Back to Long Tests report for BioC 3.22

This page was generated on 2026-02-21 23:55 -0500 (Sat, 21 Feb 2026).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 4890
merida1macOS 12.7.6 Montereyx86_644.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 4680
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: 2026-02-21 09:55 -0500 (Sat, 21 Feb 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: 2026-02-21 16:02:19 -0500 (Sat, 21 Feb 2026)
EndedAt: 2026-02-21 16:03:22 -0500 (Sat, 21 Feb 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"
Copyright (C) 2025 The R Foundation for Statistical Computing
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 [2026-02-21 16:03:19.303][biodb::testContext]
biodb.INFO [2026-02-21 16:03:19.305][biodb::testContext] ********************************************************************************
biodb.INFO [2026-02-21 16:03:19.306][biodb::testContext] Test context - Generic long tests
biodb.INFO [2026-02-21 16:03:19.307][biodb::testContext] ********************************************************************************
biodb.INFO [2026-02-21 16:03:19.308][biodb::testContext]
biodb.INFO [2026-02-21 16:03:19.314][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.18.0.
biodb.DEBUG[2026-02-21 16:03:19.315][self$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.22-bioc/R/site-library/biodb/definitions.yml".
biodb.DEBUG[2026-02-21 16:03:19.322][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2026-02-21 16:03:19.323][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2026-02-21 16:03:19.324][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2026-02-21 16:03:19.324][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:03:19.325][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:03:19.326][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-21 16:03:19.327][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2026-02-21 16:03:19.343][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2026-02-21 16:03:19.344][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:03:19.345][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:03:19.346][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-21 16:03:19.347][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2026-02-21 16:03:19.348][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2026-02-21 16:03:19.348][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:03:19.349][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:03:19.350][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-21 16:03:19.351][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2026-02-21 16:03:19.352][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2026-02-21 16:03:19.353][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2026-02-21 16:03:19.354][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:03:19.354][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:03:19.355][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-21 16:03:19.356][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2026-02-21 16:03:19.357][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2026-02-21 16:03:19.358][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2026-02-21 16:03:19.359][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:03:19.360][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:03:19.361][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-21 16:03:19.361][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2026-02-21 16:03:19.362][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2026-02-21 16:03:19.363][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:03:19.364][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:03:19.365][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-21 16:03:19.366][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2026-02-21 16:03:19.367][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2026-02-21 16:03:19.368][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2026-02-21 16:03:19.369][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:03:19.369][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:03:19.370][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-21 16:03:19.371][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2026-02-21 16:03:19.372][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2026-02-21 16:03:19.373][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:03:19.374][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:03:19.375][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-21 16:03:19.376][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2026-02-21 16:03:19.377][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2026-02-21 16:03:19.378][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2026-02-21 16:03:19.379][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:03:19.379][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:03:19.380][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-21 16:03:19.381][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2026-02-21 16:03:19.382][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2026-02-21 16:03:19.383][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2026-02-21 16:03:19.384][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2026-02-21 16:03:19.385][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2026-02-21 16:03:19.386][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2026-02-21 16:03:19.387][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:03:19.387][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:03:19.388][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-21 16:03:19.389][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2026-02-21 16:03:19.390][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2026-02-21 16:03:19.391][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:03:19.392][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:03:19.393][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-21 16:03:19.394][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2026-02-21 16:03:19.394][self$set] Set key entries.sep to "|".
biodb.DEBUG[2026-02-21 16:03:19.395][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:03:19.396][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:03:19.397][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-21 16:03:19.398][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2026-02-21 16:03:19.399][self$set] Set key offline to FALSE.
biodb.DEBUG[2026-02-21 16:03:19.400][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:03:19.400][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:03:19.401][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-21 16:03:19.402][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2026-02-21 16:03:19.403][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2026-02-21 16:03:19.404][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2026-02-21 16:03:19.405][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:03:19.406][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:03:19.407][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-21 16:03:19.407][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2026-02-21 16:03:19.408][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2026-02-21 16:03:19.412][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2026-02-21 16:03:19.413][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:03:19.414][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:03:19.415][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-21 16:03:19.416][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2026-02-21 16:03:19.417][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2026-02-21 16:03:19.418][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2026-02-21 16:03:19.418][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:03:19.419][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:03:19.420][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-21 16:03:19.423][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2026-02-21 16:03:19.454][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2026-02-21 16:03:19.474][self$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[2026-02-21 16:03:19.475][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-02-21 16:03:19.476][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-02-21 16:03:19.477][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-02-21 16:03:19.478][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-02-21 16:03:19.479][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2026-02-21 16:03:19.480][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-02-21 16:03:19.481][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2026-02-21 16:03:19.482][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-02-21 16:03:19.483][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2026-02-21 16:03:19.483][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2026-02-21 16:03:19.484][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-02-21 16:03:19.485][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2026-02-21 16:03:19.486][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2026-02-21 16:03:19.487][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2026-02-21 16:03:19.487][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2026-02-21 16:03:19.487][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2026-02-21 16:03:19.487][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2026-02-21 16:03:19.487][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2026-02-21 16:03:19.488][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2026-02-21 16:03:19.489][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-02-21 16:03:19.490][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-02-21 16:03:19.491][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-02-21 16:03:19.492][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-02-21 16:03:19.492][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-02-21 16:03:19.493][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-02-21 16:03:19.494][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2026-02-21 16:03:19.495][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-02-21 16:03:19.496][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-02-21 16:03:19.497][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2026-02-21 16:03:19.498][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-02-21 16:03:19.499][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2026-02-21 16:03:19.500][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2026-02-21 16:03:19.501][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2026-02-21 16:03:19.502][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-02-21 16:03:19.503][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-02-21 16:03:19.504][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-02-21 16:03:19.505][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-02-21 16:03:19.506][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2026-02-21 16:03:19.507][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-02-21 16:03:19.508][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2026-02-21 16:03:19.509][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-02-21 16:03:19.510][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2026-02-21 16:03:19.511][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2026-02-21 16:03:19.512][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-02-21 16:03:19.513][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2026-02-21 16:03:19.513][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2026-02-21 16:03:19.514][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2026-02-21 16:03:19.514][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2026-02-21 16:03:19.514][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2026-02-21 16:03:19.514][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2026-02-21 16:03:19.514][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2026-02-21 16:03:19.515][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2026-02-21 16:03:19.516][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-02-21 16:03:19.517][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-02-21 16:03:19.518][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-02-21 16:03:19.519][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-02-21 16:03:19.520][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-02-21 16:03:19.521][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-02-21 16:03:19.522][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2026-02-21 16:03:19.522][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-02-21 16:03:19.523][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-02-21 16:03:19.524][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2026-02-21 16:03:19.525][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-02-21 16:03:19.526][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2026-02-21 16:03:19.528][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2026-02-21 16:03:19.529][self$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[2026-02-21 16:03:19.530][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-02-21 16:03:19.531][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-02-21 16:03:19.532][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-02-21 16:03:19.532][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-02-21 16:03:19.533][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2026-02-21 16:03:19.534][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-02-21 16:03:19.535][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2026-02-21 16:03:19.536][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-02-21 16:03:19.537][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2026-02-21 16:03:19.538][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2026-02-21 16:03:19.539][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-02-21 16:03:19.540][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2026-02-21 16:03:19.541][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2026-02-21 16:03:19.542][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2026-02-21 16:03:19.543][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2026-02-21 16:03:19.544][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-02-21 16:03:19.544][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-02-21 16:03:19.545][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-02-21 16:03:19.546][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-02-21 16:03:19.547][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-02-21 16:03:19.548][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-02-21 