274][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2026-01-31 16:02:20.276][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2026-01-31 16:02:20.277][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:20.278][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:20.279][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2026-01-31 16:02:20.281][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2026-01-31 16:02:20.282][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:20.283][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:20.284][ef$get] Asked field names are: molecular.weight.
biodb.TRACE[2026-01-31 16:02:20.286][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2026-01-31 16:02:20.287][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:20.288][ef$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:20.289][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.weight.
biodb.TRACE[2026-01-31 16:02:20.291][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2026-01-31 16:02:20.292][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:20.293][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:20.304][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2026-01-31 16:02:20.306][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2026-01-31 16:02:20.307][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:20.308][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:20.310][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2026-01-31 16:02:20.311][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2026-01-31 16:02:20.312][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:20.313][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:20.314][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2026-01-31 16:02:20.316][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2026-01-31 16:02:20.317][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:20.318][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:20.319][ef$get] Asked field names are: formula.
biodb.TRACE[2026-01-31 16:02:20.321][ef$get] Realnames of fields are: formula.
biodb.TRACE[2026-01-31 16:02:20.322][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:20.323][ef$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:20.324][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2026-01-31 16:02:20.326][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2026-01-31 16:02:20.327][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:20.328][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:20.340][self$getBiodb()$getEntryFields()$get] Asked field names are: logp.
biodb.TRACE[2026-01-31 16:02:20.341][self$getBiodb()$getEntryFields()$get] Realnames of fields are: logp.
biodb.TRACE[2026-01-31 16:02:20.342][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:20.344][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:20.345][self$getBiodb()$getEntryFields()$get] Asked field names are: logp.
biodb.TRACE[2026-01-31 16:02:20.346][self$getBiodb()$getEntryFields()$get] Realnames of fields are: logp.
biodb.TRACE[2026-01-31 16:02:20.348][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:20.349][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:20.350][self$getBiodb()$getEntryFields()$get] Asked field names are: logp.
biodb.TRACE[2026-01-31 16:02:20.351][self$getBiodb()$getEntryFields()$get] Realnames of fields are: logp.
biodb.TRACE[2026-01-31 16:02:20.353][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:20.354][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:20.355][ef$get] Asked field names are: logp.
biodb.TRACE[2026-01-31 16:02:20.356][ef$get] Realnames of fields are: logp.
biodb.TRACE[2026-01-31 16:02:20.358][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:20.359][ef$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:20.360][self$getBiodb()$getEntryFields()$get] Asked field names are: logp.
biodb.TRACE[2026-01-31 16:02:20.361][self$getBiodb()$getEntryFields()$get] Realnames of fields are: logp.
biodb.TRACE[2026-01-31 16:02:20.363][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:20.364][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:20.376][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.canonical.
biodb.TRACE[2026-01-31 16:02:20.377][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2026-01-31 16:02:20.379][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:20.380][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:20.381][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.canonical.
biodb.TRACE[2026-01-31 16:02:20.383][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2026-01-31 16:02:20.384][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:20.385][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:20.386][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.canonical.
biodb.TRACE[2026-01-31 16:02:20.388][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2026-01-31 16:02:20.389][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:20.390][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:20.392][ef$get] Asked field names are: smiles.canonical.
biodb.TRACE[2026-01-31 16:02:20.393][ef$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2026-01-31 16:02:20.394][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:20.395][ef$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:20.397][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.canonical.
biodb.TRACE[2026-01-31 16:02:20.398][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2026-01-31 16:02:20.399][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:20.400][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:20.413][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2026-01-31 16:02:20.414][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2026-01-31 16:02:20.415][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:20.417][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:20.418][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2026-01-31 16:02:20.424][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2026-01-31 16:02:20.426][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:20.427][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:20.429][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2026-01-31 16:02:20.430][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2026-01-31 16:02:20.431][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:20.432][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:20.434][ef$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2026-01-31 16:02:20.435][ef$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2026-01-31 16:02:20.436][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:20.437][ef$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:20.439][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2026-01-31 16:02:20.440][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2026-01-31 16:02:20.441][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:20.442][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:20.455][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2026-01-31 16:02:20.456][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2026-01-31 16:02:20.457][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:20.459][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:20.460][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2026-01-31 16:02:20.461][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2026-01-31 16:02:20.463][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:20.464][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:20.465][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2026-01-31 16:02:20.467][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2026-01-31 16:02:20.468][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:20.469][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:20.470][ef$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2026-01-31 16:02:20.472][ef$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2026-01-31 16:02:20.473][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:20.474][ef$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:20.475][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2026-01-31 16:02:20.477][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2026-01-31 16:02:20.478][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:20.479][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:20.491][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2026-01-31 16:02:20.493][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2026-01-31 16:02:20.494][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:20.495][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:20.496][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2026-01-31 16:02:20.498][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2026-01-31 16:02:20.499][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:20.500][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:20.501][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2026-01-31 16:02:20.503][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2026-01-31 16:02:20.504][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:20.505][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:20.506][ef$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2026-01-31 16:02:20.508][ef$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2026-01-31 16:02:20.509][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:20.510][ef$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:20.511][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2026-01-31 16:02:20.513][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2026-01-31 16:02:20.514][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:20.515][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:20.526][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2026-01-31 16:02:20.528][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2026-01-31 16:02:20.529][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:20.531][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:20.532][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2026-01-31 16:02:20.533][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2026-01-31 16:02:20.535][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:20.536][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:20.537][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2026-01-31 16:02:20.538][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2026-01-31 16:02:20.540][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:20.541][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:20.542][ef$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2026-01-31 16:02:20.544][ef$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2026-01-31 16:02:20.545][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:20.546][ef$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:20.547][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2026-01-31 16:02:20.548][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2026-01-31 16:02:20.550][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:20.551][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:20.563][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2026-01-31 16:02:20.564][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2026-01-31 16:02:20.565][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:20.566][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:20.568][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2026-01-31 16:02:20.569][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2026-01-31 16:02:20.570][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:20.571][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:20.573][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2026-01-31 16:02:20.574][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2026-01-31 16:02:20.575][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:20.576][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:20.578][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2026-01-31 16:02:20.579][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2026-01-31 16:02:20.580][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:20.581][ef$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:20.582][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2026-01-31 16:02:20.584][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2026-01-31 16:02:20.585][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:20.586][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:20.598][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2026-01-31 16:02:20.599][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2026-01-31 16:02:20.601][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:20.607][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:20.608][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2026-01-31 16:02:20.609][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2026-01-31 16:02:20.611][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:20.612][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:20.613][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2026-01-31 16:02:20.614][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2026-01-31 16:02:20.616][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:20.617][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:20.618][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2026-01-31 16:02:20.619][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2026-01-31 16:02:20.621][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:20.622][ef$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:20.623][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2026-01-31 16:02:20.624][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2026-01-31 16:02:20.625][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:20.627][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:20.638][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-01-31 16:02:20.640][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-01-31 16:02:20.641][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:20.642][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:20.643][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-01-31 16:02:20.645][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-01-31 16:02:20.646][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:20.647][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:20.648][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-01-31 16:02:20.650][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-01-31 16:02:20.651][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:20.652][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:20.653][ef$get] Asked field names are: name.
biodb.TRACE[2026-01-31 16:02:20.655][ef$get] Realnames of fields are: name.
biodb.TRACE[2026-01-31 16:02:20.656][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:20.657][ef$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:20.658][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-01-31 16:02:20.660][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-01-31 16:02:20.661][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:20.662][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:20.673][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-01-31 16:02:20.675][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-01-31 16:02:20.676][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:20.677][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:20.678][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-01-31 16:02:20.680][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-01-31 16:02:20.681][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:20.682][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:20.683][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-01-31 16:02:20.685][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-01-31 16:02:20.686][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:20.687][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:20.688][ef$get] Asked field names are: inchikey.
biodb.TRACE[2026-01-31 16:02:20.690][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-01-31 16:02:20.691][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:20.692][ef$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:20.693][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-01-31 16:02:20.695][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-01-31 16:02:20.696][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:20.697][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:20.709][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2026-01-31 16:02:20.710][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2026-01-31 16:02:20.711][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:20.713][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:20.714][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2026-01-31 16:02:20.715][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2026-01-31 16:02:20.716][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:20.718][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:20.719][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2026-01-31 16:02:20.720][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2026-01-31 16:02:20.721][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:20.722][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:20.724][ef$get] Asked field names are: inchi.
biodb.TRACE[2026-01-31 16:02:20.725][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2026-01-31 16:02:20.726][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:20.727][ef$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:20.729][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2026-01-31 16:02:20.730][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2026-01-31 16:02:20.731][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:20.732][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:20.744][ef$get] Asked field names are: accession.
biodb.TRACE[2026-01-31 16:02:20.746][ef$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-31 16:02:20.747][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:20.748][ef$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:20.754][ef$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2026-01-31 16:02:20.756][ef$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2026-01-31 16:02:20.757][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:20.758][ef$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:20.765][ef$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2026-01-31 16:02:20.766][ef$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2026-01-31 16:02:20.767][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:20.769][ef$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:20.775][ef$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2026-01-31 16:02:20.777][ef$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2026-01-31 16:02:20.778][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:20.779][ef$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:20.791][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2026-01-31 16:02:20.793][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2026-01-31 16:02:20.794][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:20.795][ef$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:20.802][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2026-01-31 16:02:20.803][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2026-01-31 16:02:20.804][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:20.805][ef$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:20.812][ef$get] Asked field names are: formula.
biodb.TRACE[2026-01-31 16:02:20.813][ef$get] Realnames of fields are: formula.
biodb.TRACE[2026-01-31 16:02:20.815][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:20.816][ef$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:20.822][ef$get] Asked field names are: inchi.
biodb.TRACE[2026-01-31 16:02:20.824][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2026-01-31 16:02:20.825][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:20.826][ef$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:20.832][ef$get] Asked field names are: inchikey.
biodb.TRACE[2026-01-31 16:02:20.834][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-01-31 16:02:20.835][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:20.836][ef$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:20.843][ef$get] Asked field names are: logp.
biodb.TRACE[2026-01-31 16:02:20.844][ef$get] Realnames of fields are: logp.
biodb.TRACE[2026-01-31 16:02:20.845][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:20.847][ef$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:20.853][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2026-01-31 16:02:20.854][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2026-01-31 16:02:20.856][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:20.857][ef$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:20.863][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2026-01-31 16:02:20.865][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2026-01-31 16:02:20.866][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:20.867][ef$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:20.873][ef$get] Asked field names are: name.
biodb.TRACE[2026-01-31 16:02:20.875][ef$get] Realnames of fields are: name.
biodb.TRACE[2026-01-31 16:02:20.876][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:20.877][ef$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:20.884][ef$get] Asked field names are: smiles.canonical.
biodb.TRACE[2026-01-31 16:02:20.885][ef$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2026-01-31 16:02:20.886][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:20.887][ef$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:20.894][ef$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2026-01-31 16:02:20.895][ef$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2026-01-31 16:02:20.897][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:20.898][ef$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:20.905][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNcbi.Rcheck/biodbNcbi/testref/entry-ncbi.pubchem.comp-65124-content.xml".
biodb.DEBUG[2026-01-31 16:02:20.906][biodb$getFactory()$createEntryFromCo ...] Creating PubChem Compound entries from 1 content(s).
biodb.DEBUG[2026-01-31 16:02:20.908][biodb$getFactory()$createEntryFromCo ...] Parsing 1 PubChem Compound entries.
biodb.DEBUG[2026-01-31 16:02:20.910][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2026-01-31 16:02:20.911][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2026-01-31 16:02:20.912][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-01-31 16:02:20.918][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2026-01-31 16:02:20.919][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-31 16:02:20.921][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:20.922][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2026-01-31 16:02:20.925][ef$get] Asked field names are: accession.
biodb.TRACE[2026-01-31 16:02:20.927][ef$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-31 16:02:20.928][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:20.929][ef$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:20.931][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-31 16:02:20.932][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-31 16:02:20.933][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:20.934][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:20.936][ef$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2026-01-31 16:02:20.937][ef$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2026-01-31 16:02:20.938][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:20.940][ef$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:20.942][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2026-01-31 16:02:20.943][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2026-01-31 16:02:20.944][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:20.945][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:20.947][ef$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2026-01-31 16:02:20.949][ef$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2026-01-31 16:02:20.950][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:20.951][ef$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:20.953][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2026-01-31 16:02:20.954][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2026-01-31 16:02:20.955][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:20.956][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:20.958][ef$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2026-01-31 16:02:20.959][ef$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2026-01-31 16:02:20.960][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:20.962][ef$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:20.963][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2026-01-31 16:02:20.965][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2026-01-31 16:02:20.966][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:20.967][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:20.968][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2026-01-31 16:02:20.970][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2026-01-31 16:02:20.971][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:20.972][ef$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:20.974][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2026-01-31 16:02:20.975][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2026-01-31 16:02:20.982][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:20.984][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:20.985][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2026-01-31 16:02:20.987][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2026-01-31 16:02:20.988][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:20.989][ef$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:20.991][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2026-01-31 16:02:20.992][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2026-01-31 16:02:20.994][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:20.995][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:20.996][ef$get] Asked field names are: exact.mass.
biodb.TRACE[2026-01-31 16:02:20.998][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2026-01-31 16:02:20.999][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:21.000][ef$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:21.002][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2026-01-31 16:02:21.003][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2026-01-31 16:02:21.004][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:21.005][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:21.007][ef$get] Asked field names are: formula.
biodb.TRACE[2026-01-31 16:02:21.008][ef$get] Realnames of fields are: formula.
biodb.TRACE[2026-01-31 16:02:21.009][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:21.010][ef$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:21.012][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2026-01-31 16:02:21.013][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2026-01-31 16:02:21.014][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:21.016][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:21.017][ef$get] Asked field names are: inchi.
biodb.TRACE[2026-01-31 16:02:21.018][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2026-01-31 16:02:21.019][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:21.021][ef$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:21.022][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2026-01-31 16:02:21.024][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2026-01-31 16:02:21.025][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:21.026][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:21.027][ef$get] Asked field names are: inchikey.
biodb.TRACE[2026-01-31 16:02:21.029][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-01-31 16:02:21.030][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:21.031][ef$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:21.033][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-01-31 16:02:21.034][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-01-31 16:02:21.035][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:21.036][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:21.038][ef$get] Asked field names are: logp.
biodb.TRACE[2026-01-31 16:02:21.039][ef$get] Realnames of fields are: logp.
biodb.TRACE[2026-01-31 16:02:21.040][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:21.041][ef$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:21.043][self$getBiodb()$getEntryFields()$get] Asked field names are: logp.
