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 nebbiolo2

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: /home/biocbuild/bbs-3.22-bioc/R/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 16:02:18 -0500 (Sat, 31 Jan 2026)
EndedAt: 2026-01-31 16:03:21 -0500 (Sat, 31 Jan 2026)
EllapsedTime: 63.1 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"
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Platform: x86_64-pc-linux-gnu

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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 16:03:18.715][biodb::testContext]
biodb.INFO [2026-01-31 16:03:18.717][biodb::testContext] ********************************************************************************
biodb.INFO [2026-01-31 16:03:18.717][biodb::testContext] Test context - Generic long tests
biodb.INFO [2026-01-31 16:03:18.718][biodb::testContext] ********************************************************************************
biodb.INFO [2026-01-31 16:03:18.719][biodb::testContext]
biodb.INFO [2026-01-31 16:03:18.725][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.18.0.
biodb.DEBUG[2026-01-31 16:03:18.727][self$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.22-bioc/R/site-library/biodb/definitions.yml".
biodb.DEBUG[2026-01-31 16:03:18.733][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2026-01-31 16:03:18.734][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2026-01-31 16:03:18.735][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2026-01-31 16:03:18.736][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:03:18.736][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:03:18.737][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:03:18.738][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2026-01-31 16:03:18.754][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2026-01-31 16:03:18.755][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:03:18.756][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:03:18.757][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:03:18.758][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2026-01-31 16:03:18.759][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2026-01-31 16:03:18.759][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:03:18.760][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:03:18.761][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:03:18.762][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2026-01-31 16:03:18.763][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2026-01-31 16:03:18.764][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2026-01-31 16:03:18.765][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:03:18.766][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:03:18.766][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:03:18.767][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2026-01-31 16:03:18.768][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2026-01-31 16:03:18.769][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2026-01-31 16:03:18.770][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:03:18.771][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:03:18.772][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:03:18.772][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2026-01-31 16:03:18.773][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2026-01-31 16:03:18.774][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:03:18.775][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:03:18.776][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:03:18.777][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2026-01-31 16:03:18.778][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2026-01-31 16:03:18.779][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2026-01-31 16:03:18.779][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:03:18.780][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:03:18.781][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:03:18.782][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2026-01-31 16:03:18.783][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2026-01-31 16:03:18.784][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:03:18.785][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:03:18.786][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:03:18.787][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2026-01-31 16:03:18.788][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2026-01-31 16:03:18.789][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2026-01-31 16:03:18.790][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:03:18.791][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:03:18.791][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:03:18.792][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2026-01-31 16:03:18.793][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2026-01-31 16:03:18.794][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2026-01-31 16:03:18.795][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2026-01-31 16:03:18.796][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2026-01-31 16:03:18.797][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2026-01-31 16:03:18.798][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:03:18.799][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:03:18.799][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:03:18.800][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2026-01-31 16:03:18.801][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2026-01-31 16:03:18.802][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:03:18.803][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:03:18.804][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:03:18.805][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2026-01-31 16:03:18.806][self$set] Set key entries.sep to "|".
biodb.DEBUG[2026-01-31 16:03:18.806][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:03:18.807][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:03:18.808][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:03:18.809][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2026-01-31 16:03:18.810][self$set] Set key offline to FALSE.
biodb.DEBUG[2026-01-31 16:03:18.811][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:03:18.811][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:03:18.812][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:03:18.813][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2026-01-31 16:03:18.814][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2026-01-31 16:03:18.815][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2026-01-31 16:03:18.816][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:03:18.817][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:03:18.818][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:03:18.818][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2026-01-31 16:03:18.819][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2026-01-31 16:03:18.822][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2026-01-31 16:03:18.823][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:03:18.824][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:03:18.825][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:03:18.826][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2026-01-31 16:03:18.827][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2026-01-31 16:03:18.828][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2026-01-31 16:03:18.828][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:03:18.829][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:03:18.830][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:03:18.833][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2026-01-31 16:03:18.863][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2026-01-31 16:03:18.883][self$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 16:03:18.884][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-01-31 16:03:18.885][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-01-31 16:03:18.886][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-01-31 16:03:18.887][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-01-31 16:03:18.888][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2026-01-31 16:03:18.889][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-01-31 16:03:18.890][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2026-01-31 16:03:18.891][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-01-31 16:03:18.891][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2026-01-31 16:03:18.892][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2026-01-31 16:03:18.893][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-01-31 16:03:18.894][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2026-01-31 16:03:18.895][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2026-01-31 16:03:18.896][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2026-01-31 16:03:18.896][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2026-01-31 16:03:18.896][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2026-01-31 16:03:18.896][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2026-01-31 16:03:18.896][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2026-01-31 16:03:18.897][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2026-01-31 16:03:18.898][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-01-31 16:03:18.899][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-01-31 16:03:18.900][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-01-31 16:03:18.900][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-01-31 16:03:18.901][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-01-31 16:03:18.902][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-01-31 16:03:18.903][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2026-01-31 16:03:18.904][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-01-31 16:03:18.905][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-01-31 16:03:18.906][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2026-01-31 16:03:18.907][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-01-31 16:03:18.908][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2026-01-31 16:03:18.909][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2026-01-31 16:03:18.910][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2026-01-31 16:03:18.911][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-01-31 16:03:18.912][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-01-31 16:03:18.913][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-01-31 16:03:18.914][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-01-31 16:03:18.915][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2026-01-31 16:03:18.916][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-01-31 16:03:18.917][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2026-01-31 16:03:18.917][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-01-31 16:03:18.918][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2026-01-31 16:03:18.919][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2026-01-31 16:03:18.920][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-01-31 16:03:18.921][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2026-01-31 16:03:18.922][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2026-01-31 16:03:18.923][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2026-01-31 16:03:18.923][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2026-01-31 16:03:18.923][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2026-01-31 16:03:18.923][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2026-01-31 16:03:18.923][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2026-01-31 16:03:18.924][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2026-01-31 16:03:18.925][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-01-31 16:03:18.926][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-01-31 16:03:18.927][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-01-31 16:03:18.927][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-01-31 16:03:18.928][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-01-31 16:03:18.929][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-01-31 16:03:18.930][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2026-01-31 16:03:18.931][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-01-31 16:03:18.932][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-01-31 16:03:18.933][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2026-01-31 16:03:18.934][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-01-31 16:03:18.935][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2026-01-31 16:03:18.936][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2026-01-31 16:03:18.937][self$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 16:03:18.938][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-01-31 16:03:18.939][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-01-31 16:03:18.940][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-01-31 16:03:18.941][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-01-31 16:03:18.942][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2026-01-31 16:03:18.943][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-01-31 16:03:18.944][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2026-01-31 16:03:18.944][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-01-31 16:03:18.945][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2026-01-31 16:03:18.946][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2026-01-31 16:03:18.947][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-01-31 16:03:18.948][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2026-01-31 16:03:18.949][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2026-01-31 16:03:18.950][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2026-01-31 16:03:18.951][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2026-01-31 16:03:18.952][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-01-31 16:03:18.953][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-01-31 16:03:18.954][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-01-31 16:03:18.954][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-01-31 16:03:18.955][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-01-31 16:03:18.956][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-01-31 16:03:18.957][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2026-01-31 16:03:18.958][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-01-31 16:03:18.959][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-01-31 16:03:18.960][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2026-01-31 16:03:18.961][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-01-31 16:03:18.962][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2026-01-31 16:03:18.963][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2026-01-31 16:03:18.964][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2026-01-31 16:03:18.965][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-01-31 16:03:18.966][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-01-31 16:03:18.967][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-01-31 16:03:18.968][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-01-31 16:03:18.969][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2026-01-31 16:03:18.970][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-01-31 16:03:18.971][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2026-01-31 16:03:18.972][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-01-31 16:03:18.973][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2026-01-31 16:03:18.973][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2026-01-31 16:03:18.974][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-01-31 16:03:18.975][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2026-01-31 16:03:18.976][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2026-01-31 16:03:18.977][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2026-01-31 16:03:18.978][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2026-01-31 16:03:18.979][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-01-31 16:03:18.980][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-01-31 16:03:18.981][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-01-31 16:03:18.982][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-01-31 16:03:18.982][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-01-31 16:03:18.983][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-01-31 16:03:18.984][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2026-01-31 16:03:18.985][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-01-31 16:03:18.986][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-01-31 16:03:18.987][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2026-01-31 16:03:18.988][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-01-31 16:03:18.991][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2026-01-31 16:03:18.992][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:03:18.993][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:03:18.994][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:03:18.994][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-31 16:03:18.995][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 16:03:18.996][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:03:18.997][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:03:18.998][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:03:18.999][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-31 16:03:18.999][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 16:03:19.000][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:03:19.001][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:03:19.002][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:03:19.003][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-31 16:03:19.003][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 16:03:19.004][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:03:19.005][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:03:19.006][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:03:19.007][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-31 16:03:19.008][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-31 16:03:19.008][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:03:19.009][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:03:19.010][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:03:19.011][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-31 