16:03:19.549][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2026-02-21 16:03:19.550][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-02-21 16:03:19.550][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-02-21 16:03:19.551][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2026-02-21 16:03:19.552][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-02-21 16:03:19.553][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2026-02-21 16:03:19.555][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2026-02-21 16:03:19.556][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2026-02-21 16:03:19.557][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-02-21 16:03:19.558][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-02-21 16:03:19.559][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-02-21 16:03:19.560][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-02-21 16:03:19.561][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2026-02-21 16:03:19.561][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-02-21 16:03:19.562][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2026-02-21 16:03:19.563][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-02-21 16:03:19.564][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2026-02-21 16:03:19.565][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2026-02-21 16:03:19.566][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-02-21 16:03:19.567][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2026-02-21 16:03:19.568][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2026-02-21 16:03:19.569][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2026-02-21 16:03:19.570][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2026-02-21 16:03:19.571][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-02-21 16:03:19.572][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-02-21 16:03:19.573][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-02-21 16:03:19.573][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-02-21 16:03:19.574][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-02-21 16:03:19.575][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-02-21 16:03:19.576][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2026-02-21 16:03:19.577][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-02-21 16:03:19.578][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-02-21 16:03:19.579][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2026-02-21 16:03:19.580][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-02-21 16:03:19.583][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2026-02-21 16:03:19.584][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:03:19.585][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-21 16:03:19.586][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:03:19.587][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-21 16:03:19.587][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-21 16:03:19.588][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:03:19.589][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-21 16:03:19.590][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:03:19.591][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-21 16:03:19.592][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-21 16:03:19.593][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:03:19.593][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-21 16:03:19.594][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:03:19.595][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-21 16:03:19.596][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-21 16:03:19.597][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:03:19.598][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-21 16:03:19.598][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:03:19.599][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-21 16:03:19.600][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-21 16:03:19.601][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:03:19.602][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-21 16:03:19.603][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:03:19.603][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-21 16:03:19.604][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-21 16:03:19.605][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:03:19.606][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-21 16:03:19.607][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:03:19.608][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-21 16:03:19.608][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-21 16:03:19.609][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:03:19.610][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-21 16:03:19.611][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:03:19.612][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-21 16:03:19.613][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-21 16:03:19.613][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:03:19.614][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-21 16:03:19.615][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:03:19.616][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-21 16:03:19.617][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-21 16:03:19.618][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:03:19.618][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-21 16:03:19.619][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:03:19.620][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-21 16:03:19.621][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-21 16:03:19.622][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:03:19.623][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-21 16:03:19.624][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:03:19.632][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-21 16:03:19.634][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-21 16:03:19.635][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:03:19.636][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-21 16:03:19.637][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:03:19.638][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-21 16:03:19.639][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-21 16:03:19.640][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:03:19.641][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-21 16:03:19.642][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:03:19.642][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-21 16:03:19.643][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-21 16:03:19.644][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:03:19.645][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-21 16:03:19.646][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:03:19.647][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-21 16:03:19.648][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-21 16:03:19.649][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:03:19.650][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-21 16:03:19.651][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:03:19.652][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-21 16:03:19.653][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-21 16:03:19.654][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:03:19.655][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-21 16:03:19.656][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:03:19.657][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-21 16:03:19.658][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-21 16:03:19.658][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:03:19.659][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-21 16:03:19.660][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:03:19.661][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-21 16:03:19.662][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-21 16:03:19.663][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:03:19.664][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-21 16:03:19.665][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2026-02-21 16:03:19.671][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2026-02-21 16:03:19.672][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2026-02-21 16:03:19.674][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2026-02-21 16:03:19.675][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2026-02-21 16:03:19.677][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2026-02-21 16:03:19.678][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2026-02-21 16:03:19.680][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2026-02-21 16:03:19.681][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2026-02-21 16:03:19.683][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2026-02-21 16:03:19.701][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2026-02-21 16:03:19.702][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2026-02-21 16:03:19.704][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2026-02-21 16:03:19.705][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2026-02-21 16:03:19.707][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2026-02-21 16:03:19.708][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2026-02-21 16:03:19.710][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2026-02-21 16:03:19.711][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2026-02-21 16:03:19.712][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2026-02-21 16:03:19.714][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2026-02-21 16:03:19.715][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2026-02-21 16:03:19.717][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2026-02-21 16:03:19.718][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2026-02-21 16:03:19.720][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2026-02-21 16:03:19.721][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2026-02-21 16:03:19.723][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2026-02-21 16:03:19.724][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2026-02-21 16:03:19.726][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2026-02-21 16:03:19.727][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2026-02-21 16:03:19.728][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2026-02-21 16:03:19.730][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2026-02-21 16:03:19.731][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2026-02-21 16:03:19.733][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2026-02-21 16:03:19.734][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2026-02-21 16:03:19.736][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2026-02-21 16:03:19.737][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2026-02-21 16:03:19.738][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2026-02-21 16:03:19.740][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2026-02-21 16:03:19.741][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2026-02-21 16:03:19.743][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2026-02-21 16:03:19.744][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2026-02-21 16:03:19.745][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2026-02-21 16:03:19.747][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2026-02-21 16:03:19.748][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2026-02-21 16:03:19.750][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2026-02-21 16:03:19.751][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2026-02-21 16:03:19.753][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2026-02-21 16:03:19.754][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2026-02-21 16:03:19.755][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2026-02-21 16:03:19.757][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2026-02-21 16:03:19.758][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2026-02-21 16:03:19.760][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2026-02-21 16:03:19.761][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2026-02-21 16:03:19.762][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2026-02-21 16:03:19.764][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2026-02-21 16:03:19.765][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2026-02-21 16:03:19.767][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2026-02-21 16:03:19.768][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2026-02-21 16:03:19.770][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2026-02-21 16:03:19.771][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2026-02-21 16:03:19.772][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2026-02-21 16:03:19.774][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2026-02-21 16:03:19.775][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2026-02-21 16:03:19.777][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2026-02-21 16:03:19.778][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2026-02-21 16:03:19.779][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2026-02-21 16:03:19.781][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2026-02-21 16:03:19.782][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2026-02-21 16:03:19.783][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2026-02-21 16:03:19.785][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2026-02-21 16:03:19.786][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2026-02-21 16:03:19.788][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2026-02-21 16:03:19.789][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2026-02-21 16:03:19.790][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2026-02-21 16:03:19.792][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2026-02-21 16:03:19.793][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2026-02-21 16:03:19.795][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2026-02-21 16:03:19.796][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2026-02-21 16:03:19.798][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2026-02-21 16:03:19.799][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2026-02-21 16:03:19.800][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2026-02-21 16:03:19.802][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2026-02-21 16:03:19.803][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2026-02-21 16:03:19.810][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2026-02-21 16:03:19.811][initialize] This is biodb version 1.18.0.