biodb.TRACE[2026-01-31 16:02:21.044][self$getBiodb()$getEntryFields()$get] Realnames of fields are: logp.
biodb.TRACE[2026-01-31 16:02:21.045][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:21.047][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:21.048][ef$get] Asked field names are: molecular.weight.
biodb.TRACE[2026-01-31 16:02:21.049][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2026-01-31 16:02:21.051][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:21.052][ef$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:21.053][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.weight.
biodb.TRACE[2026-01-31 16:02:21.055][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2026-01-31 16:02:21.056][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:21.057][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:21.058][ef$get] Asked field names are: smiles.canonical.
biodb.TRACE[2026-01-31 16:02:21.060][ef$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2026-01-31 16:02:21.061][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:21.062][ef$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:21.064][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.canonical.
biodb.TRACE[2026-01-31 16:02:21.065][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2026-01-31 16:02:21.066][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:21.067][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:21.069][ef$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2026-01-31 16:02:21.070][ef$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2026-01-31 16:02:21.071][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:21.072][ef$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:21.074][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2026-01-31 16:02:21.075][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2026-01-31 16:02:21.077][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:21.078][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:21.079][self$getBiodb()$getEntryFields()$get] Asked field names are: COMP.IUPAC.NAME.PREF.
biodb.TRACE[2026-01-31 16:02:21.081][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2026-01-31 16:02:21.082][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:21.083][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:21.084][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2026-01-31 16:02:21.086][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2026-01-31 16:02:21.087][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:21.088][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:21.089][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2026-01-31 16:02:21.090][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2026-01-31 16:02:21.092][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:21.093][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:21.094][self$getBiodb()$getEntryFields()$get] Asked field names are: COMP.IUPAC.NAME.ALLOWED.
biodb.TRACE[2026-01-31 16:02:21.095][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2026-01-31 16:02:21.097][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:21.098][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:21.099][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2026-01-31 16:02:21.100][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2026-01-31 16:02:21.102][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:21.103][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:21.104][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2026-01-31 16:02:21.105][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2026-01-31 16:02:21.107][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:21.108][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:21.109][self$getBiodb()$getEntryFields()$get] Asked field names are: COMP.IUPAC.NAME.TRAD.
biodb.TRACE[2026-01-31 16:02:21.110][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2026-01-31 16:02:21.112][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:21.113][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:21.114][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2026-01-31 16:02:21.115][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2026-01-31 16:02:21.117][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:21.118][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:21.119][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2026-01-31 16:02:21.120][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2026-01-31 16:02:21.121][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:21.123][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:21.124][self$getBiodb()$getEntryFields()$get] Asked field names are: COMP.IUPAC.NAME.SYST.
biodb.TRACE[2026-01-31 16:02:21.125][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2026-01-31 16:02:21.126][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:21.128][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:21.129][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2026-01-31 16:02:21.130][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2026-01-31 16:02:21.131][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:21.132][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:21.134][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2026-01-31 16:02:21.135][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2026-01-31 16:02:21.136][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:21.137][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:21.139][self$getBiodb()$getEntryFields()$get] Asked field names are: COMP.IUPAC.NAME.CAS.
biodb.TRACE[2026-01-31 16:02:21.140][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2026-01-31 16:02:21.141][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:21.142][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:21.144][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2026-01-31 16:02:21.145][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2026-01-31 16:02:21.146][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:21.147][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:21.148][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2026-01-31 16:02:21.150][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2026-01-31 16:02:21.151][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:21.152][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:21.158][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-01-31 16:02:21.159][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-01-31 16:02:21.160][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:21.162][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:21.163][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-01-31 16:02:21.164][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-01-31 16:02:21.166][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:21.167][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:21.168][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-01-31 16:02:21.169][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-01-31 16:02:21.171][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:21.172][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:21.173][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-31 16:02:21.174][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-31 16:02:21.175][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:21.177][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:21.178][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-01-31 16:02:21.179][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-01-31 16:02:21.180][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:21.182][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:21.183][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-31 16:02:21.184][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-31 16:02:21.185][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:21.187][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:21.188][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-31 16:02:21.189][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-31 16:02:21.190][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:21.192][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:21.193][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-31 16:02:21.194][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-31 16:02:21.195][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:21.197][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:21.198][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-31 16:02:21.199][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-31 16:02:21.201][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:21.202][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:21.203][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-31 16:02:21.204][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-31 16:02:21.206][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:21.207][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:21.208][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-31 16:02:21.209][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-31 16:02:21.210][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:21.212][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2026-01-31 16:02:21.213][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 65124.
biodb.TRACE[2026-01-31 16:02:21.215][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2026-01-31 16:02:21.217][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2026-01-31 16:02:21.218][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:21.219][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:21.220][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2026-01-31 16:02:21.222][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2026-01-31 16:02:21.223][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:21.224][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:21.225][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2026-01-31 16:02:21.227][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2026-01-31 16:02:21.228][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:21.229][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:21.230][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2026-01-31 16:02:21.232][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2026-01-31 16:02:21.233][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:21.234][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:21.235][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2026-01-31 16:02:21.237][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2026-01-31 16:02:21.238][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:21.239][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:21.240][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2026-01-31 16:02:21.242][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2026-01-31 16:02:21.243][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:21.244][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:21.245][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2026-01-31 16:02:21.247][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2026-01-31 16:02:21.248][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:21.249][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:21.252][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-31 16:02:21.253][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-31 16:02:21.254][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:21.255][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:21.262][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-01-31 16:02:21.263][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-01-31 16:02:21.265][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:21.266][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:21.273][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-31 16:02:21.274][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-31 16:02:21.275][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:21.277][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:21.278][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-31 16:02:21.279][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-31 16:02:21.281][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:21.282][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:21.283][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-31 16:02:21.284][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-31 16:02:21.286][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:21.287][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:21.290][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-31 16:02:21.291][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-31 16:02:21.293][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:21.294][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:21.295][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-31 16:02:21.297][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-31 16:02:21.298][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:21.299][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:21.300][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-31 16:02:21.302][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-31 16:02:21.303][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:21.304][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:21.306][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-01-31 16:02:21.307][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-01-31 16:02:21.308][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:21.310][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:21.311][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-01-31 16:02:21.312][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-01-31 16:02:21.313][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:21.315][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:21.316][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-01-31 16:02:21.317][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-01-31 16:02:21.318][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:21.320][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:21.329][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-31 16:02:21.330][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-31 16:02:21.331][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:21.337][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:21.339][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-31 16:02:21.340][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-31 16:02:21.342][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:21.343][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:21.344][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-31 16:02:21.346][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-31 16:02:21.347][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:21.348][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:21.349][ef$get] Asked field names are: accession.
biodb.TRACE[2026-01-31 16:02:21.351][ef$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-31 16:02:21.352][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:21.353][ef$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:21.354][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-31 16:02:21.356][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-31 16:02:21.357][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:21.358][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:21.369][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2026-01-31 16:02:21.371][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2026-01-31 16:02:21.372][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:21.373][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:21.374][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2026-01-31 16:02:21.376][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2026-01-31 16:02:21.377][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:21.378][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:21.379][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2026-01-31 16:02:21.381][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2026-01-31 16:02:21.382][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:21.383][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:21.384][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2026-01-31 16:02:21.386][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2026-01-31 16:02:21.387][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:21.388][ef$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:21.389][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2026-01-31 16:02:21.391][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2026-01-31 16:02:21.392][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:21.393][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:21.404][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2026-01-31 16:02:21.406][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2026-01-31 16:02:21.407][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:21.408][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:21.410][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2026-01-31 16:02:21.411][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2026-01-31 16:02:21.412][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:21.413][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:21.415][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2026-01-31 16:02:21.416][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2026-01-31 16:02:21.417][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:21.418][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:21.420][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2026-01-31 16:02:21.421][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2026-01-31 16:02:21.422][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:21.423][ef$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:21.424][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2026-01-31 16:02:21.426][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2026-01-31 16:02:21.427][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:21.428][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:21.440][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2026-01-31 16:02:21.441][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2026-01-31 16:02:21.442][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:21.444][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:21.445][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2026-01-31 16:02:21.446][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2026-01-31 16:02:21.447][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:21.448][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:21.450][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2026-01-31 16:02:21.451][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2026-01-31 16:02:21.452][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:21.453][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:21.455][ef$get] Asked field names are: formula.
biodb.TRACE[2026-01-31 16:02:21.456][ef$get] Realnames of fields are: formula.
biodb.TRACE[2026-01-31 16:02:21.457][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:21.458][ef$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:21.460][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2026-01-31 16:02:21.461][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2026-01-31 16:02:21.462][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:21.463][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:21.476][self$getBiodb()$getEntryFields()$get] Asked field names are: logp.
biodb.TRACE[2026-01-31 16:02:21.477][self$getBiodb()$getEntryFields()$get] Realnames of fields are: logp.
biodb.TRACE[2026-01-31 16:02:21.478][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:21.480][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:21.481][self$getBiodb()$getEntryFields()$get] Asked field names are: logp.
biodb.TRACE[2026-01-31 16:02:21.482][self$getBiodb()$getEntryFields()$get] Realnames of fields are: logp.
biodb.TRACE[2026-01-31 16:02:21.483][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:21.485][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:21.486][self$getBiodb()$getEntryFields()$get] Asked field names are: logp.
biodb.TRACE[2026-01-31 16:02:21.487][self$getBiodb()$getEntryFields()$get] Realnames of fields are: logp.
biodb.TRACE[2026-01-31 16:02:21.488][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:21.490][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:21.491][ef$get] Asked field names are: logp.
biodb.TRACE[2026-01-31 16:02:21.492][ef$get] Realnames of fields are: logp.
biodb.TRACE[2026-01-31 16:02:21.493][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:21.495][ef$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:21.496][self$getBiodb()$getEntryFields()$get] Asked field names are: logp.
biodb.TRACE[2026-01-31 16:02:21.497][self$getBiodb()$getEntryFields()$get] Realnames of fields are: logp.
biodb.TRACE[2026-01-31 16:02:21.498][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:21.499][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:21.517][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.canonical.
biodb.TRACE[2026-01-31 16:02:21.518][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2026-01-31 16:02:21.520][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:21.521][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:21.522][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.canonical.
biodb.TRACE[2026-01-31 16:02:21.524][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2026-01-31 16:02:21.525][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:21.526][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:21.527][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.canonical.
biodb.TRACE[2026-01-31 16:02:21.528][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2026-01-31 16:02:21.530][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:21.531][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:21.532][ef$get] Asked field names are: smiles.canonical.
biodb.TRACE[2026-01-31 16:02:21.534][ef$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2026-01-31 16:02:21.535][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:21.536][ef$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:21.537][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.canonical.
biodb.TRACE[2026-01-31 16:02:21.538][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2026-01-31 16:02:21.540][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:21.541][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:21.552][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2026-01-31 16:02:21.554][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2026-01-31 16:02:21.555][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:21.556][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:21.558][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2026-01-31 16:02:21.559][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2026-01-31 16:02:21.560][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:21.561][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:21.563][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2026-01-31 16:02:21.564][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2026-01-31 16:02:21.565][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:21.566][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:21.568][ef$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2026-01-31 16:02:21.569][ef$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2026-01-31 16:02:21.570][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:21.571][ef$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:21.573][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2026-01-31 16:02:21.574][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2026-01-31 16:02:21.575][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:21.576][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:21.588][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-01-31 16:02:21.590][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-01-31 16:02:21.591][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:21.592][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:21.593][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-01-31 16:02:21.595][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-01-31 16:02:21.596][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:21.597][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:21.599][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-01-31 16:02:21.600][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-01-31 16:02:21.601][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:21.602][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:21.604][ef$get] Asked field names are: inchikey.
biodb.TRACE[2026-01-31 16:02:21.605][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-01-31 16:02:21.606][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:21.608][ef$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:21.609][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-01-31 16:02:21.610][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-01-31 16:02:21.611][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:21.613][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:21.625][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2026-01-31 16:02:21.626][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2026-01-31 16:02:21.627][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:21.629][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:21.630][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2026-01-31 16:02:21.631][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2026-01-31 16:02:21.633][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:21.634][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:21.635][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2026-01-31 16:02:21.637][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2026-01-31 16:02:21.638][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:21.639][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:21.641][ef$get] Asked field names are: inchi.
biodb.TRACE[2026-01-31 16:02:21.642][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2026-01-31 16:02:21.643][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:21.645][ef$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:21.646][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2026-01-31 16:02:21.647][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2026-01-31 16:02:21.649][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:21.650][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:21.662][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2026-01-31 16:02:21.664][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2026-01-31 16:02:21.665][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:21.667][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:21.668][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2026-01-31 16:02:21.669][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2026-01-31 16:02:21.671][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:21.672][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:21.673][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2026-01-31 16:02:21.674][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2026-01-31 16:02:21.676][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:21.677][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:21.678][ef$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2026-01-31 16:02:21.680][ef$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2026-01-31 16:02:21.681][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:21.682][ef$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:21.683][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2026-01-31 16:02:21.685][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2026-01-31 16:02:21.686][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:21.687][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:21.706][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2026-01-31 16:02:21.707][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2026-01-31 16:02:21.709][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:21.710][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:21.712][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2026-01-31 16:02:21.713][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2026-01-31 16:02:21.714][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:21.716][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:21.717][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2026-01-31 16:02:21.719][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2026-01-31 16:02:21.720][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:21.721][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:21.723][ef$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2026-01-31 16:02:21.725][ef$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2026-01-31 16:02:21.726][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:21.728][ef$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:21.729][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2026-01-31 16:02:21.731][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2026-01-31 16:02:21.733][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:21.734][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:21.747][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2026-01-31 16:02:21.749][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2026-01-31 16:02:21.750][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:21.751][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:21.752][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2026-01-31 16:02:21.754][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2026-01-31 16:02:21.755][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:21.756][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:21.757][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2026-01-31 16:02:21.759][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2026-01-31 16:02:21.760][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:21.761][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:21.763][ef$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2026-01-31 16:02:21.764][ef$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2026-01-31 16:02:21.765][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:21.767][ef$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:21.768][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2026-01-31 16:02:21.769][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2026-01-31 16:02:21.770][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:21.772][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:21.783][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2026-01-31 16:02:21.785][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2026-01-31 16:02:21.786][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:21.787][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:21.789][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2026-01-31 16:02:21.790][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2026-01-31 16:02:21.791][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:21.793][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:21.794][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2026-01-31 16:02:21.795][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2026-01-31 16:02:21.796][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:21.798][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:21.799][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2026-01-31 16:02:21.800][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2026-01-31 16:02:21.802][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:21.803][ef$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:21.804][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2026-01-31 16:02:21.805][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2026-01-31 16:02:21.807][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:21.808][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:21.820][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2026-01-31 16:02:21.821][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2026-01-31 16:02:21.822][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:21.824][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:21.825][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2026-01-31 16:02:21.826][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2026-01-31 16:02:21.828][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:21.829][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:21.830][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2026-01-31 16:02:21.831][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2026-01-31 16:02:21.833][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:21.834][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:21.835][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2026-01-31 16:02:21.837][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2026-01-31 16:02:21.838][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:21.839][ef$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:21.840][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2026-01-31 16:02:21.842][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2026-01-31 16:02:21.843][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:21.844][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:21.856][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-01-31 16:02:21.857][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-01-31 16:02:21.859][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:21.860][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:21.861][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-01-31 16:02:21.863][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-01-31 16:02:21.864][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:21.865][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:21.866][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-01-31 16:02:21.868][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-01-31 16:02:21.869][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:21.870][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:21.871][ef$get] Asked field names are: name.