16:03:19.012][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 16:03:19.013][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:03:19.013][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:03:19.014][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:03:19.015][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-31 16:03:19.016][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 16:03:19.017][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:03:19.018][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:03:19.018][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:03:19.019][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-31 16:03:19.020][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 16:03:19.021][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:03:19.022][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:03:19.022][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:03:19.023][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-31 16:03:19.024][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 16:03:19.025][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:03:19.026][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:03:19.027][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:03:19.027][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-31 16:03:19.028][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 16:03:19.029][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:03:19.030][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:03:19.031][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:03:19.031][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-31 16:03:19.032][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 16:03:19.033][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:03:19.034][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:03:19.035][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:03:19.036][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-31 16:03:19.036][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-31 16:03:19.037][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:03:19.038][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:03:19.039][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:03:19.040][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-31 16:03:19.041][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 16:03:19.041][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:03:19.042][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:03:19.043][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:03:19.044][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-31 16:03:19.045][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 16:03:19.045][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:03:19.046][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:03:19.047][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:03:19.048][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-31 16:03:19.049][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 16:03:19.050][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:03:19.050][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:03:19.051][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:03:19.052][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-31 16:03:19.053][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 16:03:19.054][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:03:19.054][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:03:19.055][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:03:19.056][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-31 16:03:19.057][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 16:03:19.058][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:03:19.059][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 16:03:19.059][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2026-01-31 16:03:19.064][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2026-01-31 16:03:19.065][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2026-01-31 16:03:19.066][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2026-01-31 16:03:19.068][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2026-01-31 16:03:19.069][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2026-01-31 16:03:19.070][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2026-01-31 16:03:19.071][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2026-01-31 16:03:19.073][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2026-01-31 16:03:19.074][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2026-01-31 16:03:19.096][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2026-01-31 16:03:19.099][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2026-01-31 16:03:19.100][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2026-01-31 16:03:19.102][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2026-01-31 16:03:19.103][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2026-01-31 16:03:19.105][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2026-01-31 16:03:19.106][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2026-01-31 16:03:19.108][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2026-01-31 16:03:19.109][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2026-01-31 16:03:19.111][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2026-01-31 16:03:19.112][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2026-01-31 16:03:19.114][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2026-01-31 16:03:19.115][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2026-01-31 16:03:19.117][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2026-01-31 16:03:19.118][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2026-01-31 16:03:19.120][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2026-01-31 16:03:19.121][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2026-01-31 16:03:19.122][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2026-01-31 16:03:19.124][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2026-01-31 16:03:19.126][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2026-01-31 16:03:19.127][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2026-01-31 16:03:19.128][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2026-01-31 16:03:19.130][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2026-01-31 16:03:19.131][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2026-01-31 16:03:19.133][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2026-01-31 16:03:19.134][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2026-01-31 16:03:19.136][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2026-01-31 16:03:19.137][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2026-01-31 16:03:19.138][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2026-01-31 16:03:19.140][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2026-01-31 16:03:19.141][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2026-01-31 16:03:19.143][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2026-01-31 16:03:19.144][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2026-01-31 16:03:19.145][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2026-01-31 16:03:19.147][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2026-01-31 16:03:19.148][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2026-01-31 16:03:19.150][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2026-01-31 16:03:19.151][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2026-01-31 16:03:19.153][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2026-01-31 16:03:19.154][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2026-01-31 16:03:19.155][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2026-01-31 16:03:19.157][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2026-01-31 16:03:19.158][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2026-01-31 16:03:19.160][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2026-01-31 16:03:19.161][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2026-01-31 16:03:19.162][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2026-01-31 16:03:19.164][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2026-01-31 16:03:19.165][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2026-01-31 16:03:19.167][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2026-01-31 16:03:19.168][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2026-01-31 16:03:19.170][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2026-01-31 16:03:19.171][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2026-01-31 16:03:19.172][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2026-01-31 16:03:19.174][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2026-01-31 16:03:19.175][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2026-01-31 16:03:19.177][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2026-01-31 16:03:19.178][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2026-01-31 16:03:19.179][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2026-01-31 16:03:19.181][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2026-01-31 16:03:19.182][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2026-01-31 16:03:19.184][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2026-01-31 16:03:19.185][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2026-01-31 16:03:19.187][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2026-01-31 16:03:19.188][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2026-01-31 16:03:19.189][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2026-01-31 16:03:19.191][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2026-01-31 16:03:19.192][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2026-01-31 16:03:19.194][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2026-01-31 16:03:19.195][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2026-01-31 16:03:19.196][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2026-01-31 16:03:19.198][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2026-01-31 16:03:19.199][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2026-01-31 16:03:19.201][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2026-01-31 16:03:19.207][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2026-01-31 16:03:19.209][initialize] This is biodb version 1.18.0.
biodb.DEBUG[2026-01-31 16:03:19.213][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2026-01-31 16:03:19.214][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2026-01-31 16:03:19.215][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 16:03:19.215][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:03:19.216][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:03:19.221][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:03:19.222][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-01-31 16:03:19.223][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-01-31 16:03:19.224][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-31 16:03:19.225][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 16:03:19.226][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:03:19.227][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:03:19.228][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:03:19.229][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-01-31 16:03:19.229][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-01-31 16:03:19.230][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-31 16:03:19.231][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 16:03:19.232][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:03:19.233][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:03:19.234][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:03:19.235][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-01-31 16:03:19.236][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-01-31 16:03:19.237][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-31 16:03:19.238][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 16:03:19.239][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:03:19.240][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:03:19.240][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:03:19.241][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-01-31 16:03:19.242][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-01-31 16:03:19.243][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-31 16:03:19.244][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 16:03:19.245][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:03:19.246][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 16:03:19.247][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:03:19.248][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-01-31 16:03:19.249][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-01-31 16:03:19.250][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-31 16:03:19.251][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 16:03:19.251][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:03:19.252][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 16:03:19.253][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:03:19.254][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-01-31 16:03:19.255][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-01-31 16:03:19.256][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-31 16:03:19.257][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 16:03:19.258][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:03:19.259][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:03:19.260][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:03:19.261][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-01-31 16:03:19.262][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-01-31 16:03:19.262][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-31 16:03:19.263][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 16:03:19.264][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:03:19.265][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:03:19.266][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:03:19.267][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-01-31 16:03:19.268][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-01-31 16:03:19.269][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-31 16:03:19.270][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 16:03:19.271][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:03:19.272][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:03:19.272][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:03:19.273][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-01-31 16:03:19.274][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-01-31 16:03:19.275][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-31 16:03:19.276][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-31 16:03:19.277][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:03:19.278][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:03:19.279][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:03:19.280][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-01-31 16:03:19.281][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-01-31 16:03:19.281][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-31 16:03:19.282][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 16:03:19.283][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:03:19.284][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:03:19.285][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:03:19.286][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-01-31 16:03:19.287][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-01-31 16:03:19.288][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-31 16:03:19.289][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 16:03:19.290][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:03:19.290][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:03:19.291][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:03:19.292][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-01-31 16:03:19.293][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-01-31 16:03:19.294][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-31 16:03:19.295][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 16:03:19.296][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:03:19.297][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:03:19.298][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:03:19.298][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-01-31 16:03:19.299][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-01-31 16:03:19.300][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-31 16:03:19.301][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 16:03:19.302][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:03:19.303][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:03:19.304][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:03:19.305][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-01-31 16:03:19.306][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-01-31 16:03:19.314][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-31 16:03:19.315][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 16:03:19.316][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:03:19.316][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:03:19.317][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:03:19.318][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-01-31 16:03:19.319][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-01-31 16:03:19.320][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-31 16:03:19.320][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-31 16:03:19.321][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:03:19.322][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:03:19.323][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:03:19.324][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-01-31 16:03:19.324][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-01-31 16:03:19.325][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-31 16:03:19.326][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 16:03:19.327][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:03:19.328][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:03:19.329][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNci.Rcheck/biodbNci/definitions.yml".