biodb.DEBUG[2026-02-21 16:03:19.815][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2026-02-21 16:03:19.816][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2026-02-21 16:03:19.816][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-21 16:03:19.817][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:03:19.818][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[2026-02-21 16:03:19.823][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:03:19.824][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-21 16:03:19.825][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-21 16:03:19.826][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-21 16:03:19.827][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-21 16:03:19.828][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:03:19.829][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-21 16:03:19.830][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:03:19.830][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-21 16:03:19.831][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-21 16:03:19.832][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-21 16:03:19.833][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-21 16:03:19.834][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:03:19.835][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-21 16:03:19.836][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:03:19.837][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-21 16:03:19.838][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-21 16:03:19.839][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-21 16:03:19.839][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-21 16:03:19.840][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:03:19.841][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-21 16:03:19.842][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:03:19.843][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-21 16:03:19.844][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-21 16:03:19.845][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-21 16:03:19.846][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-21 16:03:19.847][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:03:19.848][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-21 16:03:19.849][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:03:19.849][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-21 16:03:19.850][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-21 16:03:19.851][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-21 16:03:19.852][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-21 16:03:19.853][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:03:19.854][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[2026-02-21 16:03:19.855][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:03:19.856][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-21 16:03:19.857][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-21 16:03:19.858][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-21 16:03:19.859][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-21 16:03:19.859][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:03:19.860][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-21 16:03:19.861][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:03:19.862][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-21 16:03:19.863][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-21 16:03:19.864][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-21 16:03:19.864][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-21 16:03:19.865][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:03:19.866][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-21 16:03:19.867][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:03:19.868][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-21 16:03:19.869][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-21 16:03:19.869][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-21 16:03:19.870][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-21 16:03:19.871][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:03:19.872][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-21 16:03:19.873][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:03:19.874][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-21 16:03:19.874][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-21 16:03:19.875][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-21 16:03:19.876][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-21 16:03:19.877][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:03:19.878][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[2026-02-21 16:03:19.879][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:03:19.879][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-21 16:03:19.880][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-21 16:03:19.881][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-21 16:03:19.882][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-21 16:03:19.883][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:03:19.884][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[2026-02-21 16:03:19.884][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:03:19.885][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-21 16:03:19.886][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-21 16:03:19.887][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-21 16:03:19.888][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-21 16:03:19.889][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:03:19.889][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-21 16:03:19.890][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:03:19.891][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-21 16:03:19.892][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-21 16:03:19.893][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-21 16:03:19.894][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-21 16:03:19.894][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:03:19.895][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-21 16:03:19.896][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:03:19.897][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-21 16:03:19.898][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-21 16:03:19.899][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-21 16:03:19.899][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-21 16:03:19.900][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:03:19.901][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-21 16:03:19.902][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:03:19.903][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-21 16:03:19.908][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-21 16:03:19.909][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-21 16:03:19.910][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-21 16:03:19.911][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:03:19.911][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-21 16:03:19.912][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:03:19.913][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-21 16:03:19.914][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-21 16:03:19.915][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-21 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[2026-02-21 16:03:19.916][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 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.DEBUG[2026-02-21 16:03:19.918][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:03:19.919][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-21 16:03:19.920][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-21 16:03:19.920][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-21 16:03:19.921][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-21 16:03:19.922][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:03:19.923][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-21 16:03:19.925][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNci.Rcheck/biodbNci/definitions.yml".
biodb.DEBUG[2026-02-21 16:03:19.934][self$getDbsInfo()$define] Define connector nci.cactus.
biodb.DEBUG[2026-02-21 16:03:19.935][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2026-02-21 16:03:19.936][self$setPropertyValue] Setting property "description" to "National Cancer Institute (USA) CACTUS Database.".
biodb.DEBUG[2026-02-21 16:03:19.937][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-02-21 16:03:19.938][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-02-21 16:03:19.939][self$setPropertyValue] Setting property "downloadable" to "TRUE".
biodb.DEBUG[2026-02-21 16:03:19.940][self$setPropertyValue] Setting property "dwnld.ext" to "gz".
biodb.DEBUG[2026-02-21 16:03:19.941][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2026-02-21 16:03:19.942][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-02-21 16:03:19.943][self$setPropertyValue] Setting property "entry.content.type" to "sdf".
biodb.DEBUG[2026-02-21 16:03:19.944][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-02-21 16:03:19.945][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2026-02-21 16:03:19.946][self$setPropertyValue] Setting property "name" to "NCI CACTUS".
biodb.DEBUG[2026-02-21 16:03:19.947][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-02-21 16:03:19.948][self$setPropertyValue] Setting property "parsing.expr" to "NSC".
biodb.DEBUG[2026-02-21 16:03:19.948][self$setPropertyValue] Setting property "parsing.expr" to "DTP names".
biodb.DEBUG[2026-02-21 16:03:19.948][self$setPropertyValue] Setting property "parsing.expr" to "Standard InChI".
biodb.DEBUG[2026-02-21 16:03:19.948][self$setPropertyValue] Setting property "parsing.expr" to "c("Standard InChIKey", "^InChIKey=(.*)$")".
biodb.DEBUG[2026-02-21 16:03:19.948][self$setPropertyValue] Setting property "parsing.expr" to "Formula".
biodb.DEBUG[2026-02-21 16:03:19.948][self$setPropertyValue] Setting property "parsing.expr" to "Molecular Weight".
biodb.DEBUG[2026-02-21 16:03:19.948][self$setPropertyValue] Setting property "parsing.expr" to "CAS".
biodb.DEBUG[2026-02-21 16:03:19.949][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2026-02-21 16:03:19.950][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2026-02-21 16:03:19.951][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2026-02-21 16:03:19.952][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-02-21 16:03:19.952][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-02-21 16:03:19.953][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-02-21 16:03:19.954][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-02-21 16:03:19.955][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-02-21 16:03:19.956][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-02-21 16:03:19.957][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/".
biodb.DEBUG[2026-02-21 16:03:19.957][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/".
biodb.DEBUG[2026-02-21 16:03:19.957][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/download/nci/".
biodb.DEBUG[2026-02-21 16:03:19.957][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/download/nci/NCI-Open_2012-05-01.sdf.gz".
biodb.DEBUG[2026-02-21 16:03:19.958][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-02-21 16:03:19.959][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-02-21 16:03:19.960][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2026-02-21 16:03:19.961][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-02-21 16:03:19.966][self$getEntryFields()$define] Define field nci.cactus.id.
biodb.DEBUG[2026-02-21 16:03:19.987][super$initialize] Initialize connector nci.cactus.
biodb.DEBUG[2026-02-21 16:03:20.002][biodb$getFactory()$createConn] Creating new connector nci.cactus for database class nci.cactus .
