Back to Long Tests report for BioC 3.22

This page was generated on 2026-01-31 23:55 -0500 (Sat, 31 Jan 2026).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 4888
merida1macOS 12.7.6 Montereyx86_644.5.2 (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

Package 8/31HostnameOS / ArchCHECK
biodbNci 1.14.0  (landing page)
Pierrick Roger
Snapshot Date: 2026-01-31 09:55 -0500 (Sat, 31 Jan 2026)
git_url: https://git.bioconductor.org/packages/biodbNci
git_branch: RELEASE_3_22
git_last_commit: 4ce22d8
git_last_commit_date: 2025-10-29 11:15:34 -0500 (Wed, 29 Oct 2025)
nebbiolo2Linux (Ubuntu 24.04.3 LTS) / x86_64  ERROR  
merida1macOS 12.7.6 Monterey / x86_64  ERROR  

CHECK results for biodbNci on merida1

To the developers/maintainers of the biodbNci 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: biodbNci
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 biodbNci_1.14.0.tar.gz
StartedAt: 2026-01-31 16:01:16 -0500 (Sat, 31 Jan 2026)
EndedAt: 2026-01-31 16:02:37 -0500 (Sat, 31 Jan 2026)
EllapsedTime: 80.9 seconds
RetCode: 1
Status:   ERROR  
CheckDir: biodbNci.Rcheck
Warnings: NA