biodb.DEBUG[2026-01-31 16:03:19.338][self$getDbsInfo()$define] Define connector nci.cactus.
biodb.DEBUG[2026-01-31 16:03:19.340][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2026-01-31 16:03:19.341][self$setPropertyValue] Setting property "description" to "National Cancer Institute (USA) CACTUS Database.".
biodb.DEBUG[2026-01-31 16:03:19.342][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-01-31 16:03:19.343][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-01-31 16:03:19.344][self$setPropertyValue] Setting property "downloadable" to "TRUE".
biodb.DEBUG[2026-01-31 16:03:19.345][self$setPropertyValue] Setting property "dwnld.ext" to "gz".
biodb.DEBUG[2026-01-31 16:03:19.346][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2026-01-31 16:03:19.346][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-01-31 16:03:19.347][self$setPropertyValue] Setting property "entry.content.type" to "sdf".
biodb.DEBUG[2026-01-31 16:03:19.348][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-01-31 16:03:19.349][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2026-01-31 16:03:19.350][self$setPropertyValue] Setting property "name" to "NCI CACTUS".
biodb.DEBUG[2026-01-31 16:03:19.351][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-01-31 16:03:19.352][self$setPropertyValue] Setting property "parsing.expr" to "NSC".
biodb.DEBUG[2026-01-31 16:03:19.352][self$setPropertyValue] Setting property "parsing.expr" to "DTP names".
biodb.DEBUG[2026-01-31 16:03:19.352][self$setPropertyValue] Setting property "parsing.expr" to "Standard InChI".
biodb.DEBUG[2026-01-31 16:03:19.352][self$setPropertyValue] Setting property "parsing.expr" to "c("Standard InChIKey", "^InChIKey=(.*)$")".
biodb.DEBUG[2026-01-31 16:03:19.352][self$setPropertyValue] Setting property "parsing.expr" to "Formula".
biodb.DEBUG[2026-01-31 16:03:19.352][self$setPropertyValue] Setting property "parsing.expr" to "Molecular Weight".
biodb.DEBUG[2026-01-31 16:03:19.352][self$setPropertyValue] Setting property "parsing.expr" to "CAS".
biodb.DEBUG[2026-01-31 16:03:19.353][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2026-01-31 16:03:19.354][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2026-01-31 16:03:19.355][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2026-01-31 16:03:19.356][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-01-31 16:03:19.357][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-01-31 16:03:19.357][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-01-31 16:03:19.358][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-01-31 16:03:19.359][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-01-31 16:03:19.360][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-01-31 16:03:19.361][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/".
biodb.DEBUG[2026-01-31 16:03:19.361][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/".
biodb.DEBUG[2026-01-31 16:03:19.361][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/download/nci/".
biodb.DEBUG[2026-01-31 16:03:19.361][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/download/nci/NCI-Open_2012-05-01.sdf.gz".
biodb.DEBUG[2026-01-31 16:03:19.362][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-01-31 16:03:19.363][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-01-31 16:03:19.364][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2026-01-31 16:03:19.365][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-01-31 16:03:19.370][self$getEntryFields()$define] Define field nci.cactus.id.
biodb.DEBUG[2026-01-31 16:03:19.390][super$initialize] Initialize connector nci.cactus.
biodb.DEBUG[2026-01-31 16:03:19.405][biodb$getFactory()$createConn] Creating new connector nci.cactus for database class nci.cactus .
biodb.INFO [2026-01-31 16:03:19.413][biodb::testThat]
biodb.INFO [2026-01-31 16:03:19.414][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2026-01-31 16:03:19.415][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-01-31 16:03:19.415][biodb::testThat]
biodb.TRACE[2026-01-31 16:03:19.418][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNci.Rcheck/biodbNci/testref/entry-nci.cactus-749674-content.sdf".
biodb.DEBUG[2026-01-31 16:03:19.420][biodb$getFactory()$createEntryFromCo ...] Creating NCI CACTUS entries from 1 content(s).
biodb.DEBUG[2026-01-31 16:03:19.423][biodb$getFactory()$createEntryFromCo ...] Parsing 1 NCI CACTUS entries.
biodb.DEBUG[2026-01-31 16:03:19.431][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2026-01-31 16:03:19.432][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2026-01-31 16:03:19.433][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-01-31 16:03:19.445][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2026-01-31 16:03:19.445][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-31 16:03:19.446][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:03:19.447][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2026-01-31 16:03:19.464][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-31 16:03:19.465][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-31 16:03:19.466][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:03:19.467][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:03:19.468][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-31 16:03:19.480][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-31 16:03:19.481][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:03:19.482][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:03:19.484][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2026-01-31 16:03:19.485][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2026-01-31 16:03:19.486][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:03:19.487][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:03:19.511][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2026-01-31 16:03:19.512][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2026-01-31 16:03:19.513][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:03:19.514][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:03:19.515][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2026-01-31 16:03:19.516][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2026-01-31 16:03:19.517][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:03:19.518][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:03:19.527][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2026-01-31 16:03:19.528][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2026-01-31 16:03:19.529][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:03:19.530][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:03:19.532][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2026-01-31 16:03:19.533][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2026-01-31 16:03:19.533][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:03:19.534][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:03:19.535][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2026-01-31 16:03:19.536][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2026-01-31 16:03:19.537][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:03:19.538][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:03:19.539][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-01-31 16:03:19.540][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-01-31 16:03:19.541][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:03:19.542][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:03:19.543][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-01-31 16:03:19.544][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-01-31 16:03:19.545][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:03:19.546][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:03:19.547][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2026-01-31 16:03:19.548][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2026-01-31 16:03:19.549][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:03:19.550][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:03:19.551][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2026-01-31 16:03:19.552][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2026-01-31 16:03:19.553][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:03:19.554][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:03:19.555][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-31 16:03:19.556][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-31 16:03:19.556][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:03:19.557][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:03:19.558][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2026-01-31 16:03:19.559][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2026-01-31 16:03:19.560][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:03:19.561][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:03:19.562][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-31 16:03:19.563][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-31 16:03:19.564][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:03:19.565][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:03:19.566][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-31 16:03:19.567][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-31 16:03:19.567][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:03:19.568][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:03:19.569][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-31 16:03:19.570][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-31 16:03:19.571][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:03:19.572][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:03:19.603][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-31 16:03:19.604][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-31 16:03:19.605][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:03:19.606][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:03:19.607][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-31 16:03:19.608][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-31 16:03:19.608][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:03:19.609][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:03:19.610][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-31 16:03:19.611][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-31 16:03:19.612][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:03:19.613][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2026-01-31 16:03:19.614][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 749674.
biodb.TRACE[2026-01-31 16:03:19.616][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2026-01-31 16:03:19.617][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2026-01-31 16:03:19.618][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:03:19.619][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:03:19.620][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2026-01-31 16:03:19.621][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2026-01-31 16:03:19.622][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:03:19.623][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:03:19.624][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2026-01-31 16:03:19.624][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2026-01-31 16:03:19.625][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:03:19.626][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:03:19.627][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2026-01-31 16:03:19.628][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2026-01-31 16:03:19.629][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:03:19.630][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:03:19.632][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-31 16:03:19.633][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-31 16:03:19.634][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:03:19.635][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:03:19.647][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2026-01-31 16:03:19.648][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2026-01-31 16:03:19.649][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:03:19.650][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:03:19.654][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-31 16:03:19.655][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-31 16:03:19.656][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:03:19.657][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:03:19.657][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-31 16:03:19.658][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-31 16:03:19.659][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:03:19.660][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:03:19.661][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-31 16:03:19.662][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-31 16:03:19.663][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:03:19.664][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:03:19.666][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-31 16:03:19.667][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-31 16:03:19.668][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:03:19.669][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:03:19.670][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-31 16:03:19.671][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-31 16:03:19.672][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:03:19.673][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:03:19.674][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-31 16:03:19.675][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-31 16:03:19.676][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:03:19.677][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:03:19.681][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2026-01-31 16:03:19.682][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2026-01-31 16:03:19.683][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:03:19.684][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:03:19.685][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2026-01-31 16:03:19.686][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2026-01-31 16:03:19.687][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:03:19.688][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:03:19.689][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2026-01-31 16:03:19.690][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2026-01-31 16:03:19.691][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:03:19.691][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:03:19.698][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-31 16:03:19.699][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-31 16:03:19.700][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:03:19.701][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:03:19.702][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-31 16:03:19.703][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-31 16:03:19.704][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:03:19.705][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:03:19.706][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-31 16:03:19.706][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-31 16:03:19.707][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:03:19.708][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:03:19.709][ef$get] Asked field names are: accession.