biodb.TRACE[2026-01-31 16:02:21.873][ef$get] Realnames of fields are: name.
biodb.TRACE[2026-01-31 16:02:21.874][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:21.875][ef$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:21.876][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-01-31 16:02:21.878][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-01-31 16:02:21.879][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:21.880][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:21.898][ef$get] Asked field names are: accession.
biodb.TRACE[2026-01-31 16:02:21.899][ef$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-31 16:02:21.901][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:21.902][ef$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:21.908][ef$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2026-01-31 16:02:21.910][ef$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2026-01-31 16:02:21.911][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:21.912][ef$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:21.919][ef$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2026-01-31 16:02:21.920][ef$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2026-01-31 16:02:21.922][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:21.923][ef$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:21.930][ef$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2026-01-31 16:02:21.932][ef$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2026-01-31 16:02:21.933][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:21.935][ef$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:21.941][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2026-01-31 16:02:21.943][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2026-01-31 16:02:21.944][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:21.945][ef$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:21.952][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2026-01-31 16:02:21.954][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2026-01-31 16:02:21.955][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:21.956][ef$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:21.963][ef$get] Asked field names are: formula.
biodb.TRACE[2026-01-31 16:02:21.965][ef$get] Realnames of fields are: formula.
biodb.TRACE[2026-01-31 16:02:21.966][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:21.967][ef$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:21.974][ef$get] Asked field names are: inchi.
biodb.TRACE[2026-01-31 16:02:21.976][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2026-01-31 16:02:21.977][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:21.978][ef$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:21.985][ef$get] Asked field names are: inchikey.
biodb.TRACE[2026-01-31 16:02:21.986][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-01-31 16:02:21.988][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:21.989][ef$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:21.995][ef$get] Asked field names are: logp.
biodb.TRACE[2026-01-31 16:02:21.997][ef$get] Realnames of fields are: logp.
biodb.TRACE[2026-01-31 16:02:21.998][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:21.999][ef$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:22.006][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2026-01-31 16:02:22.007][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2026-01-31 16:02:22.008][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:22.010][ef$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:22.016][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2026-01-31 16:02:22.018][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2026-01-31 16:02:22.019][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:22.020][ef$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:22.027][ef$get] Asked field names are: name.
biodb.TRACE[2026-01-31 16:02:22.028][ef$get] Realnames of fields are: name.
biodb.TRACE[2026-01-31 16:02:22.029][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:22.031][ef$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:22.037][ef$get] Asked field names are: smiles.canonical.
biodb.TRACE[2026-01-31 16:02:22.039][ef$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2026-01-31 16:02:22.040][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:22.041][ef$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:22.048][ef$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2026-01-31 16:02:22.049][ef$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2026-01-31 16:02:22.050][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:22.052][ef$get] fields variable is a list.
biodb.INFO [2026-01-31 16:02:22.062][biodb::testThat]
biodb.INFO [2026-01-31 16:02:22.063][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2026-01-31 16:02:22.064][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-01-31 16:02:22.066][biodb::testThat]
biodb.DEBUG[2026-01-31 16:02:22.069][private$loadEntries] Creating entries from ids [2]: "2, 65124".
biodb.DEBUG[2026-01-31 16:02:22.072][conn$getEntryContent] Get PubChem Compound entry content(s) for 2 id(s)...
fscache.INFO [2026-01-31 16:02:22.074][cch$loadContents] Load 2 contents, from /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/ncbi.pubchem.comp-e80afa72f6aa7425ca0c72f99f7b9d75.
biodb.DEBUG[2026-01-31 16:02:22.076][conn$getEntryContent] 0 PubChem Compound entry content(s) loaded from cache.
biodb.DEBUG[2026-01-31 16:02:22.077][conn$getEntryContent] 2 entry content(s) need to be fetched from PubChem Compound database "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2026-01-31 16:02:22.078][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2026-01-31 16:02:22.079][conn$getEntryContent] 1 chunk(s) to download.
biodb.INFO [2026-01-31 16:02:22.081][private$retrieveContents] Get entry content(s) for 2 id(s)...
Saving _problems/test_long_300_pubchem.comp-38.R
biodb.INFO [2026-01-31 16:02:22.144][biodb::testThat]
biodb.INFO [2026-01-31 16:02:22.145][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2026-01-31 16:02:22.146][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-01-31 16:02:22.147][biodb::testThat]
biodb.TRACE[2026-01-31 16:02:22.152][ef$get] Asked field names are: name.
biodb.TRACE[2026-01-31 16:02:22.153][ef$get] Realnames of fields are: name.
biodb.TRACE[2026-01-31 16:02:22.154][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:22.156][ef$get] fields variable is a list.
biodb.DEBUG[2026-01-31 16:02:22.157][function(conn, opt)] Testing searchForEntries() with entry "2" and field "name".
biodb.DEBUG[2026-01-31 16:02:22.169][private$loadEntries] Creating entries from ids [1]: "2".
biodb.DEBUG[2026-01-31 16:02:22.170][conn$getEntryContent] Get PubChem Compound entry content(s) for 1 id(s)...
fscache.INFO [2026-01-31 16:02:22.172][cch$loadContents] Load 1 contents, from /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/ncbi.pubchem.comp-e80afa72f6aa7425ca0c72f99f7b9d75.
biodb.DEBUG[2026-01-31 16:02:22.173][conn$getEntryContent] 0 PubChem Compound entry content(s) loaded from cache.
biodb.DEBUG[2026-01-31 16:02:22.175][conn$getEntryContent] 1 entry content(s) need to be fetched from PubChem Compound database "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2026-01-31 16:02:22.176][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2026-01-31 16:02:22.177][conn$getEntryContent] 1 chunk(s) to download.
biodb.INFO [2026-01-31 16:02:22.178][private$retrieveContents] Get entry content(s) for 1 id(s)...
Saving _problems/test_long_300_pubchem.comp-38.R
biodb.INFO [2026-01-31 16:02:22.236][biodb::testThat]
biodb.INFO [2026-01-31 16:02:22.237][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2026-01-31 16:02:22.239][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-01-31 16:02:22.240][biodb::testThat]
biodb.DEBUG[2026-01-31 16:02:22.254][private$loadEntries] Creating entries from ids [1]: "2".
biodb.DEBUG[2026-01-31 16:02:22.256][conn$getEntryContent] Get PubChem Compound entry content(s) for 1 id(s)...
fscache.INFO [2026-01-31 16:02:22.258][cch$loadContents] Load 1 contents, from /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/ncbi.pubchem.comp-e80afa72f6aa7425ca0c72f99f7b9d75.
biodb.DEBUG[2026-01-31 16:02:22.259][conn$getEntryContent] 0 PubChem Compound entry content(s) loaded from cache.
biodb.DEBUG[2026-01-31 16:02:22.260][conn$getEntryContent] 1 entry content(s) need to be fetched from PubChem Compound database "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2026-01-31 16:02:22.262][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2026-01-31 16:02:22.263][conn$getEntryContent] 1 chunk(s) to download.
biodb.INFO [2026-01-31 16:02:22.264][private$retrieveContents] Get entry content(s) for 1 id(s)...
Saving _problems/test_long_300_pubchem.comp-38.R
biodb.INFO [2026-01-31 16:02:22.321][biodb::testThat]
biodb.INFO [2026-01-31 16:02:22.322][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2026-01-31 16:02:22.323][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-01-31 16:02:22.324][biodb::testThat]
biodb.DEBUG[2026-01-31 16:02:22.329][private$loadEntries] Creating entries from ids [1]: "2".
biodb.DEBUG[2026-01-31 16:02:22.331][conn$getEntryContent] Get PubChem Compound entry content(s) for 1 id(s)...
fscache.INFO [2026-01-31 16:02:22.332][cch$loadContents] Load 1 contents, from /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/ncbi.pubchem.comp-e80afa72f6aa7425ca0c72f99f7b9d75.
biodb.DEBUG[2026-01-31 16:02:22.334][conn$getEntryContent] 0 PubChem Compound entry content(s) loaded from cache.
biodb.DEBUG[2026-01-31 16:02:22.335][conn$getEntryContent] 1 entry content(s) need to be fetched from PubChem Compound database "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2026-01-31 16:02:22.336][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2026-01-31 16:02:22.337][conn$getEntryContent] 1 chunk(s) to download.
biodb.INFO [2026-01-31 16:02:22.339][private$retrieveContents] Get entry content(s) for 1 id(s)...
Saving _problems/test_long_300_pubchem.comp-38.R
biodb.INFO [2026-01-31 16:02:22.396][biodb::testThat]
biodb.INFO [2026-01-31 16:02:22.397][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2026-01-31 16:02:22.399][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-01-31 16:02:22.400][biodb::testThat]
Saving _problems/test_long_300_pubchem.comp-38.R
biodb.INFO [2026-01-31 16:02:22.465][biodb::testThat]
biodb.INFO [2026-01-31 16:02:22.467][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2026-01-31 16:02:22.468][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-01-31 16:02:22.469][biodb::testThat]
Saving _problems/test_long_300_pubchem.comp-38.R
biodb.INFO [2026-01-31 16:02:22.528][biodb::testThat]
biodb.INFO [2026-01-31 16:02:22.529][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2026-01-31 16:02:22.530][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-01-31 16:02:22.532][biodb::testThat]
Saving _problems/test_long_300_pubchem.comp-38.R
biodb.INFO [2026-01-31 16:02:22.595][biodb::testThat]
biodb.INFO [2026-01-31 16:02:22.596][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2026-01-31 16:02:22.597][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-01-31 16:02:22.599][biodb::testThat]
Saving _problems/test_long_300_pubchem.comp-38.R
biodb.TRACE[2026-01-31 16:02:22.668][ef$get] Asked field names are: name.
biodb.TRACE[2026-01-31 16:02:22.670][ef$get] Realnames of fields are: name.
biodb.TRACE[2026-01-31 16:02:22.671][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:22.672][ef$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:22.674][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2026-01-31 16:02:22.675][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2026-01-31 16:02:22.676][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:22.677][ef$get] fields variable is a list.
biodb.INFO [2026-01-31 16:02:22.679][biodb::testThat]
biodb.INFO [2026-01-31 16:02:22.681][biodb::testThat] Running test function  test.searchCompound  (" We can search for a compound ").
biodb.INFO [2026-01-31 16:02:22.682][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-01-31 16:02:22.683][biodb::testThat]
biodb.DEBUG[2026-01-31 16:02:22.692][private$loadEntries] Creating entries from ids [1]: "2".
biodb.DEBUG[2026-01-31 16:02:22.694][conn$getEntryContent] Get PubChem Compound entry content(s) for 1 id(s)...
fscache.INFO [2026-01-31 16:02:22.696][cch$loadContents] Load 1 contents, from /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/ncbi.pubchem.comp-e80afa72f6aa7425ca0c72f99f7b9d75.
biodb.DEBUG[2026-01-31 16:02:22.697][conn$getEntryContent] 0 PubChem Compound entry content(s) loaded from cache.
biodb.DEBUG[2026-01-31 16:02:22.698][conn$getEntryContent] 1 entry content(s) need to be fetched from PubChem Compound database "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2026-01-31 16:02:22.700][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2026-01-31 16:02:22.701][conn$getEntryContent] 1 chunk(s) to download.
biodb.INFO [2026-01-31 16:02:22.702][private$retrieveContents] Get entry content(s) for 1 id(s)...
Saving _problems/test_long_300_pubchem.comp-38.R
biodb.INFO [2026-01-31 16:02:22.766][biodb::testThat]
biodb.INFO [2026-01-31 16:02:22.767][biodb::testThat] Running test function  test_annotateMzValues_input_vector  (" annotateMzValues() accepts a single vector. ").
biodb.INFO [2026-01-31 16:02:22.768][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-01-31 16:02:22.769][biodb::testThat]
biodb.DEBUG[2026-01-31 16:02:22.773][private$loadEntries] Creating entries from ids [2]: "2, 65124".
biodb.DEBUG[2026-01-31 16:02:22.775][conn$getEntryContent] Get PubChem Compound entry content(s) for 2 id(s)...
fscache.INFO [2026-01-31 16:02:22.777][cch$loadContents] Load 2 contents, from /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/ncbi.pubchem.comp-e80afa72f6aa7425ca0c72f99f7b9d75.
biodb.DEBUG[2026-01-31 16:02:22.778][conn$getEntryContent] 0 PubChem Compound entry content(s) loaded from cache.
biodb.DEBUG[2026-01-31 16:02:22.779][conn$getEntryContent] 2 entry content(s) need to be fetched from PubChem Compound database "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2026-01-31 16:02:22.781][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2026-01-31 16:02:22.782][conn$getEntryContent] 1 chunk(s) to download.
biodb.INFO [2026-01-31 16:02:22.783][private$retrieveContents] Get entry content(s) for 2 id(s)...
Saving _problems/test_long_300_pubchem.comp-38.R
biodb.INFO [2026-01-31 16:02:22.841][biodb::testThat]
biodb.INFO [2026-01-31 16:02:22.842][biodb::testThat] Running test function  test_annotateMzValues_ppm_tol  (" ppm tolerance works in annotateMzValues() ").
biodb.INFO [2026-01-31 16:02:22.843][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-01-31 16:02:22.845][biodb::testThat]
biodb.DEBUG[2026-01-31 16:02:22.849][private$loadEntries] Creating entries from ids [2]: "2, 65124".
biodb.DEBUG[2026-01-31 16:02:22.850][conn$getEntryContent] Get PubChem Compound entry content(s) for 2 id(s)...
fscache.INFO [2026-01-31 16:02:22.852][cch$loadContents] Load 2 contents, from /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/ncbi.pubchem.comp-e80afa72f6aa7425ca0c72f99f7b9d75.
biodb.DEBUG[2026-01-31 16:02:22.853][conn$getEntryContent] 0 PubChem Compound entry content(s) loaded from cache.
biodb.DEBUG[2026-01-31 16:02:22.855][conn$getEntryContent] 2 entry content(s) need to be fetched from PubChem Compound database "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2026-01-31 16:02:22.856][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2026-01-31 16:02:22.857][conn$getEntryContent] 1 chunk(s) to download.
biodb.INFO [2026-01-31 16:02:22.859][private$retrieveContents] Get entry content(s) for 2 id(s)...