Tests output

biodbNci.Rcheck/tests/testthat.Rout.fail


R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"
Copyright (C) 2025 The R Foundation for Statistical Computing
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("biodbNci")
biodb.INFO [2026-01-31 16:02:32.130][biodb::testContext]
biodb.INFO [2026-01-31 16:02:32.134][biodb::testContext] ********************************************************************************
biodb.INFO [2026-01-31 16:02:32.136][biodb::testContext] Test context - Generic long tests
biodb.INFO [2026-01-31 16:02:32.137][biodb::testContext] ********************************************************************************
biodb.INFO [2026-01-31 16:02:32.138][biodb::testContext]
biodb.INFO [2026-01-31 16:02:32.145][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.18.0.
biodb.DEBUG[2026-01-31 16:02:32.147][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2026-01-31 16:02:32.154][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2026-01-31 16:02:32.156][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2026-01-31 16:02:32.157][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2026-01-31 16:02:32.158][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:32.159][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:32.160][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:02:32.162][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2026-01-31 16:02:32.185][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2026-01-31 16:02:32.186][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:32.188][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:32.189][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 16:02:32.190][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2026-01-31 16:02:32.191][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2026-01-31 16:02:32.192][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:32.193][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:32.195][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:02:32.196][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2026-01-31 16:02:32.197][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2026-01-31 16:02:32.198][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2026-01-31 16:02:32.200][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:32.201][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:32.202][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 16:02:32.203][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2026-01-31 16:02:32.204][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2026-01-31 16:02:32.206][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2026-01-31 16:02:32.207][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:32.208][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:32.209][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:02:32.210][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2026-01-31 16:02:32.212][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2026-01-31 16:02:32.213][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:32.214][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:32.215][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 16:02:32.216][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2026-01-31 16:02:32.217][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2026-01-31 16:02:32.219][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2026-01-31 16:02:32.220][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:32.221][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:32.222][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:02:32.223][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2026-01-31 16:02:32.225][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2026-01-31 16:02:32.226][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:32.227][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:32.228][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 16:02:32.229][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2026-01-31 16:02:32.230][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2026-01-31 16:02:32.232][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2026-01-31 16:02:32.233][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:32.234][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:32.235][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:02:32.236][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2026-01-31 16:02:32.238][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2026-01-31 16:02:32.239][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2026-01-31 16:02:32.240][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2026-01-31 16:02:32.241][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2026-01-31 16:02:32.243][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2026-01-31 16:02:32.244][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:32.245][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:32.246][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 16:02:32.247][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2026-01-31 16:02:32.249][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2026-01-31 16:02:32.250][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:32.251][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:32.252][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:02:32.253][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2026-01-31 16:02:32.255][self$set] Set key entries.sep to "|".
biodb.DEBUG[2026-01-31 16:02:32.256][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:32.257][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:32.258][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 16:02:32.259][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2026-01-31 16:02:32.261][self$set] Set key offline to FALSE.
biodb.DEBUG[2026-01-31 16:02:32.262][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:32.263][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:32.264][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:02:32.265][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2026-01-31 16:02:32.267][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2026-01-31 16:02:32.268][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2026-01-31 16:02:32.269][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:32.270][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:32.271][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 16:02:32.273][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2026-01-31 16:02:32.274][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2026-01-31 16:02:32.285][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2026-01-31 16:02:32.286][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:32.287][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:32.288][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:02:32.290][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2026-01-31 16:02:32.291][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2026-01-31 16:02:32.292][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2026-01-31 16:02:32.293][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:32.294][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:32.295][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 16:02:32.299][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2026-01-31 16:02:32.342][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2026-01-31 16:02:32.370][self$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 16:02:32.371][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-01-31 16:02:32.373][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-01-31 16:02:32.374][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-01-31 16:02:32.375][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-01-31 16:02:32.376][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2026-01-31 16:02:32.378][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-01-31 16:02:32.379][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2026-01-31 16:02:32.380][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-01-31 16:02:32.381][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2026-01-31 16:02:32.383][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2026-01-31 16:02:32.384][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-01-31 16:02:32.385][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2026-01-31 16:02:32.386][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2026-01-31 16:02:32.388][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2026-01-31 16:02:32.388][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2026-01-31 16:02:32.388][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2026-01-31 16:02:32.388][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2026-01-31 16:02:32.388][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2026-01-31 16:02:32.389][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2026-01-31 16:02:32.390][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-01-31 16:02:32.391][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-01-31 16:02:32.393][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-01-31 16:02:32.394][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-01-31 16:02:32.395][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-01-31 16:02:32.396][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-01-31 16:02:32.397][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2026-01-31 16:02:32.398][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-01-31 16:02:32.400][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-01-31 16:02:32.401][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2026-01-31 16:02:32.402][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-01-31 16:02:32.403][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2026-01-31 16:02:32.406][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2026-01-31 16:02:32.407][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2026-01-31 16:02:32.408][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-01-31 16:02:32.409][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-01-31 16:02:32.410][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-01-31 16:02:32.412][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-01-31 16:02:32.413][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2026-01-31 16:02:32.414][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-01-31 16:02:32.415][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2026-01-31 16:02:32.417][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-01-31 16:02:32.418][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2026-01-31 16:02:32.419][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2026-01-31 16:02:32.420][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-01-31 16:02:32.422][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2026-01-31 16:02:32.423][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2026-01-31 16:02:32.424][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2026-01-31 16:02:32.424][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2026-01-31 16:02:32.424][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2026-01-31 16:02:32.424][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2026-01-31 16:02:32.424][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2026-01-31 16:02:32.426][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2026-01-31 16:02:32.427][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-01-31 16:02:32.428][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-01-31 16:02:32.429][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-01-31 16:02:32.430][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-01-31 16:02:32.431][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-01-31 16:02:32.433][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-01-31 16:02:32.434][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2026-01-31 16:02:32.435][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-01-31 16:02:32.436][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-01-31 16:02:32.437][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2026-01-31 16:02:32.439][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-01-31 16:02:32.440][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2026-01-31 16:02:32.442][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2026-01-31 16:02:32.444][self$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 16:02:32.445][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-01-31 16:02:32.446][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-01-31 16:02:32.447][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-01-31 16:02:32.449][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-01-31 16:02:32.450][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2026-01-31 16:02:32.451][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-01-31 16:02:32.452][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2026-01-31 16:02:32.454][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-01-31 16:02:32.455][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2026-01-31 16:02:32.456][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2026-01-31 16:02:32.457][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-01-31 16:02:32.459][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2026-01-31 16:02:32.460][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2026-01-31 16:02:32.461][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2026-01-31 16:02:32.462][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2026-01-31 16:02:32.464][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-01-31 16:02:32.465][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-01-31 16:02:32.466][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-01-31 16:02:32.467][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-01-31 16:02:32.468][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-01-31 16:02:32.470][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-01-31 16:02:32.471][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2026-01-31 16:02:32.472][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-01-31 16:02:32.473][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-01-31 16:02:32.474][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2026-01-31 16:02:32.476][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-01-31 16:02:32.477][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2026-01-31 16:02:32.480][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2026-01-31 16:02:32.481][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2026-01-31 16:02:32.482][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-01-31 16:02:32.483][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-01-31 16:02:32.485][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-01-31 16:02:32.486][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-01-31 16:02:32.487][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2026-01-31 16:02:32.488][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-01-31 16:02:32.490][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2026-01-31 16:02:32.491][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-01-31 16:02:32.492][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2026-01-31 16:02:32.494][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2026-01-31 16:02:32.495][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-01-31 16:02:32.496][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2026-01-31 16:02:32.497][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2026-01-31 16:02:32.499][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2026-01-31 16:02:32.500][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2026-01-31 16:02:32.501][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-01-31 16:02:32.502][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-01-31 16:02:32.503][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-01-31 16:02:32.505][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-01-31 16:02:32.506][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-01-31 16:02:32.507][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-01-31 16:02:32.508][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2026-01-31 16:02:32.510][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-01-31 16:02:32.511][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-01-31 16:02:32.512][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2026-01-31 16:02:32.513][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-01-31 16:02:32.517][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2026-01-31 16:02:32.519][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:32.520][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 16:02:32.521][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:32.522][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-31 16:02:32.523][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 16:02:32.524][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:32.525][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 16:02:32.527][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:32.528][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-31 16:02:32.529][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 16:02:32.530][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:32.531][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 16:02:32.532][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:32.533][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-31 16:02:32.535][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 16:02:32.536][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:32.537][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 16:02:32.538][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:32.539][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-31 16:02:32.540][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 16:02:32.541][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:32.543][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 16:02:32.544][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:32.545][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-31 16:02:32.546][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 16:02:32.547][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:32.548][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 16:02:32.549][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:32.551][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-31 16:02:32.552][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 16:02:32.553][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:32.554][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 16:02:32.555][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:32.556][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-31 16:02:32.557][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 16:02:32.559][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:32.560][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 16:02:32.561][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:32.562][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-31 16:02:32.563][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 16:02:32.564][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:32.565][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 16:02:32.567][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:32.568][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-31 16:02:32.569][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 16:02:32.570][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:32.571][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 16:02:32.573][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:32.575][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-31 16:02:32.578][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 16:02:32.579][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:32.581][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 16:02:32.582][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:32.583][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-31 16:02:32.585][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 16:02:32.586][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:32.588][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 16:02:32.589][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:32.590][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-31 16:02:32.592][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 16:02:32.593][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:32.595][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 16:02:32.597][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:32.599][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-31 16:02:32.601][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 16:02:32.603][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:32.605][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.DEBUG[2026-01-31 16:02:32.607][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:32.608][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-31 16:02:32.610][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 16:02:32.611][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:32.613][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 16:02:32.615][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:32.617][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-31 