biodb.INFO [2026-02-21 16:03:20.010][biodb::testThat]
biodb.INFO [2026-02-21 16:03:20.011][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2026-02-21 16:03:20.012][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-02-21 16:03:20.013][biodb::testThat]
biodb.TRACE[2026-02-21 16:03:20.016][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNci.Rcheck/biodbNci/testref/entry-nci.cactus-749674-content.sdf".
biodb.DEBUG[2026-02-21 16:03:20.018][biodb$getFactory()$createEntryFromCo ...] Creating NCI CACTUS entries from 1 content(s).
biodb.DEBUG[2026-02-21 16:03:20.021][biodb$getFactory()$createEntryFromCo ...] Parsing 1 NCI CACTUS entries.
biodb.DEBUG[2026-02-21 16:03:20.029][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2026-02-21 16:03:20.030][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-21 16:03:20.031][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-21 16:03:20.043][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2026-02-21 16:03:20.044][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-21 16:03:20.045][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:03:20.046][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2026-02-21 16:03:20.063][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-21 16:03:20.064][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-21 16:03:20.065][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:03:20.066][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:03:20.067][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-21 16:03:20.079][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-21 16:03:20.080][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:03:20.081][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:03:20.083][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2026-02-21 16:03:20.085][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2026-02-21 16:03:20.085][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:03:20.086][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:03:20.111][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2026-02-21 16:03:20.112][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2026-02-21 16:03:20.113][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:03:20.114][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:03:20.115][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2026-02-21 16:03:20.116][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2026-02-21 16:03:20.117][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:03:20.128][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:03:20.129][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2026-02-21 16:03:20.130][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2026-02-21 16:03:20.130][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:03:20.131][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:03:20.133][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2026-02-21 16:03:20.134][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2026-02-21 16:03:20.135][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:03:20.136][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:03:20.137][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2026-02-21 16:03:20.138][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2026-02-21 16:03:20.139][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:03:20.140][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:03:20.141][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-02-21 16:03:20.142][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-02-21 16:03:20.143][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:03:20.144][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:03:20.145][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-02-21 16:03:20.146][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-02-21 16:03:20.147][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:03:20.148][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:03:20.149][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2026-02-21 16:03:20.150][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2026-02-21 16:03:20.151][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:03:20.152][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:03:20.153][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2026-02-21 16:03:20.154][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2026-02-21 16:03:20.155][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:03:20.156][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:03:20.157][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-21 16:03:20.158][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-21 16:03:20.159][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:03:20.160][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:03:20.161][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2026-02-21 16:03:20.162][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2026-02-21 16:03:20.162][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:03:20.163][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:03:20.164][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-21 16:03:20.165][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-21 16:03:20.166][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:03:20.167][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:03:20.168][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-21 16:03:20.169][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-21 16:03:20.170][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:03:20.171][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:03:20.172][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-21 16:03:20.173][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-21 16:03:20.174][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:03:20.175][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:03:20.207][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-21 16:03:20.208][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-21 16:03:20.209][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:03:20.210][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:03:20.211][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-21 16:03:20.212][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-21 16:03:20.212][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:03:20.213][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:03:20.214][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-21 16:03:20.215][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-21 16:03:20.216][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:03:20.217][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2026-02-21 16:03:20.218][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 749674.
biodb.TRACE[2026-02-21 16:03:20.220][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2026-02-21 16:03:20.221][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2026-02-21 16:03:20.222][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:03:20.223][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:03:20.224][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2026-02-21 16:03:20.225][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2026-02-21 16:03:20.226][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:03:20.227][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:03:20.228][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2026-02-21 16:03:20.229][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2026-02-21 16:03:20.230][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:03:20.231][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:03:20.232][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2026-02-21 16:03:20.233][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2026-02-21 16:03:20.233][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:03:20.234][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:03:20.236][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-21 16:03:20.237][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-21 16:03:20.238][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:03:20.239][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:03:20.251][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2026-02-21 16:03:20.252][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2026-02-21 16:03:20.253][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:03:20.254][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:03:20.258][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-21 16:03:20.259][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-21 16:03:20.260][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:03:20.261][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:03:20.262][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-21 16:03:20.263][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-21 16:03:20.264][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:03:20.265][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:03:20.266][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-21 16:03:20.267][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-21 16:03:20.268][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:03:20.269][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:03:20.271][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-21 16:03:20.272][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-21 16:03:20.273][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:03:20.274][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:03:20.275][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-21 16:03:20.276][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-21 16:03:20.277][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:03:20.278][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:03:20.279][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-21 16:03:20.280][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-21 16:03:20.284][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:03:20.285][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:03:20.286][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2026-02-21 16:03:20.287][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2026-02-21 16:03:20.288][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:03:20.289][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:03:20.290][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2026-02-21 16:03:20.291][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2026-02-21 16:03:20.292][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:03:20.293][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:03:20.294][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2026-02-21 16:03:20.294][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2026-02-21 16:03:20.295][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:03:20.296][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:03:20.303][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-21 16:03:20.304][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-21 16:03:20.305][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:03:20.306][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:03:20.307][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-21 16:03:20.308][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-21 16:03:20.309][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:03:20.309][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:03:20.310][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-21 16:03:20.311][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-21 16:03:20.312][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:03:20.313][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:03:20.314][ef$get] Asked field names are: accession.
biodb.TRACE[2026-02-21 16:03:20.315][ef$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-21 16:03:20.316][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:03:20.317][ef$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:03:20.318][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-21 16:03:20.319][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-21 16:03:20.320][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:03:20.321][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:03:20.329][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2026-02-21 16:03:20.330][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2026-02-21 16:03:20.331][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:03:20.332][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:03:20.332][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2026-02-21 16:03:20.333][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2026-02-21 16:03:20.334][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:03:20.335][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:03:20.336][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2026-02-21 16:03:20.337][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2026-02-21 16:03:20.338][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:03:20.339][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:03:20.340][ef$get] Asked field names are: formula.
biodb.TRACE[2026-02-21 16:03:20.341][ef$get] Realnames of fields are: formula.
biodb.TRACE[2026-02-21 16:03:20.342][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:03:20.343][ef$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:03:20.344][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2026-02-21 16:03:20.345][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2026-02-21 16:03:20.346][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:03:20.346][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:03:20.354][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2026-02-21 16:03:20.355][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2026-02-21 16:03:20.356][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:03:20.357][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:03:20.358][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2026-02-21 16:03:20.359][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2026-02-21 16:03:20.360][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:03:20.361][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:03:20.362][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2026-02-21 16:03:20.363][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2026-02-21 16:03:20.364][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:03:20.364][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:03:20.365][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2026-02-21 16:03:20.366][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2026-02-21 16:03:20.367][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:03:20.368][ef$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:03:20.369][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2026-02-21 16:03:20.370][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2026-02-21 16:03:20.371][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:03:20.372][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:03:20.380][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2026-02-21 16:03:20.381][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2026-02-21 16:03:20.381][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:03:20.382][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:03:20.383][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2026-02-21 16:03:20.384][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2026-02-21 16:03:20.385][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:03:20.386][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:03:20.387][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2026-02-21 16:03:20.388][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2026-02-21 16:03:20.389][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:03:20.390][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:03:20.391][ef$get] Asked field names are: inchi.