Saving _problems/test_long_300_pubchem.comp-38.R
biodb.INFO [2026-01-31 16:02:22.921][biodb::testThat]
biodb.INFO [2026-01-31 16:02:22.922][biodb::testThat] Running test function  test_annotateMzValues_input_dataframe_untouched  (" Input data frame is not modified by annotateMzValues() ").
biodb.INFO [2026-01-31 16:02:22.923][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-01-31 16:02:22.924][biodb::testThat]
biodb.DEBUG[2026-01-31 16:02:22.928][private$loadEntries] Creating entries from ids [2]: "2, 65124".
biodb.DEBUG[2026-01-31 16:02:22.930][conn$getEntryContent] Get PubChem Compound entry content(s) for 2 id(s)...
fscache.INFO [2026-01-31 16:02:22.932][cch$loadContents] Load 2 contents, from /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/ncbi.pubchem.comp-e80afa72f6aa7425ca0c72f99f7b9d75.
biodb.DEBUG[2026-01-31 16:02:22.933][conn$getEntryContent] 0 PubChem Compound entry content(s) loaded from cache.
biodb.DEBUG[2026-01-31 16:02:22.934][conn$getEntryContent] 2 entry content(s) need to be fetched from PubChem Compound database "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2026-01-31 16:02:22.935][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2026-01-31 16:02:22.937][conn$getEntryContent] 1 chunk(s) to download.
biodb.INFO [2026-01-31 16:02:22.938][private$retrieveContents] Get entry content(s) for 2 id(s)...
Saving _problems/test_long_300_pubchem.comp-38.R
biodb.TRACE[2026-01-31 16:02:22.994][ef$get] Asked field names are: name.
biodb.TRACE[2026-01-31 16:02:22.996][ef$get] Realnames of fields are: name.
biodb.TRACE[2026-01-31 16:02:22.997][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:22.998][ef$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:22.999][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2026-01-31 16:02:23.001][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2026-01-31 16:02:23.002][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:23.003][ef$get] fields variable is a list.
biodb.INFO [2026-01-31 16:02:23.005][biodb::testThat]
biodb.INFO [2026-01-31 16:02:23.006][biodb::testThat] Running test function  test.annotateMzValues_real_values  (" annotateMzValues() works correctly with real values. ").
biodb.INFO [2026-01-31 16:02:23.007][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-01-31 16:02:23.009][biodb::testThat]
biodb.DEBUG[2026-01-31 16:02:23.012][private$loadEntries] Creating entries from ids [2]: "2, 65124".
biodb.DEBUG[2026-01-31 16:02:23.013][conn$getEntryContent] Get PubChem Compound entry content(s) for 2 id(s)...
fscache.INFO [2026-01-31 16:02:23.015][cch$loadContents] Load 2 contents, from /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/ncbi.pubchem.comp-e80afa72f6aa7425ca0c72f99f7b9d75.
biodb.DEBUG[2026-01-31 16:02:23.017][conn$getEntryContent] 0 PubChem Compound entry content(s) loaded from cache.
biodb.DEBUG[2026-01-31 16:02:23.018][conn$getEntryContent] 2 entry content(s) need to be fetched from PubChem Compound database "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2026-01-31 16:02:23.019][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2026-01-31 16:02:23.021][conn$getEntryContent] 1 chunk(s) to download.
biodb.INFO [2026-01-31 16:02:23.022][private$retrieveContents] Get entry content(s) for 2 id(s)...
Saving _problems/test_long_300_pubchem.comp-38.R
biodb.INFO [2026-01-31 16:02:23.084][biodb::testThat]
biodb.INFO [2026-01-31 16:02:23.086][biodb::testThat] Running test function  test_annotateMzValues_additional_fields  (" Additional fields are accepted in annotateMzValues() ").
biodb.INFO [2026-01-31 16:02:23.087][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-01-31 16:02:23.088][biodb::testThat]
biodb.DEBUG[2026-01-31 16:02:23.092][private$loadEntries] Creating entries from ids [2]: "2, 65124".
biodb.DEBUG[2026-01-31 16:02:23.094][conn$getEntryContent] Get PubChem Compound entry content(s) for 2 id(s)...
fscache.INFO [2026-01-31 16:02:23.096][cch$loadContents] Load 2 contents, from /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/ncbi.pubchem.comp-e80afa72f6aa7425ca0c72f99f7b9d75.
biodb.DEBUG[2026-01-31 16:02:23.097][conn$getEntryContent] 0 PubChem Compound entry content(s) loaded from cache.
biodb.DEBUG[2026-01-31 16:02:23.099][conn$getEntryContent] 2 entry content(s) need to be fetched from PubChem Compound database "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2026-01-31 16:02:23.100][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2026-01-31 16:02:23.101][conn$getEntryContent] 1 chunk(s) to download.
biodb.INFO [2026-01-31 16:02:23.102][private$retrieveContents] Get entry content(s) for 2 id(s)...
Saving _problems/test_long_300_pubchem.comp-38.R
biodb.INFO [2026-01-31 16:02:23.159][biodb$terminate] Closing BiodbMain instance...
biodb.INFO [2026-01-31 16:02:23.161][self$deleteConn] Connector "ncbi.pubchem.comp" deleted.
biodb.DEBUG[2026-01-31 16:02:23.162][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2026-01-31 16:02:23.163][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-01-31 16:02:23.164][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-01-31 16:02:23.165][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-31 16:02:23.167][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-31 16:02:23.168][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:23.169][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2026-01-31 16:02:23.174][biodb::testContext]
biodb.INFO [2026-01-31 16:02:23.176][biodb::testContext] ********************************************************************************
biodb.INFO [2026-01-31 16:02:23.177][biodb::testContext] Test context - Pubchem Subst long tests
biodb.INFO [2026-01-31 16:02:23.178][biodb::testContext] ********************************************************************************
biodb.INFO [2026-01-31 16:02:23.179][biodb::testContext]
biodb.INFO [2026-01-31 16:02:23.182][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.18.0.
biodb.DEBUG[2026-01-31 16:02:23.184][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2026-01-31 16:02:23.188][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2026-01-31 16:02:23.190][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2026-01-31 16:02:23.191][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2026-01-31 16:02:23.192][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:23.198][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:23.200][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:02:23.201][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2026-01-31 16:02:23.202][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2026-01-31 16:02:23.204][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:23.205][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:23.206][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:02:23.207][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2026-01-31 16:02:23.208][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2026-01-31 16:02:23.210][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:23.211][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:23.212][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:02:23.213][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2026-01-31 16:02:23.214][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2026-01-31 16:02:23.216][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2026-01-31 16:02:23.217][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:23.218][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:23.219][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:02:23.220][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2026-01-31 16:02:23.221][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2026-01-31 16:02:23.223][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2026-01-31 16:02:23.224][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:23.225][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:23.226][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:02:23.227][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2026-01-31 16:02:23.229][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2026-01-31 16:02:23.230][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:23.231][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:23.232][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:02:23.233][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2026-01-31 16:02:23.235][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2026-01-31 16:02:23.236][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2026-01-31 16:02:23.237][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:23.238][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:23.239][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:02:23.241][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2026-01-31 16:02:23.242][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2026-01-31 16:02:23.243][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:23.244][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:23.245][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:02:23.246][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2026-01-31 16:02:23.248][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2026-01-31 16:02:23.249][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2026-01-31 16:02:23.250][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:23.251][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:23.253][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:02:23.254][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2026-01-31 16:02:23.255][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2026-01-31 16:02:23.256][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2026-01-31 16:02:23.258][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2026-01-31 16:02:23.259][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2026-01-31 16:02:23.260][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2026-01-31 16:02:23.261][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:23.262][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:23.263][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:02:23.265][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2026-01-31 16:02:23.266][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2026-01-31 16:02:23.267][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:23.268][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:23.269][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:02:23.270][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2026-01-31 16:02:23.272][self$set] Set key entries.sep to "|".
biodb.DEBUG[2026-01-31 16:02:23.273][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:23.274][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:23.275][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:02:23.276][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2026-01-31 16:02:23.278][self$set] Set key offline to FALSE.
biodb.DEBUG[2026-01-31 16:02:23.279][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:23.280][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:23.281][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:02:23.282][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2026-01-31 16:02:23.283][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2026-01-31 16:02:23.285][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2026-01-31 16:02:23.286][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:23.287][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:23.288][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:02:23.289][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2026-01-31 16:02:23.291][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2026-01-31 16:02:23.301][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2026-01-31 16:02:23.302][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:23.304][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:23.305][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:02:23.306][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2026-01-31 16:02:23.307][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2026-01-31 16:02:23.308][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2026-01-31 16:02:23.310][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:23.311][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:23.312][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:02:23.313][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2026-01-31 16:02:23.315][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2026-01-31 16:02:23.317][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2026-01-31 16:02:23.318][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-01-31 16:02:23.319][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-01-31 16:02:23.321][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-01-31 16:02:23.322][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-01-31 16:02:23.323][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2026-01-31 16:02:23.324][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-01-31 16:02:23.326][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2026-01-31 16:02:23.327][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-01-31 16:02:23.328][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2026-01-31 16:02:23.330][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2026-01-31 16:02:23.331][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-01-31 16:02:23.332][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2026-01-31 16:02:23.333][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2026-01-31 16:02:23.335][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2026-01-31 16:02:23.335][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2026-01-31 16:02:23.335][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2026-01-31 16:02:23.335][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2026-01-31 16:02:23.335][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2026-01-31 16:02:23.336][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2026-01-31 16:02:23.337][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-01-31 16:02:23.338][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-01-31 16:02:23.339][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-01-31 16:02:23.341][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-01-31 16:02:23.342][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-01-31 16:02:23.343][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-01-31 16:02:23.344][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2026-01-31 16:02:23.345][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-01-31 16:02:23.346][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-01-31 16:02:23.348][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2026-01-31 16:02:23.349][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-01-31 16:02:23.350][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2026-01-31 16:02:23.352][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2026-01-31 16:02:23.354][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2026-01-31 16:02:23.355][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-01-31 16:02:23.356][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-01-31 16:02:23.357][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-01-31 16:02:23.359][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-01-31 16:02:23.360][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2026-01-31 16:02:23.361][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-01-31 16:02:23.362][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2026-01-31 16:02:23.364][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-01-31 16:02:23.365][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2026-01-31 16:02:23.366][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2026-01-31 16:02:23.367][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-01-31 16:02:23.368][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2026-01-31 16:02:23.374][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2026-01-31 16:02:23.375][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2026-01-31 16:02:23.375][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2026-01-31 16:02:23.375][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2026-01-31 16:02:23.375][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2026-01-31 16:02:23.375][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2026-01-31 16:02:23.377][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2026-01-31 16:02:23.378][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-01-31 16:02:23.379][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-01-31 16:02:23.380][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-01-31 16:02:23.382][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-01-31 16:02:23.383][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-01-31 16:02:23.384][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-01-31 16:02:23.385][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2026-01-31 16:02:23.386][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-01-31 16:02:23.387][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-01-31 16:02:23.389][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2026-01-31 16:02:23.390][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-01-31 16:02:23.391][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2026-01-31 16:02:23.393][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2026-01-31 16:02:23.395][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2026-01-31 16:02:23.396][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-01-31 16:02:23.397][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-01-31 16:02:23.398][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-01-31 16:02:23.400][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-01-31 16:02:23.401][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2026-01-31 16:02:23.402][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-01-31 16:02:23.403][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2026-01-31 16:02:23.405][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-01-31 16:02:23.406][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2026-01-31 16:02:23.407][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2026-01-31 16:02:23.408][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-01-31 16:02:23.410][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2026-01-31 16:02:23.411][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2026-01-31 16:02:23.412][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2026-01-31 16:02:23.413][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2026-01-31 16:02:23.414][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-01-31 16:02:23.416][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-01-31 16:02:23.417][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-01-31 16:02:23.418][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-01-31 16:02:23.419][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-01-31 16:02:23.420][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-01-31 16:02:23.422][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2026-01-31 16:02:23.423][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-01-31 16:02:23.424][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-01-31 16:02:23.425][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2026-01-31 16:02:23.426][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-01-31 16:02:23.428][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2026-01-31 16:02:23.430][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2026-01-31 16:02:23.431][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2026-01-31 16:02:23.432][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-01-31 16:02:23.434][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-01-31 16:02:23.435][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-01-31 16:02:23.436][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-01-31 16:02:23.438][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2026-01-31 16:02:23.439][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-01-31 16:02:23.440][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2026-01-31 16:02:23.441][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-01-31 16:02:23.443][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2026-01-31 16:02:23.444][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2026-01-31 16:02:23.445][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-01-31 16:02:23.447][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2026-01-31 16:02:23.448][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2026-01-31 16:02:23.449][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2026-01-31 16:02:23.450][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2026-01-31 16:02:23.451][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-01-31 16:02:23.453][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-01-31 16:02:23.454][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-01-31 16:02:23.455][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-01-31 16:02:23.456][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-01-31 16:02:23.457][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-01-31 16:02:23.458][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2026-01-31 16:02:23.460][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-01-31 16:02:23.461][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-01-31 16:02:23.462][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2026-01-31 16:02:23.463][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-01-31 16:02:23.465][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2026-01-31 16:02:23.466][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:23.467][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:02:23.468][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:23.469][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-31 16:02:23.470][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-31 16:02:23.471][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:23.473][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:02:23.474][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:23.475][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-31 16:02:23.476][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-31 16:02:23.477][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:23.478][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:02:23.479][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:23.480][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-31 16:02:23.481][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-31 16:02:23.482][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:23.484][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:02:23.485][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:23.486][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-31 16:02:23.487][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-31 16:02:23.488][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:23.489][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:02:23.490][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:23.491][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-31 16:02:23.492][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-31 16:02:23.493][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:23.495][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:02:23.496][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:23.497][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-31 16:02:23.498][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-31 16:02:23.499][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:23.500][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:02:23.501][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:23.502][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-31 16:02:23.503][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-31 16:02:23.504][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:23.506][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:02:23.507][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:23.508][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-31 16:02:23.509][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-31 16:02:23.510][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:23.511][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:02:23.512][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:23.513][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-31 16:02:23.514][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-31 16:02:23.515][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:23.516][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:02:23.518][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:23.519][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-31 16:02:23.520][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-31 16:02:23.521][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:23.522][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:02:23.523][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:23.524][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-31 16:02:23.525][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-31 16:02:23.526][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:23.528][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:02:23.529][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:23.530][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-31 16:02:23.531][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-31 16:02:23.536][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:23.538][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:02:23.539][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:23.540][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-31 16:02:23.541][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-31 16:02:23.542][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:23.543][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:02:23.545][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:23.546][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-31 16:02:23.547][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-31 16:02:23.548][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:23.549][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:02:23.550][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:23.551][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-31 16:02:23.552][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-31 16:02:23.553][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:23.554][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:02:23.555][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:23.556][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-31 16:02:23.558][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-31 16:02:23.559][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:23.560][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:02:23.561][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2026-01-31 16:02:23.563][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2026-01-31 16:02:23.564][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2026-01-31 16:02:23.566][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2026-01-31 16:02:23.568][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2026-01-31 16:02:23.570][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2026-01-31 16:02:23.571][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2026-01-31 16:02:23.573][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2026-01-31 16:02:23.575][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2026-01-31 16:02:23.576][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2026-01-31 16:02:23.578][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2026-01-31 16:02:23.580][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2026-01-31 16:02:23.581][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2026-01-31 16:02:23.583][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2026-01-31 16:02:23.585][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2026-01-31 16:02:23.587][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2026-01-31 16:02:23.588][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2026-01-31 16:02:23.590][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2026-01-31 16:02:23.592][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2026-01-31 16:02:23.593][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2026-01-31 16:02:23.595][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2026-01-31 16:02:23.597][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2026-01-31 16:02:23.599][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2026-01-31 16:02:23.600][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2026-01-31 16:02:23.602][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2026-01-31 16:02:23.604][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2026-01-31 16:02:23.605][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2026-01-31 16:02:23.607][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2026-01-31 16:02:23.609][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2026-01-31 16:02:23.610][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2026-01-31 16:02:23.612][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2026-01-31 16:02:23.614][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2026-01-31 16:02:23.616][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2026-01-31 16:02:23.617][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2026-01-31 16:02:23.619][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2026-01-31 16:02:23.621][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2026-01-31 16:02:23.622][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2026-01-31 16:02:23.624][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2026-01-31 16:02:23.626][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2026-01-31 16:02:23.628][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2026-01-31 16:02:23.630][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2026-01-31 16:02:23.631][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2026-01-31 16:02:23.633][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2026-01-31 16:02:23.635][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2026-01-31 16:02:23.637][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2026-01-31 16:02:23.638][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2026-01-31 16:02:23.640][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2026-01-31 16:02:23.642][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2026-01-31 16:02:23.643][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2026-01-31 16:02:23.645][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2026-01-31 16:02:23.647][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2026-01-31 16:02:23.648][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2026-01-31 16:02:23.650][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2026-01-31 16:02:23.652][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2026-01-31 16:02:23.653][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2026-01-31 16:02:23.655][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2026-01-31 16:02:23.657][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2026-01-31 16:02:23.659][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2026-01-31 16:02:23.660][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2026-01-31 16:02:23.662][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2026-01-31 16:02:23.664][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2026-01-31 16:02:23.665][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2026-01-31 16:02:23.667][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2026-01-31 16:02:23.669][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2026-01-31 16:02:23.670][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2026-01-31 16:02:23.672][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2026-01-31 16:02:23.674][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2026-01-31 16:02:23.676][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2026-01-31 16:02:23.677][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2026-01-31 16:02:23.679][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2026-01-31 16:02:23.681][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2026-01-31 16:02:23.683][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2026-01-31 16:02:23.684][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2026-01-31 16:02:23.686][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2026-01-31 16:02:23.688][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2026-01-31 16:02:23.690][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2026-01-31 16:02:23.701][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2026-01-31 16:02:23.703][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2026-01-31 16:02:23.705][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2026-01-31 16:02:23.707][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2026-01-31 16:02:23.709][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2026-01-31 16:02:23.711][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2026-01-31 16:02:23.713][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2026-01-31 16:02:23.714][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2026-01-31 16:02:23.717][initialize] This is biodb version 1.18.0.