16:02:32.619][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 16:02:32.621][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:32.624][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 16:02:32.626][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:32.633][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-31 16:02:32.634][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 16:02:32.636][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:32.637][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 16:02:32.638][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2026-01-31 16:02:32.643][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2026-01-31 16:02:32.645][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2026-01-31 16:02:32.647][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2026-01-31 16:02:32.649][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2026-01-31 16:02:32.651][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2026-01-31 16:02:32.653][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2026-01-31 16:02:32.654][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2026-01-31 16:02:32.656][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2026-01-31 16:02:32.658][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2026-01-31 16:02:32.659][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2026-01-31 16:02:32.661][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2026-01-31 16:02:32.663][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2026-01-31 16:02:32.664][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2026-01-31 16:02:32.667][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2026-01-31 16:02:32.670][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2026-01-31 16:02:32.671][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2026-01-31 16:02:32.673][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2026-01-31 16:02:32.675][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2026-01-31 16:02:32.676][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2026-01-31 16:02:32.678][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2026-01-31 16:02:32.680][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2026-01-31 16:02:32.682][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2026-01-31 16:02:32.683][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2026-01-31 16:02:32.685][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2026-01-31 16:02:32.687][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2026-01-31 16:02:32.688][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2026-01-31 16:02:32.690][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2026-01-31 16:02:32.692][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2026-01-31 16:02:32.694][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2026-01-31 16:02:32.695][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2026-01-31 16:02:32.697][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2026-01-31 16:02:32.699][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2026-01-31 16:02:32.700][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2026-01-31 16:02:32.702][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2026-01-31 16:02:32.704][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2026-01-31 16:02:32.706][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2026-01-31 16:02:32.707][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2026-01-31 16:02:32.709][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2026-01-31 16:02:32.711][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2026-01-31 16:02:32.712][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2026-01-31 16:02:32.714][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2026-01-31 16:02:32.716][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2026-01-31 16:02:32.718][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2026-01-31 16:02:32.719][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2026-01-31 16:02:32.721][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2026-01-31 16:02:32.723][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2026-01-31 16:02:32.724][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2026-01-31 16:02:32.726][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2026-01-31 16:02:32.728][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2026-01-31 16:02:32.730][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2026-01-31 16:02:32.731][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2026-01-31 16:02:32.733][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2026-01-31 16:02:32.735][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2026-01-31 16:02:32.736][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2026-01-31 16:02:32.738][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2026-01-31 16:02:32.740][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2026-01-31 16:02:32.741][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2026-01-31 16:02:32.743][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2026-01-31 16:02:32.745][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2026-01-31 16:02:32.747][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2026-01-31 16:02:32.748][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2026-01-31 16:02:32.750][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2026-01-31 16:02:32.752][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2026-01-31 16:02:32.753][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2026-01-31 16:02:32.755][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2026-01-31 16:02:32.757][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2026-01-31 16:02:32.758][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2026-01-31 16:02:32.760][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2026-01-31 16:02:32.762][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2026-01-31 16:02:32.763][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2026-01-31 16:02:32.765][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2026-01-31 16:02:32.767][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2026-01-31 16:02:32.769][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2026-01-31 16:02:32.770][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2026-01-31 16:02:32.772][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2026-01-31 16:02:32.774][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2026-01-31 16:02:32.775][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2026-01-31 16:02:32.777][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2026-01-31 16:02:32.779][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2026-01-31 16:02:32.780][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2026-01-31 16:02:32.782][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2026-01-31 16:02:32.784][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2026-01-31 16:02:32.791][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2026-01-31 16:02:32.794][initialize] This is biodb version 1.18.0.
biodb.DEBUG[2026-01-31 16:02:32.798][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2026-01-31 16:02:32.799][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2026-01-31 16:02:32.800][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 16:02:32.801][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:32.802][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 16:02:32.809][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:32.810][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-01-31 16:02:32.811][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-01-31 16:02:32.812][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-31 16:02:32.813][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 16:02:32.814][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:32.815][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 16:02:32.817][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:32.818][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-01-31 16:02:32.819][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-01-31 16:02:32.820][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-31 16:02:32.821][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 16:02:32.822][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:32.823][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 16:02:32.824][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:32.825][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-01-31 16:02:32.827][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-01-31 16:02:32.828][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-31 16:02:32.829][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 16:02:32.830][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:32.831][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 16:02:32.832][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:32.833][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-01-31 16:02:32.834][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-01-31 16:02:32.836][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-31 16:02:32.837][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 16:02:32.838][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:32.839][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 16:02:32.840][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:32.841][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-01-31 16:02:32.842][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-01-31 16:02:32.843][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-31 16:02:32.844][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 16:02:32.846][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:32.847][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 16:02:32.848][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:32.849][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-01-31 16:02:32.850][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-01-31 16:02:32.851][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-31 16:02:32.852][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 16:02:32.853][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:32.854][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 16:02:32.856][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:32.857][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-01-31 16:02:32.858][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-01-31 16:02:32.859][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-31 16:02:32.860][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 16:02:32.861][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:32.862][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 16:02:32.863][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:32.864][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-01-31 16:02:32.866][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-01-31 16:02:32.867][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-31 16:02:32.868][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 16:02:32.869][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:32.870][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 16:02:32.871][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:32.872][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-01-31 16:02:32.873][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-01-31 16:02:32.874][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-31 16:02:32.876][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 16:02:32.877][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:32.878][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 16:02:32.879][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:32.880][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-01-31 16:02:32.881][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-01-31 16:02:32.882][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-31 16:02:32.883][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 16:02:32.884][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:32.890][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 16:02:32.892][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:32.893][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-01-31 16:02:32.894][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-01-31 16:02:32.895][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-31 16:02:32.896][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 16:02:32.897][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:32.898][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 16:02:32.899][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:32.900][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-01-31 16:02:32.901][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-01-31 16:02:32.902][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-31 16:02:32.903][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 16:02:32.905][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:32.906][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 16:02:32.907][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:32.908][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-01-31 16:02:32.909][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-01-31 16:02:32.910][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-31 16:02:32.911][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 16:02:32.912][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:32.913][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 16:02:32.914][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:32.915][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-01-31 16:02:32.916][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-01-31 16:02:32.918][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-31 16:02:32.919][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 16:02:32.920][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:32.921][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 16:02:32.922][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:32.923][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-01-31 16:02:32.924][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-01-31 16:02:32.925][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-31 16:02:32.926][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 16:02:32.927][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:32.928][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 16:02:32.930][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:32.931][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-01-31 16:02:32.932][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-01-31 16:02:32.933][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-31 16:02:32.934][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 16:02:32.935][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:32.936][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 16:02:32.939][biodb$loadDefinitions] Load definitions from file "/Users/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNci.Rcheck/biodbNci/definitions.yml".
biodb.DEBUG[2026-01-31 16:02:32.951][self$getDbsInfo()$define] Define connector nci.cactus.
biodb.DEBUG[2026-01-31 16:02:32.953][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2026-01-31 16:02:32.955][self$setPropertyValue] Setting property "description" to "National Cancer Institute (USA) CACTUS Database.".
biodb.DEBUG[2026-01-31 16:02:32.956][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-01-31 16:02:32.957][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-01-31 16:02:32.958][self$setPropertyValue] Setting property "downloadable" to "TRUE".
biodb.DEBUG[2026-01-31 16:02:32.960][self$setPropertyValue] Setting property "dwnld.ext" to "gz".
biodb.DEBUG[2026-01-31 16:02:32.961][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2026-01-31 16:02:32.962][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-01-31 16:02:32.963][self$setPropertyValue] Setting property "entry.content.type" to "sdf".
biodb.DEBUG[2026-01-31 16:02:32.964][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-01-31 16:02:32.966][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2026-01-31 16:02:32.967][self$setPropertyValue] Setting property "name" to "NCI CACTUS".
biodb.DEBUG[2026-01-31 16:02:32.968][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-01-31 16:02:32.969][self$setPropertyValue] Setting property "parsing.expr" to "NSC".
biodb.DEBUG[2026-01-31 16:02:32.969][self$setPropertyValue] Setting property "parsing.expr" to "DTP names".
biodb.DEBUG[2026-01-31 16:02:32.969][self$setPropertyValue] Setting property "parsing.expr" to "Standard InChI".
biodb.DEBUG[2026-01-31 16:02:32.969][self$setPropertyValue] Setting property "parsing.expr" to "c("Standard InChIKey", "^InChIKey=(.*)$")".
biodb.DEBUG[2026-01-31 16:02:32.969][self$setPropertyValue] Setting property "parsing.expr" to "Formula".
biodb.DEBUG[2026-01-31 16:02:32.969][self$setPropertyValue] Setting property "parsing.expr" to "Molecular Weight".
biodb.DEBUG[2026-01-31 16:02:32.969][self$setPropertyValue] Setting property "parsing.expr" to "CAS".
biodb.DEBUG[2026-01-31 16:02:32.971][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2026-01-31 16:02:32.972][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2026-01-31 16:02:32.973][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2026-01-31 16:02:32.974][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-01-31 16:02:32.975][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-01-31 16:02:32.977][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-01-31 16:02:32.978][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-01-31 16:02:32.979][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-01-31 16:02:32.980][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-01-31 16:02:32.981][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/".
biodb.DEBUG[2026-01-31 16:02:32.981][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/".
biodb.DEBUG[2026-01-31 16:02:32.981][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/download/nci/".
biodb.DEBUG[2026-01-31 16:02:32.981][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/download/nci/NCI-Open_2012-05-01.sdf.gz".
biodb.DEBUG[2026-01-31 16:02:32.983][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-01-31 16:02:32.984][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-01-31 16:02:32.985][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2026-01-31 16:02:32.986][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-01-31 16:02:32.994][self$getEntryFields()$define] Define field nci.cactus.id.
biodb.DEBUG[2026-01-31 16:02:33.016][super$initialize] Initialize connector nci.cactus.
biodb.DEBUG[2026-01-31 16:02:33.033][biodb$getFactory()$createConn] Creating new connector nci.cactus for database class nci.cactus .
biodb.INFO [2026-01-31 16:02:33.043][biodb::testThat]
biodb.INFO [2026-01-31 16:02:33.045][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2026-01-31 16:02:33.046][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-01-31 16:02:33.047][biodb::testThat]
biodb.TRACE[2026-01-31 16:02:33.051][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNci.Rcheck/biodbNci/testref/entry-nci.cactus-749674-content.sdf".
biodb.DEBUG[2026-01-31 16:02:33.053][biodb$getFactory()$createEntryFromCo ...] Creating NCI CACTUS entries from 1 content(s).
biodb.DEBUG[2026-01-31 16:02:33.057][biodb$getFactory()$createEntryFromCo ...] Parsing 1 NCI CACTUS entries.