biodb.TRACE[2026-02-21 16:03:20.392][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2026-02-21 16:03:20.393][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:03:20.393][ef$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:03:20.394][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2026-02-21 16:03:20.395][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2026-02-21 16:03:20.396][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:03:20.397][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:03:20.405][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-02-21 16:03:20.406][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-02-21 16:03:20.407][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:03:20.408][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:03:20.409][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-02-21 16:03:20.410][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-02-21 16:03:20.410][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:03:20.411][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:03:20.412][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-02-21 16:03:20.413][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-02-21 16:03:20.414][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:03:20.415][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:03:20.416][ef$get] Asked field names are: inchikey.
biodb.TRACE[2026-02-21 16:03:20.417][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-02-21 16:03:20.418][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:03:20.419][ef$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:03:20.420][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-02-21 16:03:20.421][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-02-21 16:03:20.422][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:03:20.422][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:03:20.430][ef$get] Asked field names are: accession.
biodb.TRACE[2026-02-21 16:03:20.431][ef$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-21 16:03:20.432][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:03:20.433][ef$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:03:20.437][ef$get] Asked field names are: formula.
biodb.TRACE[2026-02-21 16:03:20.438][ef$get] Realnames of fields are: formula.
biodb.TRACE[2026-02-21 16:03:20.439][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:03:20.440][ef$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:03:20.448][ef$get] Asked field names are: inchi.
biodb.TRACE[2026-02-21 16:03:20.449][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2026-02-21 16:03:20.450][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:03:20.451][ef$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:03:20.454][ef$get] Asked field names are: inchikey.
biodb.TRACE[2026-02-21 16:03:20.455][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-02-21 16:03:20.456][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:03:20.457][ef$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:03:20.461][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2026-02-21 16:03:20.462][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2026-02-21 16:03:20.463][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:03:20.464][ef$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:03:20.479][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNci.Rcheck/biodbNci/testref/entry-nci.cactus-750690-content.sdf".
biodb.DEBUG[2026-02-21 16:03:20.513][biodb$getFactory()$createEntryFromCo ...] Creating NCI CACTUS entries from 1 content(s).
biodb.DEBUG[2026-02-21 16:03:20.514][biodb$getFactory()$createEntryFromCo ...] Parsing 1 NCI CACTUS entries.
biodb.DEBUG[2026-02-21 16:03:20.515][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2026-02-21 16:03:20.516][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-21 16:03:20.517][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-21 16:03:20.521][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2026-02-21 16:03:20.522][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-21 16:03:20.523][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:03:20.524][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2026-02-21 16:03:20.533][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-21 16:03:20.534][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-21 16:03:20.535][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:03:20.536][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:03:20.537][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-21 16:03:20.538][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-21 16:03:20.539][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:03:20.540][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:03:20.557][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2026-02-21 16:03:20.558][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2026-02-21 16:03:20.559][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:03:20.560][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:03:20.561][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2026-02-21 16:03:20.562][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2026-02-21 16:03:20.563][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:03:20.564][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:03:20.566][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2026-02-21 16:03:20.567][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2026-02-21 16:03:20.567][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:03:20.568][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:03:20.569][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2026-02-21 16:03:20.570][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2026-02-21 16:03:20.571][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:03:20.572][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:03:20.573][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2026-02-21 16:03:20.574][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2026-02-21 16:03:20.575][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:03:20.576][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:03:20.577][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2026-02-21 16:03:20.578][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2026-02-21 16:03:20.579][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:03:20.580][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:03:20.581][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-02-21 16:03:20.582][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-02-21 16:03:20.583][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:03:20.584][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:03:20.585][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-02-21 16:03:20.586][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-02-21 16:03:20.587][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:03:20.588][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:03:20.589][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-02-21 16:03:20.590][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-02-21 16:03:20.591][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:03:20.592][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:03:20.593][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-02-21 16:03:20.636][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-02-21 16:03:20.637][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:03:20.638][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:03:20.639][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-02-21 16:03:20.640][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-02-21 16:03:20.641][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:03:20.642][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:03:20.643][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-02-21 16:03:20.644][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-02-21 16:03:20.645][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:03:20.646][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:03:20.647][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-02-21 16:03:20.648][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-02-21 16:03:20.649][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:03:20.649][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:03:20.651][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2026-02-21 16:03:20.652][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2026-02-21 16:03:20.653][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:03:20.654][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:03:20.655][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2026-02-21 16:03:20.656][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2026-02-21 16:03:20.657][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:03:20.658][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:03:20.659][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-02-21 16:03:20.660][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-02-21 16:03:20.661][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:03:20.662][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:03:20.663][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-02-21 16:03:20.664][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-02-21 16:03:20.665][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:03:20.666][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:03:20.667][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2026-02-21 16:03:20.668][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2026-02-21 16:03:20.669][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:03:20.670][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:03:20.671][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2026-02-21 16:03:20.672][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2026-02-21 16:03:20.673][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:03:20.674][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:03:20.675][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-21 16:03:20.676][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-21 16:03:20.677][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:03:20.678][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:03:20.679][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2026-02-21 16:03:20.680][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2026-02-21 16:03:20.681][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:03:20.681][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:03:20.682][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-21 16:03:20.683][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-21 16:03:20.684][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:03:20.685][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:03:20.686][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-21 16:03:20.687][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-21 16:03:20.688][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:03:20.689][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:03:20.690][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-21 16:03:20.691][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-21 16:03:20.692][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:03:20.693][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:03:20.694][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-21 16:03:20.695][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-21 16:03:20.696][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:03:20.697][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:03:20.698][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-21 16:03:20.699][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-21 16:03:20.700][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:03:20.700][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:03:20.701][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-21 16:03:20.702][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-21 16:03:20.703][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:03:20.704][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2026-02-21 16:03:20.705][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 750690.