biodb.TRACE[2026-01-31 16:03:19.710][ef$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-31 16:03:19.711][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:03:19.712][ef$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:03:19.713][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-31 16:03:19.714][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-31 16:03:19.715][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:03:19.716][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:03:19.724][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2026-01-31 16:03:19.725][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2026-01-31 16:03:19.726][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:03:19.726][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:03:19.727][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2026-01-31 16:03:19.728][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2026-01-31 16:03:19.729][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:03:19.730][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:03:19.731][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2026-01-31 16:03:19.732][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2026-01-31 16:03:19.733][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:03:19.734][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:03:19.735][ef$get] Asked field names are: formula.
biodb.TRACE[2026-01-31 16:03:19.736][ef$get] Realnames of fields are: formula.
biodb.TRACE[2026-01-31 16:03:19.737][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:03:19.738][ef$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:03:19.738][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2026-01-31 16:03:19.739][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2026-01-31 16:03:19.740][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:03:19.741][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:03:19.749][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2026-01-31 16:03:19.750][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2026-01-31 16:03:19.751][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:03:19.752][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:03:19.753][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2026-01-31 16:03:19.754][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2026-01-31 16:03:19.754][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:03:19.755][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:03:19.756][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2026-01-31 16:03:19.757][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2026-01-31 16:03:19.758][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:03:19.759][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:03:19.760][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2026-01-31 16:03:19.761][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2026-01-31 16:03:19.762][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:03:19.763][ef$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:03:19.764][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2026-01-31 16:03:19.765][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2026-01-31 16:03:19.766][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:03:19.766][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:03:19.774][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2026-01-31 16:03:19.775][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2026-01-31 16:03:19.776][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:03:19.777][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:03:19.778][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2026-01-31 16:03:19.779][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2026-01-31 16:03:19.780][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:03:19.781][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:03:19.781][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2026-01-31 16:03:19.782][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2026-01-31 16:03:19.783][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:03:19.784][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:03:19.785][ef$get] Asked field names are: inchi.
biodb.TRACE[2026-01-31 16:03:19.786][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2026-01-31 16:03:19.787][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:03:19.788][ef$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:03:19.789][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2026-01-31 16:03:19.790][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2026-01-31 16:03:19.791][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:03:19.792][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:03:19.799][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-01-31 16:03:19.800][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-01-31 16:03:19.801][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:03:19.802][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:03:19.803][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-01-31 16:03:19.804][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-01-31 16:03:19.805][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:03:19.806][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:03:19.807][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-01-31 16:03:19.808][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-01-31 16:03:19.808][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:03:19.809][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:03:19.810][ef$get] Asked field names are: inchikey.
biodb.TRACE[2026-01-31 16:03:19.811][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-01-31 16:03:19.812][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:03:19.813][ef$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:03:19.814][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-01-31 16:03:19.815][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-01-31 16:03:19.816][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:03:19.817][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:03:19.824][ef$get] Asked field names are: accession.
biodb.TRACE[2026-01-31 16:03:19.825][ef$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-31 16:03:19.826][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:03:19.827][ef$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:03:19.831][ef$get] Asked field names are: formula.
biodb.TRACE[2026-01-31 16:03:19.832][ef$get] Realnames of fields are: formula.
biodb.TRACE[2026-01-31 16:03:19.833][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:03:19.834][ef$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:03:19.837][ef$get] Asked field names are: inchi.
biodb.TRACE[2026-01-31 16:03:19.838][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2026-01-31 16:03:19.843][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:03:19.844][ef$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:03:19.848][ef$get] Asked field names are: inchikey.
biodb.TRACE[2026-01-31 16:03:19.849][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-01-31 16:03:19.850][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:03:19.851][ef$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:03:19.855][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2026-01-31 16:03:19.856][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2026-01-31 16:03:19.856][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:03:19.857][ef$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:03:19.873][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNci.Rcheck/biodbNci/testref/entry-nci.cactus-750690-content.sdf".
biodb.DEBUG[2026-01-31 16:03:19.906][biodb$getFactory()$createEntryFromCo ...] Creating NCI CACTUS entries from 1 content(s).
biodb.DEBUG[2026-01-31 16:03:19.907][biodb$getFactory()$createEntryFromCo ...] Parsing 1 NCI CACTUS entries.
biodb.DEBUG[2026-01-31 16:03:19.909][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2026-01-31 16:03:19.910][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2026-01-31 16:03:19.910][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-01-31 16:03:19.915][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2026-01-31 16:03:19.915][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-31 16:03:19.916][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:03:19.917][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2026-01-31 16:03:19.926][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-31 16:03:19.927][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-31 16:03:19.928][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:03:19.929][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:03:19.930][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-31 16:03:19.931][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-31 16:03:19.932][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:03:19.933][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:03:19.950][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2026-01-31 16:03:19.951][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2026-01-31 16:03:19.952][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:03:19.953][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:03:19.954][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2026-01-31 16:03:19.955][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2026-01-31 16:03:19.956][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:03:19.957][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:03:19.958][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2026-01-31 16:03:19.959][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2026-01-31 16:03:19.960][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:03:19.961][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:03:19.962][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2026-01-31 16:03:19.963][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2026-01-31 16:03:19.964][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:03:19.965][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:03:19.966][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2026-01-31 16:03:19.967][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2026-01-31 16:03:19.968][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:03:19.969][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:03:19.969][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2026-01-31 16:03:19.970][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2026-01-31 16:03:19.971][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:03:19.972][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:03:19.974][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-01-31 16:03:19.974][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-01-31 16:03:19.975][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:03:19.976][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:03:19.977][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-01-31 16:03:19.978][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-01-31 16:03:19.979][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:03:19.980][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:03:19.981][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-01-31 16:03:19.982][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-01-31 16:03:19.983][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:03:19.984][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:03:19.985][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-01-31 16:03:19.986][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-01-31 16:03:19.987][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:03:20.027][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:03:20.028][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-01-31 16:03:20.029][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-01-31 16:03:20.030][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:03:20.031][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:03:20.032][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-01-31 16:03:20.033][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-01-31 16:03:20.033][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:03:20.034][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:03:20.035][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-01-31 16:03:20.036][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-01-31 16:03:20.037][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:03:20.038][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:03:20.040][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2026-01-31 16:03:20.041][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2026-01-31 16:03:20.042][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:03:20.042][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:03:20.043][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2026-01-31 16:03:20.044][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2026-01-31 16:03:20.045][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:03:20.046][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:03:20.047][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-01-31 16:03:20.048][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-01-31 16:03:20.049][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:03:20.050][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:03:20.051][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-01-31 16:03:20.052][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-01-31 16:03:20.053][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:03:20.054][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:03:20.055][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2026-01-31 16:03:20.056][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2026-01-31 16:03:20.057][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:03:20.058][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:03:20.059][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2026-01-31 16:03:20.060][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2026-01-31 16:03:20.061][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:03:20.062][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:03:20.063][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-31 16:03:20.064][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-31 16:03:20.065][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:03:20.065][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:03:20.066][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2026-01-31 16:03:20.067][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2026-01-31 16:03:20.068][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:03:20.069][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:03:20.070][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-31 16:03:20.071][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-31 16:03:20.072][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:03:20.073][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:03:20.074][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-31 16:03:20.075][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-31 16:03:20.076][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:03:20.077][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:03:20.077][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-31 16:03:20.078][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-31 16:03:20.079][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:03:20.080][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:03:20.081][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-31 16:03:20.082][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-31 16:03:20.083][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:03:20.084][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:03:20.085][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-31 16:03:20.086][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-31 16:03:20.087][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:03:20.088][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:03:20.089][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-31 16:03:20.090][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-31 16:03:20.090][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:03:20.091][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2026-01-31 16:03:20.092][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 750690.