biodb.DEBUG[2026-01-31 16:02:33.066][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2026-01-31 16:02:33.067][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2026-01-31 16:02:33.068][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-01-31 16:02:33.084][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2026-01-31 16:02:33.086][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-31 16:02:33.087][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:33.088][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2026-01-31 16:02:33.111][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-31 16:02:33.112][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-31 16:02:33.113][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:33.115][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:33.116][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-31 16:02:33.134][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-31 16:02:33.135][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:33.137][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:33.140][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2026-01-31 16:02:33.142][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2026-01-31 16:02:33.144][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:33.145][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:33.190][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2026-01-31 16:02:33.192][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2026-01-31 16:02:33.193][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:33.194][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:33.196][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2026-01-31 16:02:33.197][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2026-01-31 16:02:33.198][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:33.200][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:33.201][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2026-01-31 16:02:33.202][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2026-01-31 16:02:33.204][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:33.205][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:33.208][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2026-01-31 16:02:33.210][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2026-01-31 16:02:33.211][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:33.212][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:33.214][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2026-01-31 16:02:33.215][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2026-01-31 16:02:33.216][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:33.217][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:33.219][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-01-31 16:02:33.221][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-01-31 16:02:33.222][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:33.223][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:33.224][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-01-31 16:02:33.226][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-01-31 16:02:33.227][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:33.228][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:33.230][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2026-01-31 16:02:33.232][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2026-01-31 16:02:33.233][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:33.234][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:33.235][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2026-01-31 16:02:33.237][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2026-01-31 16:02:33.238][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:33.239][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:33.240][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-31 16:02:33.242][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-31 16:02:33.243][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:33.244][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:33.245][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2026-01-31 16:02:33.246][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2026-01-31 16:02:33.248][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:33.249][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:33.250][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-31 16:02:33.251][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-31 16:02:33.253][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:33.254][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:33.255][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-31 16:02:33.256][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-31 16:02:33.257][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:33.259][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:33.260][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-31 16:02:33.261][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-31 16:02:33.262][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:33.264][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:33.309][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-31 16:02:33.310][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-31 16:02:33.312][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:33.313][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:33.314][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-31 16:02:33.315][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-31 16:02:33.317][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:33.318][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:33.319][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-31 16:02:33.320][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-31 16:02:33.321][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:33.323][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2026-01-31 16:02:33.324][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 749674.
biodb.TRACE[2026-01-31 16:02:33.327][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2026-01-31 16:02:33.328][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2026-01-31 16:02:33.329][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:33.330][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:33.332][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2026-01-31 16:02:33.333][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2026-01-31 16:02:33.334][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:33.335][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:33.337][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2026-01-31 16:02:33.338][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2026-01-31 16:02:33.339][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:33.340][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:33.342][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2026-01-31 16:02:33.343][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2026-01-31 16:02:33.344][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:33.345][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:33.348][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-31 16:02:33.349][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-31 16:02:33.351][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:33.352][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:33.373][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2026-01-31 16:02:33.375][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2026-01-31 16:02:33.376][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:33.377][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:33.383][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-31 16:02:33.385][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-31 16:02:33.386][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:33.387][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:33.389][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-31 16:02:33.390][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-31 16:02:33.391][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:33.392][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:33.393][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-31 16:02:33.395][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-31 16:02:33.396][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:33.397][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:33.401][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-31 16:02:33.402][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-31 16:02:33.403][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:33.404][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:33.406][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-31 16:02:33.407][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-31 16:02:33.408][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:33.409][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:33.411][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-31 16:02:33.412][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-31 16:02:33.413][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:33.415][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:33.416][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2026-01-31 16:02:33.418][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2026-01-31 16:02:33.419][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:33.420][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:33.422][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2026-01-31 16:02:33.423][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2026-01-31 16:02:33.424][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:33.426][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:33.427][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2026-01-31 16:02:33.428][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2026-01-31 16:02:33.429][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:33.431][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:33.441][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-31 16:02:33.442][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-31 16:02:33.444][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:33.445][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:33.446][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-31 16:02:33.447][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-31 16:02:33.448][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:33.450][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:33.451][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-31 16:02:33.452][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-31 16:02:33.453][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:33.454][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:33.456][ef$get] Asked field names are: accession.
biodb.TRACE[2026-01-31 16:02:33.457][ef$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-31 16:02:33.458][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:33.459][ef$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:33.461][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-31 16:02:33.462][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-31 16:02:33.463][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:33.464][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:33.476][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2026-01-31 16:02:33.477][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2026-01-31 16:02:33.479][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:33.480][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:33.481][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2026-01-31 16:02:33.482][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2026-01-31 16:02:33.484][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:33.485][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:33.486][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2026-01-31 16:02:33.487][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2026-01-31 16:02:33.488][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:33.490][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:33.491][ef$get] Asked field names are: formula.
biodb.TRACE[2026-01-31 16:02:33.492][ef$get] Realnames of fields are: formula.
biodb.TRACE[2026-01-31 16:02:33.493][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:33.495][ef$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:33.496][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2026-01-31 16:02:33.497][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2026-01-31 16:02:33.498][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:33.499][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:33.511][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2026-01-31 16:02:33.513][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2026-01-31 16:02:33.514][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:33.515][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:33.516][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2026-01-31 16:02:33.518][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2026-01-31 16:02:33.519][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:33.520][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:33.521][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2026-01-31 16:02:33.523][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2026-01-31 16:02:33.524][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:33.525][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:33.526][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2026-01-31 16:02:33.528][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2026-01-31 16:02:33.529][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:33.530][ef$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:33.531][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2026-01-31 16:02:33.532][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2026-01-31 16:02:33.534][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:33.535][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:33.547][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2026-01-31 16:02:33.549][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2026-01-31 16:02:33.550][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:33.551][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:33.552][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2026-01-31 16:02:33.554][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2026-01-31 16:02:33.555][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:33.556][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:33.557][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2026-01-31 16:02:33.558][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2026-01-31 16:02:33.560][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:33.561][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:33.562][ef$get] Asked field names are: inchi.
biodb.TRACE[2026-01-31 16:02:33.563][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2026-01-31 16:02:33.565][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:33.566][ef$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:33.567][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2026-01-31 16:02:33.568][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2026-01-31 16:02:33.570][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:33.571][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:33.582][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-01-31 16:02:33.584][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-01-31 16:02:33.585][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:33.586][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:33.588][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-01-31 16:02:33.589][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-01-31 16:02:33.590][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:33.596][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:33.598][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-01-31 16:02:33.599][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-01-31 16:02:33.600][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:33.601][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:33.603][ef$get] Asked field names are: inchikey.
biodb.TRACE[2026-01-31 16:02:33.604][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-01-31 16:02:33.605][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:33.606][ef$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:33.608][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-01-31 16:02:33.609][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-01-31 16:02:33.610][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:33.611][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:33.623][ef$get] Asked field names are: accession.
biodb.TRACE[2026-01-31 16:02:33.625][ef$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-31 16:02:33.626][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:33.627][ef$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:33.634][ef$get] Asked field names are: formula.
biodb.TRACE[2026-01-31 16:02:33.635][ef$get] Realnames of fields are: formula.
biodb.TRACE[2026-01-31 16:02:33.637][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:33.638][ef$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:33.644][ef$get] Asked field names are: inchi.
biodb.TRACE[2026-01-31 16:02:33.646][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2026-01-31 16:02:33.647][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:33.648][ef$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:33.654][ef$get] Asked field names are: inchikey.
biodb.TRACE[2026-01-31 16:02:33.656][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-01-31 16:02:33.657][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:33.658][ef$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:33.665][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2026-01-31 16:02:33.666][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2026-01-31 16:02:33.667][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:33.668][ef$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:33.691][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNci.Rcheck/biodbNci/testref/entry-nci.cactus-750690-content.sdf".
biodb.DEBUG[2026-01-31 16:02:33.738][biodb$getFactory()$createEntryFromCo ...] Creating NCI CACTUS entries from 1 content(s).
biodb.DEBUG[2026-01-31 16:02:33.740][biodb$getFactory()$createEntryFromCo ...] Parsing 1 NCI CACTUS entries.
biodb.DEBUG[2026-01-31 16:02:33.742][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2026-01-31 16:02:33.743][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2026-01-31 16:02:33.744][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-01-31 16:02:33.750][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2026-01-31 16:02:33.752][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-31 16:02:33.753][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:33.754][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2026-01-31 16:02:33.769][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-31 16:02:33.771][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-31 16:02:33.772][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:33.773][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:33.775][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-31 16:02:33.776][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-31 16:02:33.777][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:33.778][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:33.838][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2026-01-31 16:02:33.840][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2026-01-31 16:02:33.841][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:33.842][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:33.843][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2026-01-31 16:02:33.845][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2026-01-31 16:02:33.846][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:33.847][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:33.849][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2026-01-31 16:02:33.850][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2026-01-31 16:02:33.851][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:33.853][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:33.854][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2026-01-31 16:02:33.855][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2026-01-31 16:02:33.856][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:33.857][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:33.859][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2026-01-31 16:02:33.861][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2026-01-31 16:02:33.862][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:33.863][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:33.864][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2026-01-31 16:02:33.865][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2026-01-31 16:02:33.867][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:33.868][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:33.869][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-01-31 16:02:33.871][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-01-31 16:02:33.872][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:33.873][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:33.874][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-01-31 16:02:33.876][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-01-31 16:02:33.877][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:33.878][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:33.880][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-01-31 16:02:33.881][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-01-31 16:02:33.882][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:33.883][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:33.884][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-01-31 16:02:33.886][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-01-31 16:02:33.887][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:33.888][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:33.889][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-01-31 16:02:33.891][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-01-31 16:02:33.892][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:33.893][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:33.894][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-01-31 16:02:33.895][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-01-31 16:02:33.897][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:33.898][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:33.899][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-01-31 16:02:33.900][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-01-31 16:02:33.902][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:33.903][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:33.906][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2026-01-31 16:02:33.907][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2026-01-31 