biodb.TRACE[2026-02-21 16:03:20.725][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2026-02-21 16:03:20.726][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2026-02-21 16:03:20.727][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:03:20.728][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:03:20.729][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2026-02-21 16:03:20.730][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2026-02-21 16:03:20.731][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:03:20.732][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:03:20.733][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2026-02-21 16:03:20.734][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2026-02-21 16:03:20.734][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:03:20.735][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:03:20.736][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2026-02-21 16:03:20.737][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2026-02-21 16:03:20.738][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:03:20.739][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:03:20.741][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-21 16:03:20.742][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-21 16:03:20.743][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:03:20.744][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:03:20.748][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2026-02-21 16:03:20.749][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2026-02-21 16:03:20.750][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:03:20.751][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:03:20.755][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-21 16:03:20.756][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-21 16:03:20.757][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:03:20.758][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:03:20.759][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-21 16:03:20.760][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-21 16:03:20.761][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:03:20.762][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:03:20.763][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-21 16:03:20.764][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-21 16:03:20.765][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:03:20.766][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:03:20.768][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-21 16:03:20.769][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-21 16:03:20.770][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:03:20.771][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:03:20.772][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-21 16:03:20.773][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-21 16:03:20.774][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:03:20.775][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:03:20.776][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-21 16:03:20.777][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-21 16:03:20.778][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:03:20.779][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:03:20.780][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2026-02-21 16:03:20.781][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2026-02-21 16:03:20.782][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:03:20.783][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:03:20.784][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2026-02-21 16:03:20.785][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2026-02-21 16:03:20.786][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:03:20.787][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:03:20.788][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2026-02-21 16:03:20.789][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2026-02-21 16:03:20.790][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:03:20.791][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:03:20.811][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-21 16:03:20.812][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-21 16:03:20.813][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:03:20.814][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:03:20.815][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-21 16:03:20.816][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-21 16:03:20.817][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:03:20.818][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:03:20.819][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-21 16:03:20.820][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-21 16:03:20.821][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:03:20.821][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:03:20.822][ef$get] Asked field names are: accession.
biodb.TRACE[2026-02-21 16:03:20.823][ef$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-21 16:03:20.824][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:03:20.825][ef$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:03:20.826][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-21 16:03:20.827][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-21 16:03:20.828][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:03:20.829][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:03:20.837][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2026-02-21 16:03:20.838][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2026-02-21 16:03:20.839][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:03:20.840][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:03:20.840][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2026-02-21 16:03:20.841][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2026-02-21 16:03:20.842][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:03:20.843][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:03:20.844][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2026-02-21 16:03:20.845][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2026-02-21 16:03:20.846][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:03:20.847][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:03:20.848][ef$get] Asked field names are: cas.id.
biodb.TRACE[2026-02-21 16:03:20.849][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2026-02-21 16:03:20.850][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:03:20.851][ef$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:03:20.852][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2026-02-21 16:03:20.853][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2026-02-21 16:03:20.854][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:03:20.854][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:03:20.862][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-02-21 16:03:20.863][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-02-21 16:03:20.864][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:03:20.865][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:03:20.866][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-02-21 16:03:20.867][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-02-21 16:03:20.868][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:03:20.869][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:03:20.870][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-02-21 16:03:20.871][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-02-21 16:03:20.872][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:03:20.873][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:03:20.874][ef$get] Asked field names are: name.
biodb.TRACE[2026-02-21 16:03:20.875][ef$get] Realnames of fields are: name.
biodb.TRACE[2026-02-21 16:03:20.876][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:03:20.876][ef$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:03:20.877][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-02-21 16:03:20.878][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-02-21 16:03:20.879][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:03:20.880][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:03:20.888][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2026-02-21 16:03:20.889][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2026-02-21 16:03:20.890][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:03:20.891][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:03:20.891][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2026-02-21 16:03:20.892][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2026-02-21 16:03:20.893][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:03:20.894][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:03:20.895][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2026-02-21 16:03:20.896][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2026-02-21 16:03:20.897][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:03:20.898][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:03:20.899][ef$get] Asked field names are: formula.
biodb.TRACE[2026-02-21 16:03:20.900][ef$get] Realnames of fields are: formula.
biodb.TRACE[2026-02-21 16:03:20.901][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:03:20.902][ef$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:03:20.903][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2026-02-21 16:03:20.904][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2026-02-21 16:03:20.905][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:03:20.905][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:03:20.913][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2026-02-21 16:03:20.914][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2026-02-21 16:03:20.915][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:03:20.916][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:03:20.917][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2026-02-21 16:03:20.918][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2026-02-21 16:03:20.919][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:03:20.919][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:03:20.920][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2026-02-21 16:03:20.921][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2026-02-21 16:03:20.922][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:03:20.923][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:03:20.924][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2026-02-21 16:03:20.925][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2026-02-21 16:03:20.926][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:03:20.927][ef$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:03:20.928][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2026-02-21 16:03:20.929][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2026-02-21 16:03:20.930][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:03:20.931][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:03:20.938][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2026-02-21 16:03:20.939][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2026-02-21 16:03:20.940][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:03:20.941][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:03:20.942][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2026-02-21 16:03:20.943][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2026-02-21 16:03:20.944][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:03:20.945][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:03:20.946][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2026-02-21 16:03:20.947][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2026-02-21 16:03:20.947][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:03:20.948][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:03:20.949][ef$get] Asked field names are: inchi.
biodb.TRACE[2026-02-21 16:03:20.950][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2026-02-21 16:03:20.951][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:03:20.952][ef$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:03:20.953][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2026-02-21 16:03:20.954][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2026-02-21 16:03:20.955][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:03:20.956][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:03:20.967][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-02-21 16:03:20.968][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-02-21 16:03:20.969][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:03:20.970][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:03:20.971][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-02-21 16:03:20.972][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-02-21 16:03:20.973][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:03:20.974][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:03:20.974][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-02-21 16:03:20.975][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-02-21 16:03:20.976][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:03:20.977][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:03:20.978][ef$get] Asked field names are: inchikey.
biodb.TRACE[2026-02-21 16:03:20.979][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-02-21 16:03:20.980][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:03:20.981][ef$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:03:20.982][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-02-21 16:03:20.983][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-02-21 16:03:20.984][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:03:20.985][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:03:20.992][ef$get] Asked field names are: accession.
biodb.TRACE[2026-02-21 16:03:20.993][ef$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-21 16:03:20.994][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:03:20.995][ef$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:03:20.999][ef$get] Asked field names are: cas.id.
biodb.TRACE[2026-02-21 16:03:21.000][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2026-02-21 16:03:21.001][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:03:21.002][ef$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:03:21.006][ef$get] Asked field names are: formula.
biodb.TRACE[2026-02-21 16:03:21.007][ef$get] Realnames of fields are: formula.
biodb.TRACE[2026-02-21 16:03:21.007][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:03:21.008][ef$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:03:21.012][ef$get] Asked field names are: inchi.
biodb.TRACE[2026-02-21 16:03:21.013][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2026-02-21 16:03:21.014][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:03:21.015][ef$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:03:21.019][ef$get] Asked field names are: inchikey.
biodb.TRACE[2026-02-21 16:03:21.020][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-02-21 16:03:21.021][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:03:21.022][ef$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:03:21.025][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2026-02-21 16:03:21.026][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2026-02-21 16:03:21.027][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:03:21.028][ef$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:03:21.032][ef$get] Asked field names are: name.
biodb.TRACE[2026-02-21 16:03:21.033][ef$get] Realnames of fields are: name.
biodb.TRACE[2026-02-21 16:03:21.034][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:03:21.035][ef$get] fields variable is a list.
biodb.INFO [2026-02-21 16:03:21.041][biodb::testThat]
biodb.INFO [2026-02-21 16:03:21.042][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2026-02-21 16:03:21.043][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-02-21 16:03:21.044][biodb::testThat]
biodb.DEBUG[2026-02-21 16:03:21.046][private$loadEntries] Creating entries from ids [2]: "749674, 750690".
biodb.DEBUG[2026-02-21 16:03:21.048][conn$getEntryContent] Get NCI CACTUS entry content(s) for 2 id(s)...
biodb.DEBUG[2026-02-21 16:03:21.051][self$isDownloaded] Database nci.cactus has already been downloaded.
biodb.DEBUG[2026-02-21 16:03:21.079][self$isDownloaded] Database nci.cactus has already been downloaded.
biodb.INFO [2026-02-21 16:03:21.080][self$download] Extract whole database of nci.cactus.
biodb.INFO [2026-02-21 16:03:21.081][private$doExtractDownload] Extracting content of downloaded biodbNci, a library for connecting to the National Cancer Institute (USA) CACTUS Database....