biodb.TRACE[2026-01-31 16:03:20.111][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2026-01-31 16:03:20.112][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2026-01-31 16:03:20.113][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:03:20.114][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:03:20.115][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2026-01-31 16:03:20.116][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2026-01-31 16:03:20.117][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:03:20.118][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:03:20.119][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2026-01-31 16:03:20.120][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2026-01-31 16:03:20.121][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:03:20.121][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:03:20.122][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2026-01-31 16:03:20.123][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2026-01-31 16:03:20.124][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:03:20.125][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:03:20.127][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-31 16:03:20.128][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-31 16:03:20.129][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:03:20.130][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:03:20.134][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2026-01-31 16:03:20.135][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2026-01-31 16:03:20.136][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:03:20.137][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:03:20.141][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-31 16:03:20.142][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-31 16:03:20.142][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:03:20.143][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:03:20.144][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-31 16:03:20.145][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-31 16:03:20.146][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:03:20.147][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:03:20.148][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-31 16:03:20.149][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-31 16:03:20.150][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:03:20.151][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:03:20.153][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-31 16:03:20.154][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-31 16:03:20.155][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:03:20.156][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:03:20.157][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-31 16:03:20.158][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-31 16:03:20.158][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:03:20.159][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:03:20.160][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-31 16:03:20.161][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-31 16:03:20.162][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:03:20.163][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:03:20.164][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2026-01-31 16:03:20.165][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2026-01-31 16:03:20.166][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:03:20.167][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:03:20.168][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2026-01-31 16:03:20.169][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2026-01-31 16:03:20.170][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:03:20.171][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:03:20.172][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2026-01-31 16:03:20.173][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2026-01-31 16:03:20.173][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:03:20.174][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:03:20.193][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-31 16:03:20.194][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-31 16:03:20.195][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:03:20.196][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:03:20.197][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-31 16:03:20.198][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-31 16:03:20.199][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:03:20.200][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:03:20.201][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-31 16:03:20.202][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-31 16:03:20.203][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:03:20.203][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:03:20.204][ef$get] Asked field names are: accession.
biodb.TRACE[2026-01-31 16:03:20.205][ef$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-31 16:03:20.206][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:03:20.207][ef$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:03:20.208][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-31 16:03:20.209][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-31 16:03:20.210][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:03:20.211][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:03:20.219][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2026-01-31 16:03:20.220][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2026-01-31 16:03:20.220][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:03:20.221][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:03:20.222][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2026-01-31 16:03:20.223][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2026-01-31 16:03:20.224][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:03:20.225][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:03:20.226][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2026-01-31 16:03:20.227][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2026-01-31 16:03:20.228][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:03:20.229][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:03:20.230][ef$get] Asked field names are: cas.id.
biodb.TRACE[2026-01-31 16:03:20.231][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2026-01-31 16:03:20.232][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:03:20.232][ef$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:03:20.233][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2026-01-31 16:03:20.234][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2026-01-31 16:03:20.235][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:03:20.236][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:03:20.245][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-01-31 16:03:20.246][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-01-31 16:03:20.247][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:03:20.248][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:03:20.249][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-01-31 16:03:20.250][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-01-31 16:03:20.250][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:03:20.251][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:03:20.252][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-01-31 16:03:20.253][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-01-31 16:03:20.254][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:03:20.255][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:03:20.256][ef$get] Asked field names are: name.
biodb.TRACE[2026-01-31 16:03:20.257][ef$get] Realnames of fields are: name.
biodb.TRACE[2026-01-31 16:03:20.258][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:03:20.259][ef$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:03:20.260][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-01-31 16:03:20.261][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-01-31 16:03:20.262][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:03:20.263][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:03:20.270][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2026-01-31 16:03:20.271][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2026-01-31 16:03:20.272][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:03:20.273][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:03:20.274][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2026-01-31 16:03:20.275][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2026-01-31 16:03:20.276][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:03:20.277][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:03:20.278][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2026-01-31 16:03:20.279][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2026-01-31 16:03:20.280][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:03:20.280][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:03:20.281][ef$get] Asked field names are: formula.
biodb.TRACE[2026-01-31 16:03:20.282][ef$get] Realnames of fields are: formula.
biodb.TRACE[2026-01-31 16:03:20.283][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:03:20.284][ef$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:03:20.285][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2026-01-31 16:03:20.286][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2026-01-31 16:03:20.287][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:03:20.288][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:03:20.295][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2026-01-31 16:03:20.296][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2026-01-31 16:03:20.297][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:03:20.298][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:03:20.299][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2026-01-31 16:03:20.300][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2026-01-31 16:03:20.301][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:03:20.302][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:03:20.303][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2026-01-31 16:03:20.304][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2026-01-31 16:03:20.305][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:03:20.306][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:03:20.307][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2026-01-31 16:03:20.308][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2026-01-31 16:03:20.308][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:03:20.309][ef$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:03:20.310][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2026-01-31 16:03:20.311][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2026-01-31 16:03:20.312][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:03:20.313][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:03:20.321][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2026-01-31 16:03:20.322][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2026-01-31 16:03:20.322][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:03:20.323][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:03:20.324][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2026-01-31 16:03:20.325][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2026-01-31 16:03:20.326][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:03:20.327][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:03:20.328][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2026-01-31 16:03:20.329][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2026-01-31 16:03:20.330][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:03:20.331][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:03:20.332][ef$get] Asked field names are: inchi.
biodb.TRACE[2026-01-31 16:03:20.333][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2026-01-31 16:03:20.333][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:03:20.334][ef$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:03:20.335][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2026-01-31 16:03:20.336][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2026-01-31 16:03:20.337][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:03:20.338][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:03:20.350][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-01-31 16:03:20.351][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-01-31 16:03:20.351][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:03:20.352][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:03:20.353][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-01-31 16:03:20.354][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-01-31 16:03:20.355][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:03:20.356][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:03:20.357][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-01-31 16:03:20.358][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-01-31 16:03:20.359][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:03:20.360][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:03:20.360][ef$get] Asked field names are: inchikey.
biodb.TRACE[2026-01-31 16:03:20.361][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-01-31 16:03:20.362][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:03:20.363][ef$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:03:20.364][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-01-31 16:03:20.365][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-01-31 16:03:20.366][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:03:20.367][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:03:20.375][ef$get] Asked field names are: accession.
biodb.TRACE[2026-01-31 16:03:20.376][ef$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-31 16:03:20.377][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:03:20.377][ef$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:03:20.381][ef$get] Asked field names are: cas.id.
biodb.TRACE[2026-01-31 16:03:20.382][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2026-01-31 16:03:20.383][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:03:20.384][ef$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:03:20.388][ef$get] Asked field names are: formula.
biodb.TRACE[2026-01-31 16:03:20.389][ef$get] Realnames of fields are: formula.
biodb.TRACE[2026-01-31 16:03:20.390][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:03:20.391][ef$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:03:20.395][ef$get] Asked field names are: inchi.
biodb.TRACE[2026-01-31 16:03:20.396][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2026-01-31 16:03:20.397][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:03:20.397][ef$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:03:20.401][ef$get] Asked field names are: inchikey.
biodb.TRACE[2026-01-31 16:03:20.402][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-01-31 16:03:20.403][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:03:20.404][ef$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:03:20.408][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2026-01-31 16:03:20.409][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2026-01-31 16:03:20.410][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:03:20.411][ef$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:03:20.415][ef$get] Asked field names are: name.
biodb.TRACE[2026-01-31 16:03:20.416][ef$get] Realnames of fields are: name.
biodb.TRACE[2026-01-31 16:03:20.416][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:03:20.417][ef$get] fields variable is a list.
biodb.INFO [2026-01-31 16:03:20.424][biodb::testThat]
biodb.INFO [2026-01-31 16:03:20.425][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2026-01-31 16:03:20.426][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-01-31 16:03:20.426][biodb::testThat]
biodb.DEBUG[2026-01-31 16:03:20.428][private$loadEntries] Creating entries from ids [2]: "749674, 750690".
biodb.DEBUG[2026-01-31 16:03:20.430][conn$getEntryContent] Get NCI CACTUS entry content(s) for 2 id(s)...
biodb.DEBUG[2026-01-31 16:03:20.433][self$isDownloaded] Database nci.cactus has already been downloaded.
biodb.DEBUG[2026-01-31 16:03:20.461][self$isDownloaded] Database nci.cactus has already been downloaded.
biodb.INFO [2026-01-31 16:03:20.462][self$download] Extract whole database of nci.cactus.
biodb.INFO [2026-01-31 16:03:20.463][private$doExtractDownload] Extracting content of downloaded biodbNci, a library for connecting to the National Cancer Institute (USA) CACTUS Database....