biodb.DEBUG[2026-01-31 16:02:23.718][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2026-01-31 16:02:23.719][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2026-01-31 16:02:23.721][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-31 16:02:23.722][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:23.723][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:02:23.724][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:23.725][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-01-31 16:02:23.726][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-01-31 16:02:23.728][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-31 16:02:23.729][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-31 16:02:23.730][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:23.731][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:02:23.732][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:23.733][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-01-31 16:02:23.734][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-01-31 16:02:23.735][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-31 16:02:23.737][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-31 16:02:23.738][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:23.739][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:02:23.740][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:23.741][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-01-31 16:02:23.742][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-01-31 16:02:23.743][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-31 16:02:23.744][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-31 16:02:23.745][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:23.746][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:02:23.748][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:23.749][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-01-31 16:02:23.750][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-01-31 16:02:23.751][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-31 16:02:23.752][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-31 16:02:23.753][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:23.754][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:02:23.755][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:23.756][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-01-31 16:02:23.757][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-01-31 16:02:23.759][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-31 16:02:23.760][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-31 16:02:23.761][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:23.762][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:02:23.763][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:23.764][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-01-31 16:02:23.765][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-01-31 16:02:23.766][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-31 16:02:23.767][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-31 16:02:23.768][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:23.770][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:02:23.771][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:23.772][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-01-31 16:02:23.773][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-01-31 16:02:23.774][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-31 16:02:23.775][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-31 16:02:23.776][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:23.777][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:02:23.778][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:23.779][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-01-31 16:02:23.780][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-01-31 16:02:23.781][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-31 16:02:23.783][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-31 16:02:23.784][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:23.785][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:02:23.786][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:23.787][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-01-31 16:02:23.788][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-01-31 16:02:23.789][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-31 16:02:23.790][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-31 16:02:23.791][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:23.792][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:02:23.794][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:23.795][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-01-31 16:02:23.796][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-01-31 16:02:23.797][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-31 16:02:23.798][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-31 16:02:23.799][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:23.800][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:02:23.801][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:23.802][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-01-31 16:02:23.803][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-01-31 16:02:23.804][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-31 16:02:23.806][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-31 16:02:23.807][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:23.808][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:02:23.809][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:23.810][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-01-31 16:02:23.811][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-01-31 16:02:23.812][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-31 16:02:23.813][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-31 16:02:23.814][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:23.815][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:02:23.817][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:23.818][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-01-31 16:02:23.819][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-01-31 16:02:23.820][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-31 16:02:23.821][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-31 16:02:23.822][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:23.823][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:02:23.824][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:23.825][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-01-31 16:02:23.826][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-01-31 16:02:23.828][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-31 16:02:23.829][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-31 16:02:23.830][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:23.831][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:02:23.832][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:23.833][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-01-31 16:02:23.834][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-01-31 16:02:23.835][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-31 16:02:23.836][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-31 16:02:23.837][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:23.839][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:02:23.840][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:23.841][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-01-31 16:02:23.842][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-01-31 16:02:23.843][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-31 16:02:23.844][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-31 16:02:23.845][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:23.846][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:02:23.849][biodb$loadDefinitions] Load definitions from file "/Users/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNcbi.Rcheck/biodbNcbi/definitions.yml".
biodb.DEBUG[2026-01-31 16:02:23.851][self$getDbsInfo()$define] Define connector ncbi.ccds.
biodb.DEBUG[2026-01-31 16:02:23.853][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2026-01-31 16:02:23.854][self$setPropertyValue] Setting property "description" to "NCBI CCDS database.".
biodb.DEBUG[2026-01-31 16:02:23.855][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-01-31 16:02:23.857][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-01-31 16:02:23.858][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-01-31 16:02:23.859][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-01-31 16:02:23.860][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2026-01-31 16:02:23.862][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-01-31 16:02:23.867][self$setPropertyValue] Setting property "entry.content.type" to "html".
biodb.DEBUG[2026-01-31 16:02:23.869][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-01-31 16:02:23.870][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2026-01-31 16:02:23.872][self$setPropertyValue] Setting property "name" to "NCBI CCDS".
biodb.DEBUG[2026-01-31 16:02:23.873][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-01-31 16:02:23.874][self$setPropertyValue] Setting property "parsing.expr" to "list(attr = "value", path = "//input[@id='DATA']")".
biodb.DEBUG[2026-01-31 16:02:23.874][self$setPropertyValue] Setting property "parsing.expr" to "//b[starts-with(.,'Nucleotide Sequence')]/../tt".
biodb.DEBUG[2026-01-31 16:02:23.876][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2026-01-31 16:02:23.877][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2026-01-31 16:02:23.878][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2026-01-31 16:02:23.879][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-01-31 16:02:23.880][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-01-31 16:02:23.882][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-01-31 16:02:23.883][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-01-31 16:02:23.884][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-01-31 16:02:23.885][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-01-31 16:02:23.886][self$setPropertyValue] Setting property "urls" to "https://www.ncbi.nlm.nih.gov/CCDS/".
biodb.DEBUG[2026-01-31 16:02:23.886][self$setPropertyValue] Setting property "urls" to "https://eutils.ncbi.nlm.nih.gov/entrez/eutils".
biodb.DEBUG[2026-01-31 16:02:23.888][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-01-31 16:02:23.889][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-01-31 16:02:23.890][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2026-01-31 16:02:23.891][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-01-31 16:02:23.893][self$getDbsInfo()$define] Define connector ncbi.gene.
biodb.DEBUG[2026-01-31 16:02:23.895][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2026-01-31 16:02:23.896][self$setPropertyValue] Setting property "description" to "NCBI Gene database.".
biodb.DEBUG[2026-01-31 16:02:23.897][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-01-31 16:02:23.899][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-01-31 16:02:23.900][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-01-31 16:02:23.901][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-01-31 16:02:23.902][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2026-01-31 16:02:23.903][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-01-31 16:02:23.905][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2026-01-31 16:02:23.906][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-01-31 16:02:23.907][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2026-01-31 16:02:23.908][self$setPropertyValue] Setting property "name" to "NCBI Gene".
biodb.DEBUG[2026-01-31 16:02:23.910][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-01-31 16:02:23.911][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-track_geneid".
biodb.DEBUG[2026-01-31 16:02:23.911][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-ref_desc".
biodb.DEBUG[2026-01-31 16:02:23.911][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-ref_maploc".
biodb.DEBUG[2026-01-31 16:02:23.911][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-ref_locus".
biodb.DEBUG[2026-01-31 16:02:23.911][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-ref_syn_E".
biodb.DEBUG[2026-01-31 16:02:23.911][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-commentary_heading[text()='UniProtKB']/..//Dbtag_db[text()='UniProtKB/Swiss-Prot']/..//Object-id_str".
biodb.DEBUG[2026-01-31 16:02:23.912][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2026-01-31 16:02:23.913][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2026-01-31 16:02:23.915][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2026-01-31 16:02:23.916][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-01-31 16:02:23.917][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-01-31 16:02:23.918][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-01-31 16:02:23.919][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-01-31 16:02:23.921][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-01-31 16:02:23.922][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-01-31 16:02:23.923][self$setPropertyValue] Setting property "urls" to "https://www.ncbi.nlm.nih.gov/".
biodb.DEBUG[2026-01-31 16:02:23.923][self$setPropertyValue] Setting property "urls" to "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/".
biodb.DEBUG[2026-01-31 16:02:23.924][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-01-31 16:02:23.925][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-01-31 16:02:23.926][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2026-01-31 16:02:23.928][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-01-31 16:02:23.929][self$getDbsInfo()$define] Define connector ncbi.pubchem.comp.
biodb.DEBUG[2026-01-31 16:02:23.932][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2026-01-31 16:02:23.933][self$setPropertyValue] Setting property "description" to "PubChem Compound database.".
biodb.DEBUG[2026-01-31 16:02:23.935][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-01-31 16:02:23.936][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-01-31 16:02:23.937][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-01-31 16:02:23.938][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-01-31 16:02:23.940][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2026-01-31 16:02:23.941][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-01-31 16:02:23.942][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2026-01-31 16:02:23.944][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-01-31 16:02:23.945][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2026-01-31 16:02:23.946][self$setPropertyValue] Setting property "name" to "PubChem Compound".
biodb.DEBUG[2026-01-31 16:02:23.948][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-01-31 16:02:23.949][self$setPropertyValue] Setting property "parsing.expr" to "//PC-CompoundType_id_cid".
biodb.DEBUG[2026-01-31 16:02:23.949][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='Allowed']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-01-31 16:02:23.949][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='CAS-like Style']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-01-31 16:02:23.949][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='Preferred']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-01-31 16:02:23.949][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='Systematic']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-01-31 16:02:23.949][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='Traditional']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-01-31 16:02:23.949][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='Mass']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-01-31 16:02:23.949][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='Molecular Formula']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-01-31 16:02:23.949][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='InChI']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-01-31 16:02:23.949][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='InChIKey']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-01-31 16:02:23.949][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='Log P']/../../..//PC-InfoData_value_fval".
biodb.DEBUG[2026-01-31 16:02:23.949][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='Molecular Weight']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-01-31 16:02:23.949][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='SMILES']/../PC-Urn_name[text()='Canonical']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-01-31 16:02:23.949][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='SMILES']/../PC-Urn_name[text()='Isomeric']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-01-31 16:02:23.951][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2026-01-31 16:02:23.952][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2026-01-31 16:02:23.952][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2026-01-31 16:02:23.952][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2026-01-31 16:02:23.953][self$setPropertyValue] Setting property "scheduler.n" to "5".
biodb.DEBUG[2026-01-31 16:02:23.954][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-01-31 16:02:23.955][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-01-31 16:02:23.957][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-01-31 16:02:23.958][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-01-31 16:02:23.959][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-01-31 16:02:23.960][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-01-31 16:02:23.961][self$setPropertyValue] Setting property "urls" to "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2026-01-31 16:02:23.961][self$setPropertyValue] Setting property "urls" to "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/".
biodb.DEBUG[2026-01-31 16:02:23.961][self$setPropertyValue] Setting property "urls" to "https://pubchem.ncbi.nlm.nih.gov/rest/pug/".
biodb.DEBUG[2026-01-31 16:02:23.963][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-01-31 16:02:23.964][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-01-31 16:02:23.965][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2026-01-31 16:02:23.966][self$setPropertyValue] Setting property "xml.ns" to "http://www.ncbi.nlm.nih.gov".
biodb.DEBUG[2026-01-31 16:02:23.968][self$getDbsInfo()$define] Define connector ncbi.pubchem.subst.