16:02:33.908][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:33.910][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:33.911][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2026-01-31 16:02:33.912][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2026-01-31 16:02:33.914][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:33.915][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:33.917][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-01-31 16:02:33.918][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-01-31 16:02:33.919][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:33.921][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:33.922][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-01-31 16:02:33.923][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-01-31 16:02:33.925][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:33.926][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:33.928][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2026-01-31 16:02:33.930][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2026-01-31 16:02:33.931][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:33.932][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:33.933][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2026-01-31 16:02:33.935][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2026-01-31 16:02:33.936][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:33.937][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:33.938][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-31 16:02:33.940][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-31 16:02:33.941][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:33.942][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:33.943][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2026-01-31 16:02:33.944][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2026-01-31 16:02:33.946][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:33.947][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:33.948][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-31 16:02:33.949][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-31 16:02:33.950][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:33.952][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:33.953][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-31 16:02:33.954][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-31 16:02:33.955][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:33.957][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:33.958][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-31 16:02:33.959][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-31 16:02:33.960][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:33.961][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:33.963][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-31 16:02:33.964][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-31 16:02:33.965][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:33.967][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:33.968][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-31 16:02:33.969][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-31 16:02:33.970][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:33.971][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:33.973][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-31 16:02:33.974][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-31 16:02:33.975][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:33.976][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2026-01-31 16:02:33.978][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 750690.
biodb.TRACE[2026-01-31 16:02:34.004][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2026-01-31 16:02:34.006][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2026-01-31 16:02:34.007][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:34.008][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:34.010][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2026-01-31 16:02:34.011][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2026-01-31 16:02:34.012][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:34.013][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:34.014][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2026-01-31 16:02:34.016][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2026-01-31 16:02:34.017][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:34.018][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:34.019][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2026-01-31 16:02:34.021][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2026-01-31 16:02:34.022][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:34.023][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:34.026][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-31 16:02:34.027][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-31 16:02:34.028][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:34.029][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:34.036][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2026-01-31 16:02:34.037][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2026-01-31 16:02:34.038][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:34.040][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:34.050][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-31 16:02:34.051][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-31 16:02:34.052][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:34.054][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:34.055][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-31 16:02:34.056][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-31 16:02:34.057][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:34.059][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:34.060][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-31 16:02:34.061][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-31 16:02:34.062][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:34.063][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:34.067][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-31 16:02:34.068][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-31 16:02:34.069][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:34.070][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:34.072][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-31 16:02:34.073][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-31 16:02:34.074][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:34.075][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:34.077][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-31 16:02:34.078][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-31 16:02:34.079][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:34.080][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:34.082][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2026-01-31 16:02:34.083][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2026-01-31 16:02:34.084][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:34.086][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:34.087][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2026-01-31 16:02:34.088][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2026-01-31 16:02:34.089][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:34.090][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:34.092][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2026-01-31 16:02:34.093][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2026-01-31 16:02:34.094][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:34.095][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:34.118][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-31 16:02:34.120][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-31 16:02:34.121][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:34.122][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:34.123][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-31 16:02:34.124][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-31 16:02:34.126][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:34.127][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:34.128][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-31 16:02:34.130][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-31 16:02:34.131][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:34.132][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:34.133][ef$get] Asked field names are: accession.
biodb.TRACE[2026-01-31 16:02:34.134][ef$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-31 16:02:34.136][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:34.137][ef$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:34.138][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-31 16:02:34.139][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-31 16:02:34.141][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:34.142][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:34.154][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2026-01-31 16:02:34.155][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2026-01-31 16:02:34.156][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:34.158][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:34.159][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2026-01-31 16:02:34.160][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2026-01-31 16:02:34.161][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:34.163][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:34.164][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2026-01-31 16:02:34.165][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2026-01-31 16:02:34.166][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:34.168][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:34.169][ef$get] Asked field names are: cas.id.
biodb.TRACE[2026-01-31 16:02:34.170][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2026-01-31 16:02:34.171][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:34.173][ef$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:34.174][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2026-01-31 16:02:34.175][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2026-01-31 16:02:34.176][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:34.178][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:34.189][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-01-31 16:02:34.191][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-01-31 16:02:34.192][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:34.193][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:34.194][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-01-31 16:02:34.196][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-01-31 16:02:34.197][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:34.198][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:34.199][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-01-31 16:02:34.201][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-01-31 16:02:34.202][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:34.203][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:34.204][ef$get] Asked field names are: name.
biodb.TRACE[2026-01-31 16:02:34.206][ef$get] Realnames of fields are: name.
biodb.TRACE[2026-01-31 16:02:34.207][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:34.208][ef$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:34.209][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-01-31 16:02:34.210][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-01-31 16:02:34.212][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:34.213][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:34.225][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2026-01-31 16:02:34.226][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2026-01-31 16:02:34.227][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:34.229][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:34.230][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2026-01-31 16:02:34.231][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2026-01-31 16:02:34.232][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:34.233][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:34.235][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2026-01-31 16:02:34.236][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2026-01-31 16:02:34.237][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:34.238][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:34.240][ef$get] Asked field names are: formula.
biodb.TRACE[2026-01-31 16:02:34.241][ef$get] Realnames of fields are: formula.
biodb.TRACE[2026-01-31 16:02:34.242][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:34.243][ef$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:34.245][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2026-01-31 16:02:34.246][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2026-01-31 16:02:34.247][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:34.248][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:34.265][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2026-01-31 16:02:34.267][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2026-01-31 16:02:34.268][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:34.269][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:34.270][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2026-01-31 16:02:34.272][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2026-01-31 16:02:34.273][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:34.274][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:34.275][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2026-01-31 16:02:34.277][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2026-01-31 16:02:34.278][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:34.279][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:34.281][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2026-01-31 16:02:34.282][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2026-01-31 16:02:34.283][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:34.284][ef$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:34.286][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2026-01-31 16:02:34.287][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2026-01-31 16:02:34.288][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:34.289][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:34.301][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2026-01-31 16:02:34.302][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2026-01-31 16:02:34.303][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:34.305][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:34.306][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2026-01-31 16:02:34.307][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2026-01-31 16:02:34.308][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:34.310][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:34.311][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2026-01-31 16:02:34.312][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2026-01-31 16:02:34.313][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:34.314][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:34.316][ef$get] Asked field names are: inchi.
biodb.TRACE[2026-01-31 16:02:34.317][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2026-01-31 16:02:34.318][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:34.319][ef$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:34.321][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2026-01-31 16:02:34.322][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2026-01-31 16:02:34.323][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:34.324][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:34.336][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-01-31 16:02:34.338][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-01-31 16:02:34.339][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:34.340][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:34.341][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-01-31 16:02:34.343][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-01-31 16:02:34.344][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:34.345][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:34.346][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-01-31 16:02:34.347][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-01-31 16:02:34.349][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:34.350][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:34.351][ef$get] Asked field names are: inchikey.
biodb.TRACE[2026-01-31 16:02:34.352][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-01-31 16:02:34.354][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:34.355][ef$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:34.356][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-01-31 16:02:34.357][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-01-31 16:02:34.359][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:34.360][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:34.371][ef$get] Asked field names are: accession.
biodb.TRACE[2026-01-31 16:02:34.373][ef$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-31 16:02:34.374][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:34.375][ef$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:34.382][ef$get] Asked field names are: cas.id.
biodb.TRACE[2026-01-31 16:02:34.383][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2026-01-31 16:02:34.384][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:34.385][ef$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:34.392][ef$get] Asked field names are: formula.
biodb.TRACE[2026-01-31 16:02:34.393][ef$get] Realnames of fields are: formula.
biodb.TRACE[2026-01-31 16:02:34.394][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:34.396][ef$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:34.402][ef$get] Asked field names are: inchi.
biodb.TRACE[2026-01-31 16:02:34.404][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2026-01-31 16:02:34.405][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:34.406][ef$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:34.412][ef$get] Asked field names are: inchikey.
biodb.TRACE[2026-01-31 16:02:34.414][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-01-31 16:02:34.415][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:34.416][ef$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:34.423][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2026-01-31 16:02:34.424][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2026-01-31 16:02:34.425][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:34.427][ef$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:34.433][ef$get] Asked field names are: name.
biodb.TRACE[2026-01-31 16:02:34.435][ef$get] Realnames of fields are: name.
biodb.TRACE[2026-01-31 16:02:34.436][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:34.437][ef$get] fields variable is a list.
biodb.INFO [2026-01-31 16:02:34.448][biodb::testThat]
biodb.INFO [2026-01-31 16:02:34.449][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2026-01-31 16:02:34.450][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-01-31 16:02:34.451][biodb::testThat]
biodb.DEBUG[2026-01-31 16:02:34.454][private$loadEntries] Creating entries from ids [2]: "749674, 750690".
biodb.DEBUG[2026-01-31 16:02:34.458][conn$getEntryContent] Get NCI CACTUS entry content(s) for 2 id(s)...
biodb.DEBUG[2026-01-31 16:02:34.462][self$isDownloaded] Database nci.cactus has already been downloaded.
biodb.DEBUG[2026-01-31 16:02:34.506][self$isDownloaded] Database nci.cactus has already been downloaded.
biodb.INFO [2026-01-31 16:02:34.507][self$download] Extract whole database of nci.cactus.
biodb.INFO [2026-01-31 16:02:34.509][private$doExtractDownload] Extracting content of downloaded biodbNci, a library for connecting to the National Cancer Institute (USA) CACTUS Database....
Saving _problems/test_long_100_generic-38.R
biodb.INFO [2026-01-31 16:02:34.689][biodb::testThat]
biodb.INFO [2026-01-31 16:02:34.691][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2026-01-31 16:02:34.692][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-01-31 16:02:34.693][biodb::testThat]
biodb.INFO [2026-01-31 16:02:34.702][biodb::testThat]
biodb.INFO [2026-01-31 16:02:34.704][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2026-01-31 16:02:34.705][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-01-31 16:02:34.706][biodb::testThat]
biodb.WARN [2026-01-31 16:02:34.729][self$searchForEntries] This database is not searchable by field "name".
biodb.WARN [2026-01-31 16:02:34.754][self$searchForEntries] This database is not searchable by field "name".
biodb.INFO [2026-01-31 16:02:34.765][biodb::testThat]
biodb.INFO [2026-01-31 16:02:34.767][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2026-01-31 16:02:34.768][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-01-31 16:02:34.769][biodb::testThat]
biodb.DEBUG[2026-01-31 16:02:34.792][private$loadEntries] Creating entries from ids [1]: "749674".
biodb.DEBUG[2026-01-31 16:02:34.857][conn$getEntryContent] Get NCI CACTUS entry content(s) for 1 id(s)...
biodb.DEBUG[2026-01-31 16:02:34.859][self$isDownloaded] Database nci.cactus has already been downloaded.