Saving _problems/test_long_100_generic-38.R
biodb.INFO [2026-01-31 16:03:20.591][biodb::testThat]
biodb.INFO [2026-01-31 16:03:20.592][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2026-01-31 16:03:20.593][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-01-31 16:03:20.594][biodb::testThat]
biodb.INFO [2026-01-31 16:03:20.600][biodb::testThat]
biodb.INFO [2026-01-31 16:03:20.601][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2026-01-31 16:03:20.602][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-01-31 16:03:20.602][biodb::testThat]
biodb.WARN [2026-01-31 16:03:20.617][self$searchForEntries] This database is not searchable by field "name".
biodb.WARN [2026-01-31 16:03:20.634][self$searchForEntries] This database is not searchable by field "name".
biodb.INFO [2026-01-31 16:03:20.647][biodb::testThat]
biodb.INFO [2026-01-31 16:03:20.648][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2026-01-31 16:03:20.649][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-01-31 16:03:20.649][biodb::testThat]
biodb.DEBUG[2026-01-31 16:03:20.665][private$loadEntries] Creating entries from ids [1]: "749674".
biodb.DEBUG[2026-01-31 16:03:20.709][conn$getEntryContent] Get NCI CACTUS entry content(s) for 1 id(s)...
biodb.DEBUG[2026-01-31 16:03:20.710][self$isDownloaded] Database nci.cactus has already been downloaded.
biodb.DEBUG[2026-01-31 16:03:20.711][self$isDownloaded] Database nci.cactus has already been downloaded.
biodb.INFO [2026-01-31 16:03:20.713][self$download] Extract whole database of nci.cactus.
biodb.INFO [2026-01-31 16:03:20.725][private$doExtractDownload] Extracting content of downloaded biodbNci, a library for connecting to the National Cancer Institute (USA) CACTUS Database....
Saving _problems/test_long_100_generic-38.R
biodb.INFO [2026-01-31 16:03:20.780][biodb::testThat]
biodb.INFO [2026-01-31 16:03:20.781][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2026-01-31 16:03:20.782][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-01-31 16:03:20.783][biodb::testThat]
biodb.INFO [2026-01-31 16:03:20.789][biodb::testThat]
biodb.INFO [2026-01-31 16:03:20.790][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2026-01-31 16:03:20.791][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-01-31 16:03:20.792][biodb::testThat]
biodb.INFO [2026-01-31 16:03:20.799][biodb::testThat]
biodb.INFO [2026-01-31 16:03:20.799][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2026-01-31 16:03:20.800][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-01-31 16:03:20.801][biodb::testThat]
biodb.INFO [2026-01-31 16:03:20.807][biodb::testThat]
biodb.INFO [2026-01-31 16:03:20.807][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2026-01-31 16:03:20.808][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-01-31 16:03:20.809][biodb::testThat]
biodb.INFO [2026-01-31 16:03:20.814][biodb$terminate] Closing BiodbMain instance...
biodb.INFO [2026-01-31 16:03:20.815][self$deleteConn] Connector "nci.cactus" deleted.
biodb.DEBUG[2026-01-31 16:03:20.816][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2026-01-31 16:03:20.817][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-01-31 16:03:20.818][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-01-31 16:03:20.819][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-31 16:03:20.820][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-31 16:03:20.821][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:03:20.821][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2026-01-31 16:03:20.830][biodb::testContext]
biodb.INFO [2026-01-31 16:03:20.831][biodb::testContext] ********************************************************************************
biodb.INFO [2026-01-31 16:03:20.832][biodb::testContext] Test context - Example long tests
biodb.INFO [2026-01-31 16:03:20.833][biodb::testContext] ********************************************************************************
biodb.INFO [2026-01-31 16:03:20.834][biodb::testContext]
biodb.INFO [2026-01-31 16:03:20.836][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.18.0.
biodb.DEBUG[2026-01-31 16:03:20.837][self$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.22-bioc/R/site-library/biodb/definitions.yml".
biodb.DEBUG[2026-01-31 16:03:20.841][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2026-01-31 16:03:20.842][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2026-01-31 16:03:20.843][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2026-01-31 16:03:20.844][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:03:20.844][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:03:20.845][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:03:20.846][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2026-01-31 16:03:20.847][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2026-01-31 16:03:20.848][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:03:20.849][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:03:20.850][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:03:20.850][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2026-01-31 16:03:20.851][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2026-01-31 16:03:20.852][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:03:20.853][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:03:20.854][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 16:03:20.855][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2026-01-31 16:03:20.856][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2026-01-31 16:03:20.857][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2026-01-31 16:03:20.858][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:03:20.858][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:03:20.859][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:03:20.860][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2026-01-31 16:03:20.861][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2026-01-31 16:03:20.862][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2026-01-31 16:03:20.863][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:03:20.864][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:03:20.865][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:03:20.865][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2026-01-31 16:03:20.866][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2026-01-31 16:03:20.867][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:03:20.868][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:03:20.869][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:03:20.870][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2026-01-31 16:03:20.871][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2026-01-31 16:03:20.872][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2026-01-31 16:03:20.872][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:03:20.873][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:03:20.874][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:03:20.875][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2026-01-31 16:03:20.876][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2026-01-31 16:03:20.877][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:03:20.878][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:03:20.878][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:03:20.879][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2026-01-31 16:03:20.880][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2026-01-31 16:03:20.881][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2026-01-31 16:03:20.882][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:03:20.883][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:03:20.884][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:03:20.885][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2026-01-31 16:03:20.886][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2026-01-31 16:03:20.886][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2026-01-31 16:03:20.887][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2026-01-31 16:03:20.888][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2026-01-31 16:03:20.889][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2026-01-31 16:03:20.890][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:03:20.891][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:03:20.892][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:03:20.893][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2026-01-31 16:03:20.894][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2026-01-31 16:03:20.894][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:03:20.895][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:03:20.896][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:03:20.897][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2026-01-31 16:03:20.898][self$set] Set key entries.sep to "|".
biodb.DEBUG[2026-01-31 16:03:20.899][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:03:20.900][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:03:20.900][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:03:20.901][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2026-01-31 16:03:20.902][self$set] Set key offline to FALSE.