Saving _problems/test_long_100_generic-38.R
biodb.INFO [2026-02-21 16:03:21.209][biodb::testThat]
biodb.INFO [2026-02-21 16:03:21.210][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2026-02-21 16:03:21.211][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-02-21 16:03:21.212][biodb::testThat]
biodb.INFO [2026-02-21 16:03:21.218][biodb::testThat]
biodb.INFO [2026-02-21 16:03:21.219][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2026-02-21 16:03:21.219][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-02-21 16:03:21.220][biodb::testThat]
biodb.WARN [2026-02-21 16:03:21.235][self$searchForEntries] This database is not searchable by field "name".
biodb.WARN [2026-02-21 16:03:21.258][self$searchForEntries] This database is not searchable by field "name".
biodb.INFO [2026-02-21 16:03:21.265][biodb::testThat]
biodb.INFO [2026-02-21 16:03:21.266][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2026-02-21 16:03:21.266][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-02-21 16:03:21.267][biodb::testThat]
biodb.DEBUG[2026-02-21 16:03:21.283][private$loadEntries] Creating entries from ids [1]: "749674".
biodb.DEBUG[2026-02-21 16:03:21.326][conn$getEntryContent] Get NCI CACTUS entry content(s) for 1 id(s)...
biodb.DEBUG[2026-02-21 16:03:21.328][self$isDownloaded] Database nci.cactus has already been downloaded.
biodb.DEBUG[2026-02-21 16:03:21.329][self$isDownloaded] Database nci.cactus has already been downloaded.
biodb.INFO [2026-02-21 16:03:21.330][self$download] Extract whole database of nci.cactus.
biodb.INFO [2026-02-21 16:03:21.342][private$doExtractDownload] Extracting content of downloaded biodbNci, a library for connecting to the National Cancer Institute (USA) CACTUS Database....
Saving _problems/test_long_100_generic-38.R
biodb.INFO [2026-02-21 16:03:21.396][biodb::testThat]
biodb.INFO [2026-02-21 16:03:21.397][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2026-02-21 16:03:21.398][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-02-21 16:03:21.399][biodb::testThat]
biodb.INFO [2026-02-21 16:03:21.405][biodb::testThat]
biodb.INFO [2026-02-21 16:03:21.406][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2026-02-21 16:03:21.407][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-02-21 16:03:21.408][biodb::testThat]
biodb.INFO [2026-02-21 16:03:21.415][biodb::testThat]
biodb.INFO [2026-02-21 16:03:21.416][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2026-02-21 16:03:21.416][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-02-21 16:03:21.417][biodb::testThat]
biodb.INFO [2026-02-21 16:03:21.423][biodb::testThat]
biodb.INFO [2026-02-21 16:03:21.424][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2026-02-21 16:03:21.425][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-02-21 16:03:21.425][biodb::testThat]
biodb.INFO [2026-02-21 16:03:21.431][biodb$terminate] Closing BiodbMain instance...
biodb.INFO [2026-02-21 16:03:21.432][self$deleteConn] Connector "nci.cactus" deleted.
biodb.DEBUG[2026-02-21 16:03:21.433][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2026-02-21 16:03:21.433][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-21 16:03:21.434][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-21 16:03:21.435][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-21 16:03:21.436][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-21 16:03:21.437][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:03:21.438][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2026-02-21 16:03:21.447][biodb::testContext]
biodb.INFO [2026-02-21 16:03:21.448][biodb::testContext] ********************************************************************************
biodb.INFO [2026-02-21 16:03:21.448][biodb::testContext] Test context - Example long tests
biodb.INFO [2026-02-21 16:03:21.449][biodb::testContext] ********************************************************************************
biodb.INFO [2026-02-21 16:03:21.450][biodb::testContext]
biodb.INFO [2026-02-21 16:03:21.452][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.18.0.
biodb.DEBUG[2026-02-21 16:03:21.454][self$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.22-bioc/R/site-library/biodb/definitions.yml".
biodb.DEBUG[2026-02-21 16:03:21.457][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2026-02-21 16:03:21.458][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2026-02-21 16:03:21.459][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2026-02-21 16:03:21.460][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:03:21.461][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:03:21.461][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-21 16:03:21.462][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2026-02-21 16:03:21.463][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2026-02-21 16:03:21.464][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:03:21.465][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:03:21.466][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-21 16:03:21.467][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2026-02-21 16:03:21.468][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2026-02-21 16:03:21.469][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:03:21.469][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:03:21.470][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-21 16:03:21.471][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2026-02-21 16:03:21.472][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2026-02-21 16:03:21.473][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2026-02-21 16:03:21.474][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:03:21.475][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:03:21.476][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-21 16:03:21.476][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2026-02-21 16:03:21.477][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2026-02-21 16:03:21.478][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2026-02-21 16:03:21.479][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:03:21.480][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:03:21.481][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-21 16:03:21.482][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2026-02-21 16:03:21.483][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2026-02-21 16:03:21.484][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:03:21.484][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:03:21.485][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-21 16:03:21.486][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2026-02-21 16:03:21.487][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2026-02-21 16:03:21.488][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2026-02-21 16:03:21.489][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:03:21.490][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:03:21.491][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-21 16:03:21.491][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2026-02-21 16:03:21.492][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2026-02-21 16:03:21.493][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:03:21.494][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:03:21.495][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-21 16:03:21.496][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2026-02-21 16:03:21.497][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2026-02-21 16:03:21.498][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2026-02-21 16:03:21.499][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:03:21.499][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:03:21.500][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-21 16:03:21.501][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2026-02-21 16:03:21.502][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2026-02-21 16:03:21.503][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2026-02-21 16:03:21.504][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2026-02-21 16:03:21.505][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2026-02-21 16:03:21.506][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2026-02-21 16:03:21.507][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:03:21.507][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:03:21.508][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-21 16:03:21.509][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2026-02-21 16:03:21.510][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2026-02-21 16:03:21.511][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:03:21.512][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:03:21.513][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-21 16:03:21.514][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2026-02-21 16:03:21.515][self$set] Set key entries.sep to "|".
biodb.DEBUG[2026-02-21 16:03:21.515][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:03:21.516][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:03:21.517][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-21 16:03:21.518][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2026-02-21 16:03:21.519][self$set] Set key offline to FALSE.