biodb.DEBUG[2026-01-31 16:02:23.970][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2026-01-31 16:02:23.972][self$setPropertyValue] Setting property "description" to "PubChem Substance database.".
biodb.DEBUG[2026-01-31 16:02:23.973][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-01-31 16:02:23.974][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-01-31 16:02:23.975][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-01-31 16:02:23.977][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-01-31 16:02:23.978][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2026-01-31 16:02:23.979][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-01-31 16:02:23.981][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2026-01-31 16:02:23.982][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-01-31 16:02:23.983][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2026-01-31 16:02:23.984][self$setPropertyValue] Setting property "name" to "PubChem Substance".
biodb.DEBUG[2026-01-31 16:02:23.986][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-01-31 16:02:23.987][self$setPropertyValue] Setting property "parsing.expr" to "//PC-ID_id".
biodb.DEBUG[2026-01-31 16:02:23.987][self$setPropertyValue] Setting property "parsing.expr" to "//PC-CompoundType_id_cid".
biodb.DEBUG[2026-01-31 16:02:23.988][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2026-01-31 16:02:23.990][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2026-01-31 16:02:23.991][self$setPropertyValue] Setting property "scheduler.n" to "5".
biodb.DEBUG[2026-01-31 16:02:23.992][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-01-31 16:02:23.993][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-01-31 16:02:23.994][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-01-31 16:02:23.995][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-01-31 16:02:23.996][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-01-31 16:02:23.998][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-01-31 16:02:23.999][self$setPropertyValue] Setting property "urls" to "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2026-01-31 16:02:23.999][self$setPropertyValue] Setting property "urls" to "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/".
biodb.DEBUG[2026-01-31 16:02:23.999][self$setPropertyValue] Setting property "urls" to "https://pubchem.ncbi.nlm.nih.gov/rest/pug/".
biodb.DEBUG[2026-01-31 16:02:24.000][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-01-31 16:02:24.001][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-01-31 16:02:24.002][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2026-01-31 16:02:24.004][self$setPropertyValue] Setting property "xml.ns" to "http://www.ncbi.nlm.nih.gov".
biodb.DEBUG[2026-01-31 16:02:24.005][self$getEntryFields()$define] Define field ncbi.ccds.id.
biodb.DEBUG[2026-01-31 16:02:24.007][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2026-01-31 16:02:24.009][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2026-01-31 16:02:24.011][self$getEntryFields()$define] Define field ncbi.pubchem.subst.id.
biodb.DEBUG[2026-01-31 16:02:24.013][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2026-01-31 16:02:24.014][self$getEntryFields()$define] Define field uniprot.id.
biodb.DEBUG[2026-01-31 16:02:24.021][super$initialize] Initialize connector ncbi.pubchem.subst.
biodb.DEBUG[2026-01-31 16:02:24.026][biodb$getFactory()$createConn] Creating new connector ncbi.pubchem.subst for database class ncbi.pubchem.subst .
biodb.INFO [2026-01-31 16:02:24.031][biodb::testThat]
biodb.INFO [2026-01-31 16:02:24.037][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2026-01-31 16:02:24.039][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-01-31 16:02:24.040][biodb::testThat]
biodb.TRACE[2026-01-31 16:02:24.043][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNcbi.Rcheck/biodbNcbi/testref/entry-ncbi.pubchem.subst-3-content.xml".
biodb.DEBUG[2026-01-31 16:02:24.045][biodb$getFactory()$createEntryFromCo ...] Creating PubChem Substance entries from 1 content(s).
biodb.DEBUG[2026-01-31 16:02:24.049][biodb$getFactory()$createEntryFromCo ...] Parsing 1 PubChem Substance entries.
biodb.DEBUG[2026-01-31 16:02:24.051][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2026-01-31 16:02:24.052][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2026-01-31 16:02:24.053][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-01-31 16:02:24.059][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2026-01-31 16:02:24.060][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-31 16:02:24.062][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:24.063][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2026-01-31 16:02:24.066][ef$get] Asked field names are: accession.
biodb.TRACE[2026-01-31 16:02:24.067][ef$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-31 16:02:24.068][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:24.070][ef$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:24.071][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-31 16:02:24.072][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-31 16:02:24.074][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:24.075][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:24.076][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-01-31 16:02:24.077][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-01-31 16:02:24.079][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:24.080][ef$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:24.081][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-01-31 16:02:24.082][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-01-31 16:02:24.084][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:24.085][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:24.086][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.subst.id.
biodb.TRACE[2026-01-31 16:02:24.088][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.subst.id.
biodb.TRACE[2026-01-31 16:02:24.089][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:24.090][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:24.091][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.subst.id.
biodb.TRACE[2026-01-31 16:02:24.093][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.subst.id.
biodb.TRACE[2026-01-31 16:02:24.094][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:24.095][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:24.096][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-31 16:02:24.097][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-31 16:02:24.099][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:24.100][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:24.101][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.subst.id.
biodb.TRACE[2026-01-31 16:02:24.102][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.subst.id.
biodb.TRACE[2026-01-31 16:02:24.104][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:24.105][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:24.106][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-31 16:02:24.107][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-31 16:02:24.109][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:24.110][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:24.111][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-31 16:02:24.112][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-31 16:02:24.113][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:24.115][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:24.116][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-31 16:02:24.117][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-31 16:02:24.118][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:24.120][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:24.121][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-31 16:02:24.122][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-31 16:02:24.124][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:24.125][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:24.126][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-31 16:02:24.127][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-31 16:02:24.128][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:24.130][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:24.131][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-31 16:02:24.132][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-31 16:02:24.133][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:24.135][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2026-01-31 16:02:24.136][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 3.
biodb.TRACE[2026-01-31 16:02:24.138][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2026-01-31 16:02:24.140][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2026-01-31 16:02:24.141][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:24.142][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:24.144][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2026-01-31 16:02:24.145][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2026-01-31 16:02:24.146][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:24.147][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:24.149][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2026-01-31 16:02:24.150][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2026-01-31 16:02:24.151][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:24.152][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:24.154][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2026-01-31 16:02:24.155][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2026-01-31 16:02:24.156][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:24.157][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:24.159][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2026-01-31 16:02:24.160][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2026-01-31 16:02:24.161][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:24.162][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:24.164][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2026-01-31 16:02:24.165][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2026-01-31 16:02:24.166][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:24.168][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:24.169][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2026-01-31 16:02:24.170][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2026-01-31 16:02:24.172][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:24.173][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:24.175][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-31 16:02:24.176][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-31 16:02:24.177][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:24.179][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:24.185][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.subst.id.
biodb.TRACE[2026-01-31 16:02:24.187][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.subst.id.
biodb.TRACE[2026-01-31 16:02:24.188][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:24.189][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:24.196][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-31 16:02:24.197][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-31 16:02:24.199][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:24.200][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:24.201][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-31 16:02:24.202][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-31 16:02:24.204][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:24.205][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:24.211][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-31 16:02:24.213][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-31 16:02:24.214][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:24.216][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:24.219][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-31 16:02:24.221][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-31 16:02:24.222][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:24.223][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:24.224][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-31 16:02:24.226][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-31 16:02:24.227][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:24.228][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:24.229][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-31 16:02:24.231][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-31 16:02:24.232][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:24.233][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:24.235][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.subst.id.
biodb.TRACE[2026-01-31 16:02:24.236][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.subst.id.
biodb.TRACE[2026-01-31 16:02:24.237][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:24.238][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:24.240][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.subst.id.
biodb.TRACE[2026-01-31 16:02:24.241][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.subst.id.
biodb.TRACE[2026-01-31 16:02:24.242][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:24.243][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:24.245][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.subst.id.
biodb.TRACE[2026-01-31 16:02:24.246][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.subst.id.
biodb.TRACE[2026-01-31 16:02:24.247][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:24.248][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:24.257][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-31 16:02:24.259][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-31 16:02:24.260][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:24.261][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:24.263][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-31 16:02:24.264][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-31 16:02:24.265][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:24.266][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:24.268][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-31 16:02:24.269][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-31 16:02:24.270][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:24.271][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:24.273][ef$get] Asked field names are: accession.
biodb.TRACE[2026-01-31 16:02:24.274][ef$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-31 16:02:24.275][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:24.277][ef$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:24.278][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-31 16:02:24.279][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-31 16:02:24.280][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:24.281][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:24.293][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-01-31 16:02:24.295][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-01-31 16:02:24.296][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:24.297][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:24.298][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-01-31 16:02:24.300][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-01-31 16:02:24.301][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:24.302][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:24.303][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-01-31 16:02:24.305][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-01-31 16:02:24.306][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:24.307][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:24.308][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-01-31 16:02:24.310][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-01-31 16:02:24.311][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:24.312][ef$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:24.313][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-01-31 16:02:24.315][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-01-31 16:02:24.316][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:24.317][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:24.329][ef$get] Asked field names are: accession.
biodb.TRACE[2026-01-31 16:02:24.330][ef$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-31 16:02:24.331][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:24.333][ef$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:24.339][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-01-31 16:02:24.340][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-01-31 16:02:24.342][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:24.343][ef$get] fields variable is a list.
biodb.INFO [2026-01-31 16:02:24.353][biodb::testThat]
biodb.INFO [2026-01-31 16:02:24.354][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2026-01-31 16:02:24.355][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-01-31 16:02:24.357][biodb::testThat]
biodb.DEBUG[2026-01-31 16:02:24.360][private$loadEntries] Creating entries from ids [1]: "3".
biodb.DEBUG[2026-01-31 16:02:24.364][conn$getEntryContent] Get PubChem Substance entry content(s) for 1 id(s)...
fscache.INFO [2026-01-31 16:02:24.366][cch$loadContents] Load 1 contents, from /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/ncbi.pubchem.subst-e80afa72f6aa7425ca0c72f99f7b9d75.
biodb.DEBUG[2026-01-31 16:02:24.367][conn$getEntryContent] 0 PubChem Substance entry content(s) loaded from cache.
biodb.DEBUG[2026-01-31 16:02:24.368][conn$getEntryContent] 1 entry content(s) need to be fetched from PubChem Substance database "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2026-01-31 16:02:24.370][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2026-01-31 16:02:24.371][conn$getEntryContent] 1 chunk(s) to download.
biodb.INFO [2026-01-31 16:02:24.372][private$retrieveContents] Get entry content(s) for 1 id(s)...
Saving _problems/test_long_400_pubchem.subst-38.R
biodb.INFO [2026-01-31 16:02:24.435][biodb::testThat]
biodb.INFO [2026-01-31 16:02:24.436][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2026-01-31 16:02:24.438][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-01-31 16:02:24.439][biodb::testThat]
biodb.INFO [2026-01-31 16:02:24.447][biodb::testThat]
biodb.INFO [2026-01-31 16:02:24.449][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2026-01-31 16:02:24.450][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-01-31 16:02:24.451][biodb::testThat]
biodb.WARN [2026-01-31 16:02:24.454][self$searchForEntries] This database is not searchable by field "name".
biodb.WARN [2026-01-31 16:02:24.459][self$searchForEntries] This database is not searchable by field "name".
biodb.INFO [2026-01-31 16:02:24.470][biodb::testThat]
biodb.INFO [2026-01-31 16:02:24.471][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2026-01-31 16:02:24.472][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-01-31 16:02:24.473][biodb::testThat]
biodb.DEBUG[2026-01-31 16:02:24.478][private$loadEntries] Creating entries from ids [1]: "3".
biodb.DEBUG[2026-01-31 16:02:24.480][conn$getEntryContent] Get PubChem Substance entry content(s) for 1 id(s)...
fscache.INFO [2026-01-31 16:02:24.482][cch$loadContents] Load 1 contents, from /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/ncbi.pubchem.subst-e80afa72f6aa7425ca0c72f99f7b9d75.
biodb.DEBUG[2026-01-31 16:02:24.483][conn$getEntryContent] 0 PubChem Substance entry content(s) loaded from cache.
biodb.DEBUG[2026-01-31 16:02:24.484][conn$getEntryContent] 1 entry content(s) need to be fetched from PubChem Substance database "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2026-01-31 16:02:24.485][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2026-01-31 16:02:24.487][conn$getEntryContent] 1 chunk(s) to download.
biodb.INFO [2026-01-31 16:02:24.488][private$retrieveContents] Get entry content(s) for 1 id(s)...
Saving _problems/test_long_400_pubchem.subst-38.R
biodb.INFO [2026-01-31 16:02:24.551][biodb::testThat]
biodb.INFO [2026-01-31 16:02:24.552][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2026-01-31 16:02:24.554][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-01-31 16:02:24.555][biodb::testThat]
Saving _problems/test_long_400_pubchem.subst-38.R
biodb.INFO [2026-01-31 16:02:24.615][biodb::testThat]
biodb.INFO [2026-01-31 16:02:24.616][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2026-01-31 16:02:24.617][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-01-31 16:02:24.619][biodb::testThat]
Saving _problems/test_long_400_pubchem.subst-38.R
biodb.INFO [2026-01-31 16:02:24.675][biodb::testThat]
biodb.INFO [2026-01-31 16:02:24.676][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2026-01-31 16:02:24.677][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-01-31 16:02:24.679][biodb::testThat]
Saving _problems/test_long_400_pubchem.subst-38.R
biodb.INFO [2026-01-31 16:02:24.742][biodb::testThat]
biodb.INFO [2026-01-31 16:02:24.743][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2026-01-31 16:02:24.744][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-01-31 16:02:24.745][biodb::testThat]
Saving _problems/test_long_400_pubchem.subst-38.R
biodb.INFO [2026-01-31 16:02:24.803][biodb$terminate] Closing BiodbMain instance...
biodb.INFO [2026-01-31 16:02:24.805][self$deleteConn] Connector "ncbi.pubchem.subst" deleted.
biodb.DEBUG[2026-01-31 16:02:24.806][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2026-01-31 16:02:24.807][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-01-31 16:02:24.809][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-01-31 16:02:24.810][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-31 16:02:24.811][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-31 16:02:24.812][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:24.813][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
[ FAIL 31 | WARN 1 | SKIP 1 | PASS 247 ]

══ Skipped tests (1) ═══════════════════════════════════════════════════════════
• empty test (1):

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test_long_100_ccds.R:37:1'): RT unit is defined when there is an RT value. ──
Error: 'BiodbUrl' is not an exported object from 'namespace:biodb'
Backtrace:
     ▆
  1. ├─base::do.call(fct, params)
  2. └─biodb (local) `<fn>`(conn = `<NcbCcdsC>`, opt = `<named list>`)
  3.   └─conn$getBiodb()$getFactory()$getEntry(...)