biodb.DEBUG[2026-01-31 16:03:20.903][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:03:20.904][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:03:20.905][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:03:20.906][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2026-01-31 16:03:20.907][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2026-01-31 16:03:20.908][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2026-01-31 16:03:20.908][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:03:20.909][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:03:20.910][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:03:20.911][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2026-01-31 16:03:20.912][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2026-01-31 16:03:20.919][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2026-01-31 16:03:20.920][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:03:20.921][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:03:20.922][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:03:20.923][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2026-01-31 16:03:20.924][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2026-01-31 16:03:20.925][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2026-01-31 16:03:20.926][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:03:20.926][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:03:20.927][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:03:20.928][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2026-01-31 16:03:20.930][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2026-01-31 16:03:20.931][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2026-01-31 16:03:20.932][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-01-31 16:03:20.933][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-01-31 16:03:20.934][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-01-31 16:03:20.935][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-01-31 16:03:20.936][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2026-01-31 16:03:20.937][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-01-31 16:03:20.938][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2026-01-31 16:03:20.938][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-01-31 16:03:20.939][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2026-01-31 16:03:20.940][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2026-01-31 16:03:20.941][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-01-31 16:03:20.942][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2026-01-31 16:03:20.943][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2026-01-31 16:03:20.944][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2026-01-31 16:03:20.944][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2026-01-31 16:03:20.944][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2026-01-31 16:03:20.944][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2026-01-31 16:03:20.944][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2026-01-31 16:03:20.945][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2026-01-31 16:03:20.946][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-01-31 16:03:20.947][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-01-31 16:03:20.948][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-01-31 16:03:20.949][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-01-31 16:03:20.949][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-01-31 16:03:20.950][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-01-31 16:03:20.951][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2026-01-31 16:03:20.952][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-01-31 16:03:20.953][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-01-31 16:03:20.954][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2026-01-31 16:03:20.955][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-01-31 16:03:20.956][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2026-01-31 16:03:20.958][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2026-01-31 16:03:20.958][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2026-01-31 16:03:20.959][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-01-31 16:03:20.960][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-01-31 16:03:20.961][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-01-31 16:03:20.962][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-01-31 16:03:20.963][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2026-01-31 16:03:20.964][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-01-31 16:03:20.965][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2026-01-31 16:03:20.966][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-01-31 16:03:20.967][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2026-01-31 16:03:20.968][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2026-01-31 16:03:20.969][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-01-31 16:03:20.970][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2026-01-31 16:03:20.971][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2026-01-31 16:03:20.972][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2026-01-31 16:03:20.972][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2026-01-31 16:03:20.972][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2026-01-31 16:03:20.972][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2026-01-31 16:03:20.972][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2026-01-31 16:03:20.972][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2026-01-31 16:03:20.973][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-01-31 16:03:20.974][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-01-31 16:03:20.975][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-01-31 16:03:20.976][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-01-31 16:03:20.977][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-01-31 16:03:20.978][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-01-31 16:03:20.979][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2026-01-31 16:03:20.980][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-01-31 16:03:20.980][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-01-31 16:03:20.981][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2026-01-31 16:03:20.982][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-01-31 16:03:20.984][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2026-01-31 16:03:20.985][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2026-01-31 16:03:20.986][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2026-01-31 16:03:20.987][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-01-31 16:03:20.988][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-01-31 16:03:20.989][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-01-31 16:03:20.990][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-01-31 16:03:20.991][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2026-01-31 16:03:20.992][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-01-31 16:03:20.993][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2026-01-31 16:03:20.994][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-01-31 16:03:20.995][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2026-01-31 16:03:20.996][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2026-01-31 16:03:20.997][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-01-31 16:03:20.998][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2026-01-31 16:03:20.999][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2026-01-31 16:03:21.000][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2026-01-31 16:03:21.001][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2026-01-31 16:03:21.002][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-01-31 16:03:21.002][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-01-31 16:03:21.003][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-01-31 16:03:21.004][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-01-31 16:03:21.005][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-01-31 16:03:21.006][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-01-31 16:03:21.007][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2026-01-31 16:03:21.008][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-01-31 16:03:21.009][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-01-31 16:03:21.009][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2026-01-31 16:03:21.010][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-01-31 16:03:21.011][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2026-01-31 16:03:21.013][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2026-01-31 16:03:21.014][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2026-01-31 16:03:21.015][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-01-31 16:03:21.016][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-01-31 16:03:21.017][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-01-31 16:03:21.018][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-01-31 16:03:21.019][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2026-01-31 16:03:21.020][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-01-31 16:03:21.021][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2026-01-31 16:03:21.021][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-01-31 16:03:21.022][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2026-01-31 16:03:21.023][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2026-01-31 16:03:21.024][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-01-31 16:03:21.025][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2026-01-31 16:03:21.026][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2026-01-31 16:03:21.027][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2026-01-31 16:03:21.028][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2026-01-31 16:03:21.029][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-01-31 16:03:21.030][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-01-31 16:03:21.031][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-01-31 16:03:21.032][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-01-31 16:03:21.032][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-01-31 16:03:21.033][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-01-31 16:03:21.034][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2026-01-31 16:03:21.035][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-01-31 16:03:21.036][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-01-31 16:03:21.037][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2026-01-31 16:03:21.038][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-01-31 16:03:21.039][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2026-01-31 16:03:21.040][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:03:21.041][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:03:21.042][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:03:21.042][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-31 16:03:21.043][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 16:03:21.044][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:03:21.045][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:03:21.046][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:03:21.047][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-31 16:03:21.047][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 16:03:21.048][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:03:21.049][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:03:21.050][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:03:21.051][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-31 16:03:21.052][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 16:03:21.052][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:03:21.053][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 16:03:21.054][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:03:21.055][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-31 16:03:21.056][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 16:03:21.057][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:03:21.057][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:03:21.058][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:03:21.059][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-31 16:03:21.060][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-31 16:03:21.061][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:03:21.062][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:03:21.062][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:03:21.063][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-31 16:03:21.064][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 16:03:21.065][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:03:21.066][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:03:21.071][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:03:21.071][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-31 16:03:21.072][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 16:03:21.073][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:03:21.074][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:03:21.075][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:03:21.076][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-31 16:03:21.076][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 16:03:21.077][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:03:21.078][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:03:21.079][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:03:21.080][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-31 16:03:21.081][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 16:03:21.081][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:03:21.082][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:03:21.083][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:03:21.084][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-31 16:03:21.085][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 16:03:21.085][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:03:21.086][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:03:21.087][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:03:21.088][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-31 16:03:21.089][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 16:03:21.090][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:03:21.090][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:03:21.091][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:03:21.092][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-31 16:03:21.093][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 16:03:21.094][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:03:21.095][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:03:21.095][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:03:21.096][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-31 16:03:21.097][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-31 16:03:21.098][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:03:21.099][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:03:21.100][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:03:21.100][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-31 16:03:21.101][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 16:03:21.102][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:03:21.103][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:03:21.104][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:03:21.105][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-31 16:03:21.105][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 16:03:21.106][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:03:21.107][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:03:21.108][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:03:21.109][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-31 16:03:21.110][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 16:03:21.110][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:03:21.111][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:03:21.112][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2026-01-31 16:03:21.113][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2026-01-31 16:03:21.115][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2026-01-31 16:03:21.116][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2026-01-31 16:03:21.117][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2026-01-31 16:03:21.119][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2026-01-31 16:03:21.120][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2026-01-31 16:03:21.121][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2026-01-31 16:03:21.123][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2026-01-31 16:03:21.124][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2026-01-31 16:03:21.125][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2026-01-31 16:03:21.127][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2026-01-31 16:03:21.128][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2026-01-31 16:03:21.129][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2026-01-31 16:03:21.130][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2026-01-31 16:03:21.132][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2026-01-31 16:03:21.133][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2026-01-31 16:03:21.134][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2026-01-31 16:03:21.136][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2026-01-31 16:03:21.137][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2026-01-31 16:03:21.138][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2026-01-31 16:03:21.139][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2026-01-31 16:03:21.141][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2026-01-31 16:03:21.142][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2026-01-31 16:03:21.143][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2026-01-31 16:03:21.145][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2026-01-31 16:03:21.146][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2026-01-31 16:03:21.147][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2026-01-31 16:03:21.149][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2026-01-31 16:03:21.150][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2026-01-31 16:03:21.151][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2026-01-31 16:03:21.152][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2026-01-31 16:03:21.154][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2026-01-31 16:03:21.155][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2026-01-31 16:03:21.156][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2026-01-31 16:03:21.158][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2026-01-31 16:03:21.159][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2026-01-31 16:03:21.160][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2026-01-31 16:03:21.162][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2026-01-31 16:03:21.163][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2026-01-31 16:03:21.164][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2026-01-31 16:03:21.165][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2026-01-31 16:03:21.167][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2026-01-31 16:03:21.168][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2026-01-31 16:03:21.169][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2026-01-31 16:03:21.171][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2026-01-31 16:03:21.172][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2026-01-31 16:03:21.173][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2026-01-31 16:03:21.175][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2026-01-31 16:03:21.176][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2026-01-31 16:03:21.177][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2026-01-31 16:03:21.178][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2026-01-31 16:03:21.180][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2026-01-31 16:03:21.181][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2026-01-31 16:03:21.182][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2026-01-31 16:03:21.184][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2026-01-31 16:03:21.185][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2026-01-31 16:03:21.186][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2026-01-31 16:03:21.187][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2026-01-31 16:03:21.189][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2026-01-31 16:03:21.190][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2026-01-31 16:03:21.191][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2026-01-31 16:03:21.193][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2026-01-31 16:03:21.194][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2026-01-31 16:03:21.195][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2026-01-31 16:03:21.196][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2026-01-31 16:03:21.198][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2026-01-31 16:03:21.199][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2026-01-31 16:03:21.200][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2026-01-31 16:03:21.202][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2026-01-31 16:03:21.203][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2026-01-31 16:03:21.204][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2026-01-31 16:03:21.205][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2026-01-31 16:03:21.207][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2026-01-31 16:03:21.208][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2026-01-31 16:03:21.209][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2026-01-31 16:03:21.211][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2026-01-31 16:03:21.212][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2026-01-31 16:03:21.218][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2026-01-31 16:03:21.219][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2026-01-31 16:03:21.220][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2026-01-31 16:03:21.221][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2026-01-31 16:03:21.223][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2026-01-31 16:03:21.224][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2026-01-31 16:03:21.226][initialize] This is biodb version 1.18.0.