biodb.DEBUG[2026-01-31 16:02:34.861][self$isDownloaded] Database nci.cactus has already been downloaded.
biodb.INFO [2026-01-31 16:02:34.863][self$download] Extract whole database of nci.cactus.
biodb.INFO [2026-01-31 16:02:34.885][private$doExtractDownload] Extracting content of downloaded biodbNci, a library for connecting to the National Cancer Institute (USA) CACTUS Database....
Saving _problems/test_long_100_generic-38.R
biodb.INFO [2026-01-31 16:02:34.958][biodb::testThat]
biodb.INFO [2026-01-31 16:02:34.959][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2026-01-31 16:02:34.961][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-01-31 16:02:34.962][biodb::testThat]
biodb.INFO [2026-01-31 16:02:34.973][biodb::testThat]
biodb.INFO [2026-01-31 16:02:34.974][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2026-01-31 16:02:34.975][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-01-31 16:02:34.977][biodb::testThat]
biodb.INFO [2026-01-31 16:02:34.987][biodb::testThat]
biodb.INFO [2026-01-31 16:02:34.988][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2026-01-31 16:02:34.990][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-01-31 16:02:34.991][biodb::testThat]
biodb.INFO [2026-01-31 16:02:35.000][biodb::testThat]
biodb.INFO [2026-01-31 16:02:35.001][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2026-01-31 16:02:35.002][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-01-31 16:02:35.003][biodb::testThat]
biodb.INFO [2026-01-31 16:02:35.012][biodb$terminate] Closing BiodbMain instance...
biodb.INFO [2026-01-31 16:02:35.014][self$deleteConn] Connector "nci.cactus" deleted.
biodb.DEBUG[2026-01-31 16:02:35.015][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2026-01-31 16:02:35.016][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-01-31 16:02:35.017][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-01-31 16:02:35.018][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-31 16:02:35.019][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-31 16:02:35.020][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:35.021][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2026-01-31 16:02:35.034][biodb::testContext]
biodb.INFO [2026-01-31 16:02:35.035][biodb::testContext] ********************************************************************************
biodb.INFO [2026-01-31 16:02:35.037][biodb::testContext] Test context - Example long tests
biodb.INFO [2026-01-31 16:02:35.038][biodb::testContext] ********************************************************************************
biodb.INFO [2026-01-31 16:02:35.039][biodb::testContext]
biodb.INFO [2026-01-31 16:02:35.041][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.18.0.
biodb.DEBUG[2026-01-31 16:02:35.043][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2026-01-31 16:02:35.048][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2026-01-31 16:02:35.049][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2026-01-31 16:02:35.050][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2026-01-31 16:02:35.051][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:35.052][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:35.053][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 16:02:35.055][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2026-01-31 16:02:35.056][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2026-01-31 16:02:35.057][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:35.058][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:35.059][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:02:35.060][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2026-01-31 16:02:35.062][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2026-01-31 16:02:35.063][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:35.064][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:35.065][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 16:02:35.066][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2026-01-31 16:02:35.072][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2026-01-31 16:02:35.073][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2026-01-31 16:02:35.074][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:35.075][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:35.076][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:02:35.077][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2026-01-31 16:02:35.079][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2026-01-31 16:02:35.080][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2026-01-31 16:02:35.081][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:35.082][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:35.083][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 16:02:35.084][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2026-01-31 16:02:35.085][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2026-01-31 16:02:35.087][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:35.088][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:35.089][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:02:35.090][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2026-01-31 16:02:35.091][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2026-01-31 16:02:35.092][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2026-01-31 16:02:35.093][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:35.094][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:35.096][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 16:02:35.097][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2026-01-31 16:02:35.098][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2026-01-31 16:02:35.099][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:35.100][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:35.101][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:02:35.102][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2026-01-31 16:02:35.104][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2026-01-31 16:02:35.105][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2026-01-31 16:02:35.106][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:35.107][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:35.108][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.DEBUG[2026-01-31 16:02:35.109][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2026-01-31 16:02:35.111][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2026-01-31 16:02:35.112][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2026-01-31 16:02:35.113][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2026-01-31 16:02:35.114][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2026-01-31 16:02:35.115][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2026-01-31 16:02:35.117][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:35.118][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:35.119][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:02:35.120][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2026-01-31 16:02:35.121][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2026-01-31 16:02:35.122][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:35.123][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:35.124][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 16:02:35.126][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2026-01-31 16:02:35.127][self$set] Set key entries.sep to "|".
biodb.DEBUG[2026-01-31 16:02:35.128][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:35.129][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:35.130][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:02:35.131][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2026-01-31 16:02:35.133][self$set] Set key offline to FALSE.
biodb.DEBUG[2026-01-31 16:02:35.134][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:35.135][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:35.136][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 16:02:35.137][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2026-01-31 16:02:35.138][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2026-01-31 16:02:35.140][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2026-01-31 16:02:35.141][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:35.142][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:35.143][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:02:35.144][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2026-01-31 16:02:35.145][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2026-01-31 16:02:35.156][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2026-01-31 16:02:35.157][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:35.158][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:35.159][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 16:02:35.161][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2026-01-31 16:02:35.162][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2026-01-31 16:02:35.163][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2026-01-31 16:02:35.165][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:35.166][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:35.167][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:02:35.168][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2026-01-31 16:02:35.170][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2026-01-31 16:02:35.172][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2026-01-31 16:02:35.173][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-01-31 16:02:35.174][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-01-31 16:02:35.175][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-01-31 16:02:35.177][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-01-31 16:02:35.178][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2026-01-31 16:02:35.179][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-01-31 16:02:35.181][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2026-01-31 16:02:35.182][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-01-31 16:02:35.183][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2026-01-31 16:02:35.184][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2026-01-31 16:02:35.186][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-01-31 16:02:35.187][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2026-01-31 16:02:35.188][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2026-01-31 16:02:35.190][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2026-01-31 16:02:35.190][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2026-01-31 16:02:35.190][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2026-01-31 16:02:35.190][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2026-01-31 16:02:35.190][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2026-01-31 16:02:35.191][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2026-01-31 16:02:35.192][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-01-31 16:02:35.193][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-01-31 16:02:35.195][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-01-31 16:02:35.196][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-01-31 16:02:35.197][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-01-31 16:02:35.198][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-01-31 16:02:35.199][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2026-01-31 16:02:35.201][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-01-31 16:02:35.202][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-01-31 16:02:35.203][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2026-01-31 16:02:35.204][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-01-31 16:02:35.206][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2026-01-31 16:02:35.208][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2026-01-31 16:02:35.209][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2026-01-31 16:02:35.211][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-01-31 16:02:35.212][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-01-31 16:02:35.213][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-01-31 16:02:35.214][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-01-31 16:02:35.216][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2026-01-31 16:02:35.217][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-01-31 16:02:35.218][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2026-01-31 16:02:35.219][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-01-31 16:02:35.221][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2026-01-31 16:02:35.222][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2026-01-31 16:02:35.223][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-01-31 16:02:35.224][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2026-01-31 16:02:35.226][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2026-01-31 16:02:35.227][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2026-01-31 16:02:35.227][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2026-01-31 16:02:35.227][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2026-01-31 16:02:35.227][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2026-01-31 16:02:35.227][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2026-01-31 16:02:35.228][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2026-01-31 16:02:35.230][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-01-31 16:02:35.231][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-01-31 16:02:35.232][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-01-31 16:02:35.233][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-01-31 16:02:35.234][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-01-31 16:02:35.235][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-01-31 16:02:35.237][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2026-01-31 16:02:35.238][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-01-31 16:02:35.239][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-01-31 16:02:35.240][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2026-01-31 16:02:35.242][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-01-31 16:02:35.243][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2026-01-31 16:02:35.245][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2026-01-31 16:02:35.247][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2026-01-31 16:02:35.248][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-01-31 16:02:35.249][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-01-31 16:02:35.250][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-01-31 16:02:35.252][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-01-31 16:02:35.253][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2026-01-31 16:02:35.254][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-01-31 16:02:35.255][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2026-01-31 16:02:35.257][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-01-31 16:02:35.258][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2026-01-31 16:02:35.259][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2026-01-31 16:02:35.261][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-01-31 16:02:35.262][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2026-01-31 16:02:35.263][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2026-01-31 16:02:35.264][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2026-01-31 16:02:35.266][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2026-01-31 16:02:35.267][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-01-31 16:02:35.268][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-01-31 16:02:35.269][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-01-31 16:02:35.275][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-01-31 16:02:35.276][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-01-31 16:02:35.277][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-01-31 16:02:35.278][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2026-01-31 16:02:35.280][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-01-31 16:02:35.281][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-01-31 16:02:35.282][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2026-01-31 16:02:35.283][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-01-31 16:02:35.285][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2026-01-31 16:02:35.287][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2026-01-31 16:02:35.288][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2026-01-31 16:02:35.289][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-01-31 16:02:35.291][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-01-31 16:02:35.292][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-01-31 16:02:35.293][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-01-31 16:02:35.294][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2026-01-31 16:02:35.296][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-01-31 16:02:35.297][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2026-01-31 16:02:35.298][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-01-31 16:02:35.299][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2026-01-31 16:02:35.301][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2026-01-31 16:02:35.302][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-01-31 16:02:35.303][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2026-01-31 16:02:35.304][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2026-01-31 16:02:35.306][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2026-01-31 16:02:35.307][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2026-01-31 16:02:35.308][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-01-31 16:02:35.309][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-01-31 16:02:35.310][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-01-31 16:02:35.312][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-01-31 16:02:35.313][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-01-31 16:02:35.314][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-01-31 16:02:35.315][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2026-01-31 16:02:35.317][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-01-31 16:02:35.318][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-01-31 16:02:35.319][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2026-01-31 16:02:35.320][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-01-31 16:02:35.322][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2026-01-31 16:02:35.323][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:35.324][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 16:02:35.325][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:35.326][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-31 16:02:35.327][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 16:02:35.329][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:35.330][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 16:02:35.331][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:35.332][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-31 16:02:35.333][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 16:02:35.334][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:35.335][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 16:02:35.337][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:35.338][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-31 16:02:35.339][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 16:02:35.340][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:35.341][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 16:02:35.342][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:35.343][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-31 16:02:35.344][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 16:02:35.346][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:35.347][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 16:02:35.348][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:35.349][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-31 16:02:35.350][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 16:02:35.351][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:35.352][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 16:02:35.353][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:35.355][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-31 16:02:35.356][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 16:02:35.357][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:35.358][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 16:02:35.359][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:35.360][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-31 16:02:35.361][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 16:02:35.362][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:35.363][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 16:02:35.365][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:35.366][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-31 16:02:35.367][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 16:02:35.368][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:35.369][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 16:02:35.370][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:35.371][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-31 16:02:35.372][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 