  4.     └─private$loadEntries(conn$getId(), missing.ids, drop = FALSE)
  5.       └─conn$getEntryContent(ids)
  6.         └─self$getEntryContentFromDb(ch.missing.ids)
  7.           └─private$doGetEntryContentFromDb(entry.id)
  8.             └─private$doGetEntryContentOneByOne(id)
  9.               └─self$getEntryContentRequest(entry.id, concatenate = FALSE)
 10.                 └─private$doGetEntryContentRequest(entry.id, concatenate = concatenate)
 11.                   └─self$getEntryPageUrl(id)
 12.                     └─private$doGetEntryPageUrl(entry.id)
 13.                       └─base::vapply(id, fct, FUN.VALUE = "")
 14.                         └─biodbNcbi (local) FUN(X[[i]], ...)
── Error ('test_long_100_ccds.R:37:1'): We can load an entry from the database. ──
Error: 'BiodbUrl' is not an exported object from 'namespace:biodb'
Backtrace:
     ▆
  1. ├─base::do.call(fct, params)
  2. └─biodb (local) `<fn>`(conn = `<NcbCcdsC>`, opt = `<named list>`)
  3.   └─opt$refEntries$getRealEntry(id)
  4.     └─self$getRealEntries(ids = id)
  5.       └─private$bdb$getFactory()$getEntry(...)
  6.         └─private$loadEntries(conn$getId(), missing.ids, drop = FALSE)
  7.           └─conn$getEntryContent(ids)
  8.             └─self$getEntryContentFromDb(ch.missing.ids)
  9.               └─private$doGetEntryContentFromDb(entry.id)
 10.                 └─private$doGetEntryContentOneByOne(id)
 11.                   └─self$getEntryContentRequest(entry.id, concatenate = FALSE)
 12.                     └─private$doGetEntryContentRequest(entry.id, concatenate = concatenate)
 13.                       └─self$getEntryPageUrl(id)
 14.                         └─private$doGetEntryPageUrl(entry.id)
 15.                           └─base::vapply(id, fct, FUN.VALUE = "")
 16.                             └─biodbNcbi (local) FUN(X[[i]], ...)
── Error ('test_long_100_ccds.R:37:1'): We can get a URL pointing to the entry page. ──
Error: 'BiodbUrl' is not an exported object from 'namespace:biodb'
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb (local) `<fn>`(conn = `<NcbCcdsC>`, opt = `<named list>`)
 3.   └─conn$getEntryPageUrl(ref.ids)
 4.     └─private$doGetEntryPageUrl(entry.id)
 5.       └─base::vapply(id, fct, FUN.VALUE = "")
 6.         └─biodbNcbi (local) FUN(X[[i]], ...)
── Error ('test_long_100_ccds.R:37:1'): The entry page URL can be downloaded. ──
Error: 'BiodbUrl' is not an exported object from 'namespace:biodb'
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb (local) `<fn>`(conn = `<NcbCcdsC>`, opt = `<named list>`)
 3.   └─conn$getEntryPageUrl(ref.ids[[1]])
 4.     └─private$doGetEntryPageUrl(entry.id)
 5.       └─base::vapply(id, fct, FUN.VALUE = "")
 6.         └─biodbNcbi (local) FUN(X[[i]], ...)
── Error ('test_long_200_gene.R:37:1'): Entry fields have a correct value ──────
Error: 'BiodbUrl' is not an exported object from 'namespace:biodb'
Backtrace:
     ▆
  1. ├─base::do.call(fct, params)
  2. └─biodb (local) `<fn>`(conn = `<NcbGnCnn>`, opt = `<named list>`)
  3.   └─opt$refEntries$saveEntriesAsJson(id, list(e))
  4.     └─private$bdb$saveEntriesAsJson(entries, json.files)
  5.       └─entries[[i]]$getFieldsAsJson(compute = compute)
  6.         └─self$computeFields()
  7.           └─private$computeField(f)
  8.             └─self$getBiodb()$getFactory()$getEntry(db, id = db.id)
  9.               └─private$loadEntries(conn$getId(), missing.ids, drop = FALSE)
 10.                 └─conn$getEntryContent(ids)
 11.                   └─self$getEntryContentFromDb(ch.missing.ids)
 12.                     └─private$doGetEntryContentFromDb(entry.id)
 13.                       └─private$doGetEntryContentOneByOne(id)
 14.                         └─self$getEntryContentRequest(entry.id, concatenate = FALSE)
 15.                           └─private$doGetEntryContentRequest(entry.id, concatenate = concatenate)
 16.                             └─self$getEntryPageUrl(id)
 17.                               └─private$doGetEntryPageUrl(entry.id)
 18.                                 └─base::vapply(id, fct, FUN.VALUE = "")
 19.                                   └─biodbNcbi (local) FUN(X[[i]], ...)
── Error ('test_long_200_gene.R:37:1'): RT unit is defined when there is an RT value. ──
Error: 'BiodbUrl' is not an exported object from 'namespace:biodb'
Backtrace:
     ▆
  1. ├─base::do.call(fct, params)
  2. └─biodb (local) `<fn>`(conn = `<NcbGnCnn>`, opt = `<named list>`)
  3.   └─conn$getBiodb()$getFactory()$getEntry(...)
  4.     └─private$loadEntries(conn$getId(), missing.ids, drop = FALSE)
  5.       └─conn$getEntryContent(ids)
  6.         └─self$getEntryContentFromDb(ch.missing.ids)
  7.           └─private$doGetEntryContentFromDb(entry.id)
  8.             └─private$retrieveContents(...)
  9.               └─self$getEntryContentRequest(id, concatenate = concatenate, max.length = URL.MAX.LENGTH)
 10.                 └─private$doGetEntryContentRequest(entry.id, concatenate = concatenate)
 11.                   └─self$wsEfetch(id, retmode = "xml", retfmt = "request")
── Error ('test_long_200_gene.R:37:1'): We can search for an entry by searchable field ──
Error: 'BiodbUrl' is not an exported object from 'namespace:biodb'
Backtrace:
     ▆
  1. ├─base::do.call(fct, params)
  2. └─biodb (local) `<fn>`(conn = `<NcbGnCnn>`, opt = `<named list>`)
  3.   └─conn$getEntry(id, drop = TRUE)
  4.     └─private$bdb$getFactory()$getEntry(self$getId(), id = id, drop = drop)
  5.       └─private$loadEntries(conn$getId(), missing.ids, drop = FALSE)
  6.         └─conn$getEntryContent(ids)
  7.           └─self$getEntryContentFromDb(ch.missing.ids)
  8.             └─private$doGetEntryContentFromDb(entry.id)
  9.               └─private$retrieveContents(...)
 10.                 └─self$getEntryContentRequest(id, concatenate = concatenate, max.length = URL.MAX.LENGTH)
 11.                   └─private$doGetEntryContentRequest(entry.id, concatenate = concatenate)
 12.                     └─self$wsEfetch(id, retmode = "xml", retfmt = "request")
── Error ('test_long_200_gene.R:37:1'): We can search for an entry by name. ────
Error: 'BiodbUrl' is not an exported object from 'namespace:biodb'
Backtrace:
     ▆
  1. ├─base::do.call(fct, params)
  2. └─biodb (local) `<fn>`(conn = `<NcbGnCnn>`, opt = `<named list>`)
  3.   └─conn$getEntry(id, drop = TRUE)
  4.     └─private$bdb$getFactory()$getEntry(self$getId(), id = id, drop = drop)
  5.       └─private$loadEntries(conn$getId(), missing.ids, drop = FALSE)
  6.         └─conn$getEntryContent(ids)
  7.           └─self$getEntryContentFromDb(ch.missing.ids)
  8.             └─private$doGetEntryContentFromDb(entry.id)
  9.               └─private$retrieveContents(...)
 10.                 └─self$getEntryContentRequest(id, concatenate = concatenate, max.length = URL.MAX.LENGTH)
 11.                   └─private$doGetEntryContentRequest(entry.id, concatenate = concatenate)
 12.                     └─self$wsEfetch(id, retmode = "xml", retfmt = "request")
── Error ('test_long_200_gene.R:37:1'): We can load an entry from the database. ──
Error: 'BiodbUrl' is not an exported object from 'namespace:biodb'
Backtrace:
     ▆
  1. ├─base::do.call(fct, params)
  2. └─biodb (local) `<fn>`(conn = `<NcbGnCnn>`, opt = `<named list>`)
  3.   └─opt$refEntries$getRealEntry(id)
  4.     └─self$getRealEntries(ids = id)
  5.       └─private$bdb$getFactory()$getEntry(...)
  6.         └─private$loadEntries(conn$getId(), missing.ids, drop = FALSE)
  7.           └─conn$getEntryContent(ids)
  8.             └─self$getEntryContentFromDb(ch.missing.ids)
  9.               └─private$doGetEntryContentFromDb(entry.id)
 10.                 └─private$retrieveContents(...)
 11.                   └─self$getEntryContentRequest(id, concatenate = concatenate, max.length = URL.MAX.LENGTH)
 12.                     └─private$doGetEntryContentRequest(entry.id, concatenate = concatenate)
 13.                       └─self$wsEfetch(id, retmode = "xml", retfmt = "request")
── Error ('test_long_200_gene.R:37:1'): We can get a URL pointing to the entry page. ──
Error: 'BiodbUrl' is not an exported object from 'namespace:biodb'
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb (local) `<fn>`(conn = `<NcbGnCnn>`, opt = `<named list>`)
 3.   └─conn$getEntryPageUrl(ref.ids)
 4.     └─private$doGetEntryPageUrl(entry.id)
 5.       └─base::vapply(id, fct, FUN.VALUE = "")
 6.         └─biodbNcbi (local) FUN(X[[i]], ...)
── Error ('test_long_200_gene.R:37:1'): The entry page URL can be downloaded. ──
Error: 'BiodbUrl' is not an exported object from 'namespace:biodb'
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb (local) `<fn>`(conn = `<NcbGnCnn>`, opt = `<named list>`)
 3.   └─conn$getEntryPageUrl(ref.ids[[1]])
 4.     └─private$doGetEntryPageUrl(entry.id)
 5.       └─base::vapply(id, fct, FUN.VALUE = "")
 6.         └─biodbNcbi (local) FUN(X[[i]], ...)
── Error ('test_long_300_pubchem.comp.R:37:1'): RT unit is defined when there is an RT value. ──
Error: 'BiodbUrl' is not an exported object from 'namespace:biodb'
Backtrace:
     ▆
  1. ├─base::do.call(fct, params)
  2. └─biodb (local) `<fn>`(conn = `<NcbPbcCC>`, opt = `<named list>`)
  3.   └─conn$getBiodb()$getFactory()$getEntry(...)
  4.     └─private$loadEntries(conn$getId(), missing.ids, drop = FALSE)
  5.       └─conn$getEntryContent(ids)
  6.         └─self$getEntryContentFromDb(ch.missing.ids)
  7.           └─private$doGetEntryContentFromDb(entry.id)
  8.             └─private$retrieveContents(...)
  9.               └─self$getEntryContentRequest(id, concatenate = concatenate, max.length = URL.MAX.LENGTH)
 10.                 └─private$doGetEntryContentRequest(entry.id, concatenate = concatenate)
── Error ('test_long_300_pubchem.comp.R:37:1'): We can search for an entry by searchable field ──
Error: 'BiodbUrl' is not an exported object from 'namespace:biodb'
Backtrace:
     ▆
  1. ├─base::do.call(fct, params)
  2. └─biodb (local) `<fn>`(conn = `<NcbPbcCC>`, opt = `<named list>`)
  3.   └─conn$getEntry(id, drop = TRUE)
  4.     └─private$bdb$getFactory()$getEntry(self$getId(), id = id, drop = drop)
  5.       └─private$loadEntries(conn$getId(), missing.ids, drop = FALSE)
  6.         └─conn$getEntryContent(ids)
  7.           └─self$getEntryContentFromDb(ch.missing.ids)
  8.             └─private$doGetEntryContentFromDb(entry.id)
  9.               └─private$retrieveContents(...)
 10.                 └─self$getEntryContentRequest(id, concatenate = concatenate, max.length = URL.MAX.LENGTH)
 11.                   └─private$doGetEntryContentRequest(entry.id, concatenate = concatenate)
── Error ('test_long_300_pubchem.comp.R:37:1'): We can search for an entry by name. ──
Error: 'BiodbUrl' is not an exported object from 'namespace:biodb'
Backtrace:
     ▆
  1. ├─base::do.call(fct, params)
  2. └─biodb (local) `<fn>`(conn = `<NcbPbcCC>`, opt = `<named list>`)
  3.   └─conn$getEntry(id, drop = TRUE)
  4.     └─private$bdb$getFactory()$getEntry(self$getId(), id = id, drop = drop)
  5.       └─private$loadEntries(conn$getId(), missing.ids, drop = FALSE)
  6.         └─conn$getEntryContent(ids)
  7.           └─self$getEntryContentFromDb(ch.missing.ids)
  8.             └─private$doGetEntryContentFromDb(entry.id)
  9.               └─private$retrieveContents(...)
 10.                 └─self$getEntryContentRequest(id, concatenate = concatenate, max.length = URL.MAX.LENGTH)
 11.                   └─private$doGetEntryContentRequest(entry.id, concatenate = concatenate)
── Error ('test_long_300_pubchem.comp.R:37:1'): We can load an entry from the database. ──
Error: 'BiodbUrl' is not an exported object from 'namespace:biodb'
Backtrace:
     ▆
  1. ├─base::do.call(fct, params)
  2. └─biodb (local) `<fn>`(conn = `<NcbPbcCC>`, opt = `<named list>`)
  3.   └─opt$refEntries$getRealEntry(id)
  4.     └─self$getRealEntries(ids = id)
  5.       └─private$bdb$getFactory()$getEntry(...)
  6.         └─private$loadEntries(conn$getId(), missing.ids, drop = FALSE)
  7.           └─conn$getEntryContent(ids)
  8.             └─self$getEntryContentFromDb(ch.missing.ids)
  9.               └─private$doGetEntryContentFromDb(entry.id)
 10.                 └─private$retrieveContents(...)
 11.                   └─self$getEntryContentRequest(id, concatenate = concatenate, max.length = URL.MAX.LENGTH)
 12.                     └─private$doGetEntryContentRequest(entry.id, concatenate = concatenate)
── Error ('test_long_300_pubchem.comp.R:37:1'): We can get a URL pointing to the entry page. ──
Error: 'BiodbUrl' is not an exported object from 'namespace:biodb'
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb (local) `<fn>`(conn = `<NcbPbcCC>`, opt = `<named list>`)
 3.   └─conn$getEntryPageUrl(ref.ids)
 4.     └─private$doGetEntryPageUrl(entry.id)
 5.       └─base::vapply(id, fct, FUN.VALUE = "")
 6.         └─biodbNcbi (local) FUN(X[[i]], ...)