biodb.DEBUG[2026-01-31 16:03:21.227][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2026-01-31 16:03:21.227][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2026-01-31 16:03:21.228][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 16:03:21.229][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:03:21.230][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:03:21.234][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:03:21.235][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-01-31 16:03:21.236][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-01-31 16:03:21.237][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-31 16:03:21.238][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 16:03:21.239][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:03:21.239][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:03:21.240][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:03:21.241][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-01-31 16:03:21.242][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-01-31 16:03:21.243][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-31 16:03:21.244][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 16:03:21.244][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:03:21.245][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:03:21.246][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:03:21.247][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-01-31 16:03:21.248][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-01-31 16:03:21.249][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-31 16:03:21.249][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 16:03:21.250][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:03:21.251][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:03:21.252][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:03:21.253][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-01-31 16:03:21.254][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-01-31 16:03:21.255][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-31 16:03:21.255][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 16:03:21.256][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:03:21.257][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:03:21.258][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:03:21.259][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-01-31 16:03:21.260][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-01-31 16:03:21.260][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-31 16:03:21.261][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 16:03:21.262][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:03:21.263][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:03:21.264][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:03:21.264][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-01-31 16:03:21.265][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-01-31 16:03:21.266][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-31 16:03:21.267][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 16:03:21.268][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:03:21.269][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:03:21.269][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:03:21.270][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-01-31 16:03:21.271][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-01-31 16:03:21.272][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-31 16:03:21.273][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 16:03:21.274][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:03:21.274][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:03:21.275][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:03:21.276][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-01-31 16:03:21.277][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-01-31 16:03:21.278][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-31 16:03:21.279][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 16:03:21.279][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:03:21.280][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:03:21.281][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:03:21.282][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-01-31 16:03:21.283][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-01-31 16:03:21.284][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-31 16:03:21.284][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-31 16:03:21.285][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:03:21.286][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:03:21.287][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:03:21.288][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-01-31 16:03:21.289][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-01-31 16:03:21.289][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-31 16:03:21.290][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 16:03:21.291][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:03:21.292][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:03:21.293][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:03:21.294][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-01-31 16:03:21.294][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-01-31 16:03:21.295][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-31 16:03:21.296][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 16:03:21.297][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:03:21.298][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:03:21.299][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:03:21.299][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-01-31 16:03:21.300][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-01-31 16:03:21.301][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-31 16:03:21.302][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 16:03:21.303][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:03:21.304][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:03:21.305][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:03:21.305][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-01-31 16:03:21.306][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-01-31 16:03:21.307][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-31 16:03:21.308][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 16:03:21.309][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:03:21.309][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:03:21.310][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:03:21.311][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-01-31 16:03:21.312][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-01-31 16:03:21.313][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-31 16:03:21.314][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 16:03:21.315][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:03:21.315][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:03:21.316][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:03:21.317][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-01-31 16:03:21.318][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-01-31 16:03:21.319][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-31 16:03:21.320][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-31 16:03:21.320][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:03:21.321][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:03:21.322][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:03:21.323][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-01-31 16:03:21.324][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-01-31 16:03:21.325][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-31 16:03:21.325][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-31 16:03:21.326][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:03:21.327][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:03:21.329][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNci.Rcheck/biodbNci/definitions.yml".
biodb.DEBUG[2026-01-31 16:03:21.330][self$getDbsInfo()$define] Define connector nci.cactus.
biodb.DEBUG[2026-01-31 16:03:21.332][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2026-01-31 16:03:21.333][self$setPropertyValue] Setting property "description" to "National Cancer Institute (USA) CACTUS Database.".
biodb.DEBUG[2026-01-31 16:03:21.334][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-01-31 16:03:21.335][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-01-31 16:03:21.335][self$setPropertyValue] Setting property "downloadable" to "TRUE".
biodb.DEBUG[2026-01-31 16:03:21.336][self$setPropertyValue] Setting property "dwnld.ext" to "gz".
biodb.DEBUG[2026-01-31 16:03:21.337][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2026-01-31 16:03:21.338][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-01-31 16:03:21.339][self$setPropertyValue] Setting property "entry.content.type" to "sdf".
biodb.DEBUG[2026-01-31 16:03:21.340][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-01-31 16:03:21.341][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2026-01-31 16:03:21.342][self$setPropertyValue] Setting property "name" to "NCI CACTUS".
biodb.DEBUG[2026-01-31 16:03:21.343][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-01-31 16:03:21.344][self$setPropertyValue] Setting property "parsing.expr" to "NSC".
biodb.DEBUG[2026-01-31 16:03:21.344][self$setPropertyValue] Setting property "parsing.expr" to "DTP names".
biodb.DEBUG[2026-01-31 16:03:21.344][self$setPropertyValue] Setting property "parsing.expr" to "Standard InChI".
biodb.DEBUG[2026-01-31 16:03:21.344][self$setPropertyValue] Setting property "parsing.expr" to "c("Standard InChIKey", "^InChIKey=(.*)$")".
biodb.DEBUG[2026-01-31 16:03:21.344][self$setPropertyValue] Setting property "parsing.expr" to "Formula".
biodb.DEBUG[2026-01-31 16:03:21.344][self$setPropertyValue] Setting property "parsing.expr" to "Molecular Weight".
biodb.DEBUG[2026-01-31 16:03:21.344][self$setPropertyValue] Setting property "parsing.expr" to "CAS".
biodb.DEBUG[2026-01-31 16:03:21.345][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2026-01-31 16:03:21.346][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2026-01-31 16:03:21.347][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2026-01-31 16:03:21.348][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-01-31 16:03:21.349][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-01-31 16:03:21.350][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-01-31 16:03:21.350][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-01-31 16:03:21.351][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-01-31 16:03:21.352][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-01-31 16:03:21.353][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/".
biodb.DEBUG[2026-01-31 16:03:21.353][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/".
biodb.DEBUG[2026-01-31 16:03:21.353][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/download/nci/".
biodb.DEBUG[2026-01-31 16:03:21.353][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/download/nci/NCI-Open_2012-05-01.sdf.gz".
biodb.DEBUG[2026-01-31 16:03:21.354][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-01-31 16:03:21.355][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-01-31 16:03:21.356][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2026-01-31 16:03:21.357][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-01-31 16:03:21.358][self$getEntryFields()$define] Define field nci.cactus.id.
biodb.DEBUG[2026-01-31 16:03:21.361][super$initialize] Initialize connector nci.cactus.
biodb.DEBUG[2026-01-31 16:03:21.368][biodb$getFactory()$createConn] Creating new connector nci.cactus for database class nci.cactus .
biodb.INFO [2026-01-31 16:03:21.369][biodb$terminate] Closing BiodbMain instance...
biodb.INFO [2026-01-31 16:03:21.370][self$deleteConn] Connector "nci.cactus" deleted.
biodb.DEBUG[2026-01-31 16:03:21.370][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2026-01-31 16:03:21.371][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-01-31 16:03:21.372][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-01-31 16:03:21.373][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-31 16:03:21.374][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 16:03:21.374][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:03:21.375][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".
[ 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:
###
###   /home/biocbuild/bbs-3.22-bioc/R/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 ‘/home/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNci.Rcheck’
* using R version 4.5.2 (2025-10-31)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* 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: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
* checking installed package size ... INFO
  installed size is  6.1Mb
  sub-directories of 1Mb or more:
    libs   5.8Mb
* 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 loading without being on the library search path ... 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
  ‘/home/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: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/testthat/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/testthat/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c extractEntries.cpp -o extractEntries.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/testthat/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c test-100-example.cpp -o test-100-example.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/testthat/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c test-runner.cpp -o test-runner.o
g++ -std=gnu++17 -shared -L/home/biocbuild/bbs-3.22-bioc/R/lib -L/usr/local/lib -o biodbNci.so RcppExports.o extractEntries.o test-100-example.o test-runner.o -L/home/biocbuild/bbs-3.22-bioc/R/lib -lR
installing to /home/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)