16:02:35.373][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:35.375][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 16:02:35.376][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:35.377][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-31 16:02:35.378][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 16:02:35.379][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:35.380][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 16:02:35.381][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:35.382][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-31 16:02:35.383][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 16:02:35.385][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:35.386][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 16:02:35.387][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:35.388][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-31 16:02:35.389][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 16:02:35.390][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:35.391][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 16:02:35.393][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:35.394][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-31 16:02:35.395][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 16:02:35.396][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:35.397][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 16:02:35.398][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:35.400][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-31 16:02:35.401][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 16:02:35.402][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:35.404][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 16:02:35.405][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:35.406][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-31 16:02:35.407][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 16:02:35.408][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:35.409][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 16:02:35.410][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:35.411][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-31 16:02:35.412][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 16:02:35.414][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:35.415][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 16:02:35.416][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2026-01-31 16:02:35.418][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2026-01-31 16:02:35.419][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2026-01-31 16:02:35.421][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2026-01-31 16:02:35.423][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2026-01-31 16:02:35.425][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2026-01-31 16:02:35.426][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2026-01-31 16:02:35.428][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2026-01-31 16:02:35.430][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2026-01-31 16:02:35.431][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2026-01-31 16:02:35.433][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2026-01-31 16:02:35.435][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2026-01-31 16:02:35.436][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2026-01-31 16:02:35.438][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2026-01-31 16:02:35.440][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2026-01-31 16:02:35.441][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2026-01-31 16:02:35.443][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2026-01-31 16:02:35.445][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2026-01-31 16:02:35.446][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2026-01-31 16:02:35.448][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2026-01-31 16:02:35.450][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2026-01-31 16:02:35.452][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2026-01-31 16:02:35.453][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2026-01-31 16:02:35.455][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2026-01-31 16:02:35.457][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2026-01-31 16:02:35.458][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2026-01-31 16:02:35.460][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2026-01-31 16:02:35.462][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2026-01-31 16:02:35.468][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2026-01-31 16:02:35.469][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2026-01-31 16:02:35.471][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2026-01-31 16:02:35.473][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2026-01-31 16:02:35.474][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2026-01-31 16:02:35.476][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2026-01-31 16:02:35.478][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2026-01-31 16:02:35.479][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2026-01-31 16:02:35.481][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2026-01-31 16:02:35.483][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2026-01-31 16:02:35.484][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2026-01-31 16:02:35.486][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2026-01-31 16:02:35.488][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2026-01-31 16:02:35.490][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2026-01-31 16:02:35.491][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2026-01-31 16:02:35.493][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2026-01-31 16:02:35.495][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2026-01-31 16:02:35.496][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2026-01-31 16:02:35.498][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2026-01-31 16:02:35.500][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2026-01-31 16:02:35.502][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2026-01-31 16:02:35.503][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2026-01-31 16:02:35.505][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2026-01-31 16:02:35.507][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2026-01-31 16:02:35.508][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2026-01-31 16:02:35.510][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2026-01-31 16:02:35.512][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2026-01-31 16:02:35.513][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2026-01-31 16:02:35.515][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2026-01-31 16:02:35.517][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2026-01-31 16:02:35.519][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2026-01-31 16:02:35.520][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2026-01-31 16:02:35.522][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2026-01-31 16:02:35.524][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2026-01-31 16:02:35.525][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2026-01-31 16:02:35.527][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2026-01-31 16:02:35.529][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2026-01-31 16:02:35.531][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2026-01-31 16:02:35.532][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2026-01-31 16:02:35.534][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2026-01-31 16:02:35.536][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2026-01-31 16:02:35.537][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2026-01-31 16:02:35.539][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2026-01-31 16:02:35.541][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2026-01-31 16:02:35.542][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2026-01-31 16:02:35.544][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2026-01-31 16:02:35.546][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2026-01-31 16:02:35.548][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2026-01-31 16:02:35.549][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2026-01-31 16:02:35.551][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2026-01-31 16:02:35.553][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2026-01-31 16:02:35.555][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2026-01-31 16:02:35.556][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2026-01-31 16:02:35.558][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2026-01-31 16:02:35.560][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2026-01-31 16:02:35.561][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2026-01-31 16:02:35.564][initialize] This is biodb version 1.18.0.
biodb.DEBUG[2026-01-31 16:02:35.565][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2026-01-31 16:02:35.566][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2026-01-31 16:02:35.567][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 16:02:35.568][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:35.569][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 16:02:35.570][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:35.572][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-01-31 16:02:35.573][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-01-31 16:02:35.574][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-31 16:02:35.575][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 16:02:35.576][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:35.577][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 16:02:35.578][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:35.579][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-01-31 16:02:35.581][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-01-31 16:02:35.582][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-31 16:02:35.583][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 16:02:35.584][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:35.585][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 16:02:35.586][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:35.587][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-01-31 16:02:35.589][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-01-31 16:02:35.590][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-31 16:02:35.591][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 16:02:35.592][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:35.593][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 16:02:35.594][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:35.595][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-01-31 16:02:35.597][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-01-31 16:02:35.598][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-31 16:02:35.599][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 16:02:35.600][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:35.601][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 16:02:35.602][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:35.603][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-01-31 16:02:35.604][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-01-31 16:02:35.606][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-31 16:02:35.607][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 16:02:35.608][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:35.609][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 16:02:35.610][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:35.611][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-01-31 16:02:35.613][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-01-31 16:02:35.614][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-31 16:02:35.615][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 16:02:35.616][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:35.617][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 16:02:35.618][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:35.620][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-01-31 16:02:35.621][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-01-31 16:02:35.622][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-31 16:02:35.623][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 16:02:35.624][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:35.625][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 16:02:35.626][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:35.628][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-01-31 16:02:35.629][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-01-31 16:02:35.630][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-31 16:02:35.631][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 16:02:35.632][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:35.633][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 16:02:35.635][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:35.636][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-01-31 16:02:35.637][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-01-31 16:02:35.638][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-31 16:02:35.639][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 16:02:35.640][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:35.641][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 16:02:35.642][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:35.644][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-01-31 16:02:35.645][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-01-31 16:02:35.646][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-31 16:02:35.647][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 16:02:35.648][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:35.649][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 16:02:35.650][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:35.651][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-01-31 16:02:35.653][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-01-31 16:02:35.658][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-31 16:02:35.659][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 16:02:35.660][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:35.661][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 16:02:35.663][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:35.664][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-01-31 16:02:35.665][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-01-31 16:02:35.666][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-31 16:02:35.667][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 16:02:35.668][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:35.669][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 16:02:35.670][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:35.671][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-01-31 16:02:35.672][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-01-31 16:02:35.673][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-31 16:02:35.675][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 16:02:35.676][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:35.677][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 16:02:35.678][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:35.679][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-01-31 16:02:35.680][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-01-31 16:02:35.681][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-31 16:02:35.682][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 16:02:35.683][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:35.684][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 16:02:35.686][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:35.687][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-01-31 16:02:35.688][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-01-31 16:02:35.689][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-31 16:02:35.690][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 16:02:35.691][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:35.692][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 16:02:35.693][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:35.694][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-01-31 16:02:35.695][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-01-31 16:02:35.697][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-31 16:02:35.698][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 16:02:35.699][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:35.700][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 16:02:35.703][biodb$loadDefinitions] Load definitions from file "/Users/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNci.Rcheck/biodbNci/definitions.yml".
biodb.DEBUG[2026-01-31 16:02:35.704][self$getDbsInfo()$define] Define connector nci.cactus.
biodb.DEBUG[2026-01-31 16:02:35.706][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2026-01-31 16:02:35.708][self$setPropertyValue] Setting property "description" to "National Cancer Institute (USA) CACTUS Database.".
biodb.DEBUG[2026-01-31 16:02:35.709][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-01-31 16:02:35.710][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-01-31 16:02:35.711][self$setPropertyValue] Setting property "downloadable" to "TRUE".
biodb.DEBUG[2026-01-31 16:02:35.713][self$setPropertyValue] Setting property "dwnld.ext" to "gz".
biodb.DEBUG[2026-01-31 16:02:35.714][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2026-01-31 16:02:35.715][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-01-31 16:02:35.716][self$setPropertyValue] Setting property "entry.content.type" to "sdf".
biodb.DEBUG[2026-01-31 16:02:35.718][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-01-31 16:02:35.719][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2026-01-31 16:02:35.720][self$setPropertyValue] Setting property "name" to "NCI CACTUS".
biodb.DEBUG[2026-01-31 16:02:35.721][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-01-31 16:02:35.723][self$setPropertyValue] Setting property "parsing.expr" to "NSC".
biodb.DEBUG[2026-01-31 16:02:35.723][self$setPropertyValue] Setting property "parsing.expr" to "DTP names".
biodb.DEBUG[2026-01-31 16:02:35.723][self$setPropertyValue] Setting property "parsing.expr" to "Standard InChI".
biodb.DEBUG[2026-01-31 16:02:35.723][self$setPropertyValue] Setting property "parsing.expr" to "c("Standard InChIKey", "^InChIKey=(.*)$")".
biodb.DEBUG[2026-01-31 16:02:35.723][self$setPropertyValue] Setting property "parsing.expr" to "Formula".
biodb.DEBUG[2026-01-31 16:02:35.723][self$setPropertyValue] Setting property "parsing.expr" to "Molecular Weight".
biodb.DEBUG[2026-01-31 16:02:35.723][self$setPropertyValue] Setting property "parsing.expr" to "CAS".
biodb.DEBUG[2026-01-31 16:02:35.724][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2026-01-31 16:02:35.725][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2026-01-31 16:02:35.727][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2026-01-31 16:02:35.728][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-01-31 16:02:35.729][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-01-31 16:02:35.730][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-01-31 16:02:35.731][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-01-31 16:02:35.732][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-01-31 16:02:35.734][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-01-31 16:02:35.735][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/".
biodb.DEBUG[2026-01-31 16:02:35.735][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/".
biodb.DEBUG[2026-01-31 16:02:35.735][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/download/nci/".
biodb.DEBUG[2026-01-31 16:02:35.735][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/download/nci/NCI-Open_2012-05-01.sdf.gz".
biodb.DEBUG[2026-01-31 16:02:35.736][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-01-31 16:02:35.737][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-01-31 16:02:35.738][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2026-01-31 16:02:35.740][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-01-31 16:02:35.741][self$getEntryFields()$define] Define field nci.cactus.id.
biodb.DEBUG[2026-01-31 16:02:35.745][super$initialize] Initialize connector nci.cactus.
biodb.DEBUG[2026-01-31 16:02:35.749][biodb$getFactory()$createConn] Creating new connector nci.cactus for database class nci.cactus .
biodb.INFO [2026-01-31 16:02:35.751][biodb$terminate] Closing BiodbMain instance...
biodb.INFO [2026-01-31 16:02:35.752][self$deleteConn] Connector "nci.cactus" deleted.
biodb.DEBUG[2026-01-31 16:02:35.753][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2026-01-31 16:02:35.754][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-01-31 16:02:35.755][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-01-31 16:02:35.756][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-31 16:02:35.758][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 16:02:35.759][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:35.760][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 2 | WARN 0 | SKIP 2 | PASS 85 ]