── Error ('test_long_300_pubchem.comp.R:37:1'): We can get a URL pointing to the entry image. ──
Error: 'BiodbUrl' is not an exported object from 'namespace:biodb'
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb (local) `<fn>`(conn = `<NcbPbcCC>`, opt = `<named list>`)
 3.   └─conn$getEntryImageUrl(ref.ids)
 4.     └─private$doGetEntryImageUrl(entry.id)
── Error ('test_long_300_pubchem.comp.R:37:1'): The entry page URL can be downloaded. ──
Error: 'BiodbUrl' is not an exported object from 'namespace:biodb'
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb (local) `<fn>`(conn = `<NcbPbcCC>`, opt = `<named list>`)
 3.   └─conn$getEntryPageUrl(ref.ids[[1]])
 4.     └─private$doGetEntryPageUrl(entry.id)
 5.       └─base::vapply(id, fct, FUN.VALUE = "")
 6.         └─biodbNcbi (local) FUN(X[[i]], ...)
── Error ('test_long_300_pubchem.comp.R:37:1'): The entry image URL can be downloaded. ──
Error: 'BiodbUrl' is not an exported object from 'namespace:biodb'
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb (local) `<fn>`(conn = `<NcbPbcCC>`, opt = `<named list>`)
 3.   └─conn$getEntryImageUrl(ref.ids[[1]])
 4.     └─private$doGetEntryImageUrl(entry.id)
── Error ('test_long_300_pubchem.comp.R:37:1'): We can search for a compound ───
Error: 'BiodbUrl' is not an exported object from 'namespace:biodb'
Backtrace:
     ▆
  1. ├─base::do.call(fct, params)
  2. └─biodb (local) `<fn>`(db = `<NcbPbcCC>`, opt = `<named list>`)
  3.   └─db$getEntry(id, drop = TRUE)
  4.     └─private$bdb$getFactory()$getEntry(self$getId(), id = id, drop = drop)
  5.       └─private$loadEntries(conn$getId(), missing.ids, drop = FALSE)
  6.         └─conn$getEntryContent(ids)
  7.           └─self$getEntryContentFromDb(ch.missing.ids)
  8.             └─private$doGetEntryContentFromDb(entry.id)
  9.               └─private$retrieveContents(...)
 10.                 └─self$getEntryContentRequest(id, concatenate = concatenate, max.length = URL.MAX.LENGTH)
 11.                   └─private$doGetEntryContentRequest(entry.id, concatenate = concatenate)
── Error ('test_long_300_pubchem.comp.R:37:1'): annotateMzValues() accepts a single vector. ──
Error: 'BiodbUrl' is not an exported object from 'namespace:biodb'
Backtrace:
     ▆
  1. ├─base::do.call(fct, params)
  2. └─biodb (local) `<fn>`(conn = `<NcbPbcCC>`, opt = `<named list>`)
  3.   └─conn$getEntry(ids, drop = FALSE)
  4.     └─private$bdb$getFactory()$getEntry(self$getId(), id = id, drop = drop)
  5.       └─private$loadEntries(conn$getId(), missing.ids, drop = FALSE)
  6.         └─conn$getEntryContent(ids)
  7.           └─self$getEntryContentFromDb(ch.missing.ids)
  8.             └─private$doGetEntryContentFromDb(entry.id)
  9.               └─private$retrieveContents(...)
 10.                 └─self$getEntryContentRequest(id, concatenate = concatenate, max.length = URL.MAX.LENGTH)
 11.                   └─private$doGetEntryContentRequest(entry.id, concatenate = concatenate)
── Error ('test_long_300_pubchem.comp.R:37:1'): ppm tolerance works in annotateMzValues() ──
Error: 'BiodbUrl' is not an exported object from 'namespace:biodb'
Backtrace:
     ▆
  1. ├─base::do.call(fct, params)
  2. └─biodb (local) `<fn>`(conn = `<NcbPbcCC>`, opt = `<named list>`)
  3.   └─conn$getEntry(ids, drop = FALSE)
  4.     └─private$bdb$getFactory()$getEntry(self$getId(), id = id, drop = drop)
  5.       └─private$loadEntries(conn$getId(), missing.ids, drop = FALSE)
  6.         └─conn$getEntryContent(ids)
  7.           └─self$getEntryContentFromDb(ch.missing.ids)
  8.             └─private$doGetEntryContentFromDb(entry.id)
  9.               └─private$retrieveContents(...)
 10.                 └─self$getEntryContentRequest(id, concatenate = concatenate, max.length = URL.MAX.LENGTH)
 11.                   └─private$doGetEntryContentRequest(entry.id, concatenate = concatenate)
── Error ('test_long_300_pubchem.comp.R:37:1'): Input data frame is not modified by annotateMzValues() ──
Error: 'BiodbUrl' is not an exported object from 'namespace:biodb'
Backtrace:
     ▆
  1. ├─base::do.call(fct, params)
  2. └─biodb (local) `<fn>`(conn = `<NcbPbcCC>`, opt = `<named list>`)
  3.   └─conn$getEntry(ids, drop = FALSE)
  4.     └─private$bdb$getFactory()$getEntry(self$getId(), id = id, drop = drop)
  5.       └─private$loadEntries(conn$getId(), missing.ids, drop = FALSE)
  6.         └─conn$getEntryContent(ids)
  7.           └─self$getEntryContentFromDb(ch.missing.ids)
  8.             └─private$doGetEntryContentFromDb(entry.id)
  9.               └─private$retrieveContents(...)
 10.                 └─self$getEntryContentRequest(id, concatenate = concatenate, max.length = URL.MAX.LENGTH)
 11.                   └─private$doGetEntryContentRequest(entry.id, concatenate = concatenate)
── Error ('test_long_300_pubchem.comp.R:37:1'): annotateMzValues() works correctly with real values. ──
Error: 'BiodbUrl' is not an exported object from 'namespace:biodb'
Backtrace:
     ▆
  1. ├─base::do.call(fct, params)
  2. └─biodb (local) `<fn>`(conn = `<NcbPbcCC>`, opt = `<named list>`)
  3.   └─conn$getEntry(ids, drop = FALSE)
  4.     └─private$bdb$getFactory()$getEntry(self$getId(), id = id, drop = drop)
  5.       └─private$loadEntries(conn$getId(), missing.ids, drop = FALSE)
  6.         └─conn$getEntryContent(ids)
  7.           └─self$getEntryContentFromDb(ch.missing.ids)
  8.             └─private$doGetEntryContentFromDb(entry.id)
  9.               └─private$retrieveContents(...)
 10.                 └─self$getEntryContentRequest(id, concatenate = concatenate, max.length = URL.MAX.LENGTH)
 11.                   └─private$doGetEntryContentRequest(entry.id, concatenate = concatenate)
── Error ('test_long_300_pubchem.comp.R:37:1'): Additional fields are accepted in annotateMzValues() ──
Error: 'BiodbUrl' is not an exported object from 'namespace:biodb'
Backtrace:
     ▆
  1. ├─base::do.call(fct, params)
  2. └─biodb (local) `<fn>`(conn = `<NcbPbcCC>`, opt = `<named list>`)
  3.   └─conn$getEntry(ids, drop = FALSE)
  4.     └─private$bdb$getFactory()$getEntry(self$getId(), id = id, drop = drop)
  5.       └─private$loadEntries(conn$getId(), missing.ids, drop = FALSE)
  6.         └─conn$getEntryContent(ids)
  7.           └─self$getEntryContentFromDb(ch.missing.ids)
  8.             └─private$doGetEntryContentFromDb(entry.id)
  9.               └─private$retrieveContents(...)
 10.                 └─self$getEntryContentRequest(id, concatenate = concatenate, max.length = URL.MAX.LENGTH)
 11.                   └─private$doGetEntryContentRequest(entry.id, concatenate = concatenate)
── Error ('test_long_400_pubchem.subst.R:37:1'): RT unit is defined when there is an RT value. ──
Error: 'BiodbUrl' is not an exported object from 'namespace:biodb'
Backtrace:
     ▆
  1. ├─base::do.call(fct, params)
  2. └─biodb (local) `<fn>`(conn = `<NcbPbcSC>`, opt = `<named list>`)
  3.   └─conn$getBiodb()$getFactory()$getEntry(...)
  4.     └─private$loadEntries(conn$getId(), missing.ids, drop = FALSE)
  5.       └─conn$getEntryContent(ids)
  6.         └─self$getEntryContentFromDb(ch.missing.ids)
  7.           └─private$doGetEntryContentFromDb(entry.id)
  8.             └─private$retrieveContents(...)
  9.               └─self$getEntryContentRequest(id, concatenate = concatenate, max.length = URL.MAX.LENGTH)
 10.                 └─private$doGetEntryContentRequest(entry.id, concatenate = concatenate)
── Error ('test_long_400_pubchem.subst.R:37:1'): We can load an entry from the database. ──
Error: 'BiodbUrl' is not an exported object from 'namespace:biodb'
Backtrace:
     ▆
  1. ├─base::do.call(fct, params)
  2. └─biodb (local) `<fn>`(conn = `<NcbPbcSC>`, opt = `<named list>`)
  3.   └─opt$refEntries$getRealEntry(id)
  4.     └─self$getRealEntries(ids = id)
  5.       └─private$bdb$getFactory()$getEntry(...)
  6.         └─private$loadEntries(conn$getId(), missing.ids, drop = FALSE)
  7.           └─conn$getEntryContent(ids)
  8.             └─self$getEntryContentFromDb(ch.missing.ids)
  9.               └─private$doGetEntryContentFromDb(entry.id)
 10.                 └─private$retrieveContents(...)
 11.                   └─self$getEntryContentRequest(id, concatenate = concatenate, max.length = URL.MAX.LENGTH)
 12.                     └─private$doGetEntryContentRequest(entry.id, concatenate = concatenate)
── Error ('test_long_400_pubchem.subst.R:37:1'): We can get a URL pointing to the entry page. ──
Error: 'BiodbUrl' is not an exported object from 'namespace:biodb'
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb (local) `<fn>`(conn = `<NcbPbcSC>`, opt = `<named list>`)
 3.   └─conn$getEntryPageUrl(ref.ids)
 4.     └─private$doGetEntryPageUrl(entry.id)
 5.       └─base::vapply(id, fct, FUN.VALUE = "")
 6.         └─biodbNcbi (local) FUN(X[[i]], ...)
── Error ('test_long_400_pubchem.subst.R:37:1'): We can get a URL pointing to the entry image. ──
Error: 'BiodbUrl' is not an exported object from 'namespace:biodb'
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb (local) `<fn>`(conn = `<NcbPbcSC>`, opt = `<named list>`)
 3.   └─conn$getEntryImageUrl(ref.ids)
 4.     └─private$doGetEntryImageUrl(entry.id)
── Error ('test_long_400_pubchem.subst.R:37:1'): The entry page URL can be downloaded. ──
Error: 'BiodbUrl' is not an exported object from 'namespace:biodb'
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb (local) `<fn>`(conn = `<NcbPbcSC>`, opt = `<named list>`)
 3.   └─conn$getEntryPageUrl(ref.ids[[1]])
 4.     └─private$doGetEntryPageUrl(entry.id)
 5.       └─base::vapply(id, fct, FUN.VALUE = "")
 6.         └─biodbNcbi (local) FUN(X[[i]], ...)
── Error ('test_long_400_pubchem.subst.R:37:1'): The entry image URL can be downloaded. ──
Error: 'BiodbUrl' is not an exported object from 'namespace:biodb'
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb (local) `<fn>`(conn = `<NcbPbcSC>`, opt = `<named list>`)
 3.   └─conn$getEntryImageUrl(ref.ids[[1]])
 4.     └─private$doGetEntryImageUrl(entry.id)

[ FAIL 31 | WARN 1 | SKIP 1 | PASS 247 ]
Error:
! Test failures.
Warning message:
In fun(libname, pkgname) :
  Package 'biodbNcbi' is deprecated and will be removed from Bioconductor
  version 3.23
Execution halted

'R CMD check' output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --test-dir=longtests --no-stop-on-test-error --no-codoc --no-examples --no-manual --ignore-vignettes --check-subdirs=no biodbNcbi_1.14.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNcbi.Rcheck’
* using R version 4.5.2 (2025-10-31)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using options ‘--no-codoc --no-examples --no-manual --ignore-vignettes --no-stop-on-test-error’
* checking for file ‘biodbNcbi/DESCRIPTION’ ... OK
* this is package ‘biodbNcbi’ version ‘1.14.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘biodbNcbi’ can be installed ... OK
* checking installed package size ... INFO
  installed size is  8.2Mb
  sub-directories of 1Mb or more:
    testref   7.6Mb
* checking package directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Title field: should not end in a period.
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking whether startup messages can be suppressed ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  NcbiCcdsConn.Rd: BiodbFactory, BiodbConn
  NcbiCcdsEntry.Rd: BiodbHtmlEntry
  NcbiEntrezConn.Rd: BiodbConn
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... SKIPPED
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... SKIPPED
* checking examples ... SKIPPED
* checking for unstated dependencies in ‘longtests’ ... OK
* checking tests in ‘longtests’ ...
  Running ‘testthat.R’
 ERROR
Running the tests in ‘longtests/testthat.R’ failed.
Last 13 lines of output:
  Backtrace:
      ▆
   1. ├─base::do.call(fct, params)
   2. └─biodb (local) `<fn>`(conn = `<NcbPbcSC>`, opt = `<named list>`)
   3.   └─conn$getEntryImageUrl(ref.ids[[1]])
   4.     └─private$doGetEntryImageUrl(entry.id)
  
  [ FAIL 31 | WARN 1 | SKIP 1 | PASS 247 ]
  Error:
  ! Test failures.
  Warning message:
  In fun(libname, pkgname) :
    Package 'biodbNcbi' is deprecated and will be removed from Bioconductor
    version 3.23
  Execution halted
* DONE

Status: 1 ERROR, 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNcbi.Rcheck/00check.log’
for details.

Installation output

biodbNcbi.Rcheck/00install.out

* installing *source* package ‘biodbNcbi’ ...
** this is package ‘biodbNcbi’ version ‘1.14.0’
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning in fun(libname, pkgname) :
  Package 'biodbNcbi' is deprecated and will be removed from Bioconductor
  version 3.23
** testing if installed package can be loaded from final location
Warning in fun(libname, pkgname) :
  Package 'biodbNcbi' is deprecated and will be removed from Bioconductor
  version 3.23
** testing if installed package keeps a record of temporary installation path
* DONE (biodbNcbi)