══ Skipped tests (2) ═══════════════════════════════════════════════════════════
• empty test (2): ,

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test_long_100_generic.R:37:1'): RT unit is defined when there is an RT value. ──
Error in `private$doExtractDownload()`: attempt to apply non-function
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb (local) `<fn>`(conn = `<NcCctsCn>`, opt = `<named list>`)
 3.   └─conn$getBiodb()$getFactory()$getEntry(...)
 4.     └─private$loadEntries(conn$getId(), missing.ids, drop = FALSE)
 5.       └─conn$getEntryContent(ids)
 6.         └─self$download()
 7.           └─private$doExtractDownload()
── Error ('test_long_100_generic.R:37:1'): We can load an entry from the database. ──
Error in `cch$getTmpFolderPath()`: attempt to apply non-function
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb (local) `<fn>`(conn = `<NcCctsCn>`, 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$getEntryContent(ids)
 8.             └─self$download()
 9.               └─private$doExtractDownload()

[ FAIL 2 | WARN 0 | SKIP 2 | PASS 85 ]
Error:
! Test failures.
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 biodbNci_1.14.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNci.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 ‘biodbNci/DESCRIPTION’ ... OK
* this is package ‘biodbNci’ 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 ‘biodbNci’ can be installed ... OK
* used C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
* used SDK: ‘MacOSX11.3.1.sdk’
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* 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:
  NciCactusConn.Rd: BiodbConn
  NciCactusEntry.Rd: BiodbSdfEntry
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 line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... 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:
      ▆
   1. ├─base::do.call(fct, params)
   2. └─biodb (local) `<fn>`(conn = `<NcCctsCn>`, 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$getEntryContent(ids)
   8.             └─self$download()
   9.               └─private$doExtractDownload()
  
  [ FAIL 2 | WARN 0 | SKIP 2 | PASS 85 ]
  Error:
  ! Test failures.
  Execution halted
* DONE

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

Installation output

biodbNci.Rcheck/00install.out

* installing *source* package ‘biodbNci’ ...
** this is package ‘biodbNci’ version ‘1.14.0’
** using staged installation
** libs
using C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
using SDK: ‘MacOSX11.3.1.sdk’
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/testthat/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c RcppExports.cpp -o RcppExports.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/testthat/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c extractEntries.cpp -o extractEntries.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/testthat/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c test-100-example.cpp -o test-100-example.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/testthat/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c test-runner.cpp -o test-runner.o
clang++ -arch x86_64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/lib -o biodbNci.so RcppExports.o extractEntries.o test-100-example.o test-runner.o -F/Library/Frameworks/R.framework/.. -framework R
installing to /Users/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNci.Rcheck/00LOCK-biodbNci/00new/biodbNci/libs
** 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 'biodbNci' is deprecated and will be removed from Bioconductor
  version 3.23
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
Warning in fun(libname, pkgname) :
  Package 'biodbNci' is deprecated and will be removed from Bioconductor
  version 3.23
** testing if installed package keeps a record of temporary installation path
* DONE (biodbNci)