biodb.DEBUG[2026-02-21 16:03:21.520][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:03:21.521][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:03:21.521][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-21 16:03:21.522][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2026-02-21 16:03:21.523][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2026-02-21 16:03:21.524][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2026-02-21 16:03:21.525][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:03:21.526][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:03:21.527][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-21 16:03:21.528][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2026-02-21 16:03:21.533][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2026-02-21 16:03:21.536][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2026-02-21 16:03:21.537][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:03:21.538][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:03:21.539][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-21 16:03:21.540][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2026-02-21 16:03:21.540][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2026-02-21 16:03:21.541][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2026-02-21 16:03:21.542][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:03:21.543][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:03:21.544][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-21 16:03:21.545][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2026-02-21 16:03:21.547][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2026-02-21 16:03:21.548][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2026-02-21 16:03:21.549][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-02-21 16:03:21.549][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-02-21 16:03:21.550][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-02-21 16:03:21.551][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-02-21 16:03:21.552][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2026-02-21 16:03:21.553][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-02-21 16:03:21.554][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2026-02-21 16:03:21.555][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-02-21 16:03:21.556][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2026-02-21 16:03:21.557][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2026-02-21 16:03:21.558][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-02-21 16:03:21.559][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2026-02-21 16:03:21.560][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2026-02-21 16:03:21.561][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2026-02-21 16:03:21.561][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2026-02-21 16:03:21.561][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2026-02-21 16:03:21.561][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2026-02-21 16:03:21.561][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2026-02-21 16:03:21.562][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2026-02-21 16:03:21.563][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-02-21 16:03:21.564][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-02-21 16:03:21.564][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-02-21 16:03:21.565][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-02-21 16:03:21.566][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-02-21 16:03:21.567][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-02-21 16:03:21.568][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2026-02-21 16:03:21.569][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-02-21 16:03:21.570][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-02-21 16:03:21.571][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2026-02-21 16:03:21.572][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-02-21 16:03:21.573][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2026-02-21 16:03:21.574][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2026-02-21 16:03:21.575][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2026-02-21 16:03:21.576][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-02-21 16:03:21.577][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-02-21 16:03:21.578][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-02-21 16:03:21.579][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-02-21 16:03:21.580][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2026-02-21 16:03:21.581][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-02-21 16:03:21.582][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2026-02-21 16:03:21.583][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-02-21 16:03:21.584][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2026-02-21 16:03:21.585][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2026-02-21 16:03:21.586][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-02-21 16:03:21.587][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2026-02-21 16:03:21.588][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2026-02-21 16:03:21.589][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2026-02-21 16:03:21.589][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2026-02-21 16:03:21.589][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2026-02-21 16:03:21.589][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2026-02-21 16:03:21.589][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2026-02-21 16:03:21.590][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2026-02-21 16:03:21.590][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-02-21 16:03:21.591][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-02-21 16:03:21.592][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-02-21 16:03:21.593][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-02-21 16:03:21.594][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-02-21 16:03:21.595][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-02-21 16:03:21.596][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2026-02-21 16:03:21.597][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-02-21 16:03:21.598][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-02-21 16:03:21.598][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2026-02-21 16:03:21.599][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-02-21 16:03:21.600][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2026-02-21 16:03:21.602][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2026-02-21 16:03:21.603][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2026-02-21 16:03:21.604][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-02-21 16:03:21.605][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-02-21 16:03:21.606][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-02-21 16:03:21.607][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-02-21 16:03:21.608][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2026-02-21 16:03:21.609][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-02-21 16:03:21.610][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2026-02-21 16:03:21.611][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-02-21 16:03:21.611][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2026-02-21 16:03:21.612][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2026-02-21 16:03:21.613][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-02-21 16:03:21.614][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2026-02-21 16:03:21.615][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2026-02-21 16:03:21.616][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2026-02-21 16:03:21.617][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2026-02-21 16:03:21.618][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-02-21 16:03:21.619][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-02-21 16:03:21.620][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-02-21 16:03:21.621][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-02-21 16:03:21.621][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-02-21 16:03:21.622][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-02-21 16:03:21.623][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2026-02-21 16:03:21.624][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-02-21 16:03:21.625][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-02-21 16:03:21.626][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2026-02-21 16:03:21.627][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-02-21 16:03:21.628][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2026-02-21 16:03:21.630][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2026-02-21 16:03:21.630][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2026-02-21 16:03:21.631][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-02-21 16:03:21.632][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-02-21 16:03:21.633][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-02-21 16:03:21.634][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-02-21 16:03:21.635][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2026-02-21 16:03:21.636][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-02-21 16:03:21.637][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2026-02-21 16:03:21.638][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-02-21 16:03:21.639][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2026-02-21 16:03:21.640][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2026-02-21 16:03:21.641][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-02-21 16:03:21.642][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2026-02-21 16:03:21.643][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2026-02-21 16:03:21.644][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2026-02-21 16:03:21.644][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2026-02-21 16:03:21.645][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-02-21 16:03:21.646][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-02-21 16:03:21.647][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-02-21 16:03:21.648][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-02-21 16:03:21.649][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-02-21 16:03:21.650][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-02-21 16:03:21.651][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2026-02-21 16:03:21.652][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-02-21 16:03:21.652][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-02-21 16:03:21.653][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2026-02-21 16:03:21.654][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-02-21 16:03:21.655][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2026-02-21 16:03:21.656][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:03:21.657][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-21 16:03:21.658][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:03:21.659][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-21 16:03:21.660][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-21 16:03:21.661][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:03:21.661][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-21 16:03:21.662][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:03:21.663][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-21 16:03:21.664][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-21 16:03:21.665][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:03:21.666][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-21 16:03:21.666][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:03:21.667][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-21 16:03:21.668][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-21 16:03:21.669][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:03:21.670][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-21 16:03:21.671][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:03:21.671][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-21 16:03:21.672][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-21 16:03:21.673][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:03:21.674][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-21 16:03:21.675][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:03:21.676][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-21 16:03:21.677][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-21 16:03:21.678][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:03:21.679][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-21 16:03:21.679][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:03:21.680][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-21 16:03:21.681][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-21 16:03:21.686][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:03:21.687][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-21 16:03:21.688][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:03:21.689][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-21 16:03:21.690][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-21 16:03:21.690][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:03:21.691][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-21 16:03:21.692][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:03:21.693][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-21 16:03:21.694][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-21 16:03:21.695][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:03:21.696][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-21 16:03:21.696][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:03:21.697][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-21 16:03:21.698][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-21 16:03:21.699][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:03:21.700][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-21 16:03:21.701][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:03:21.702][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-21 16:03:21.703][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-21 16:03:21.704][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:03:21.704][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-21 16:03:21.705][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:03:21.706][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-21 16:03:21.707][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-21 16:03:21.708][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:03:21.709][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-21 16:03:21.710][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:03:21.711][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-21 16:03:21.712][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-21 16:03:21.712][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:03:21.713][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-21 16:03:21.714][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:03:21.715][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-21 16:03:21.716][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-21 16:03:21.717][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:03:21.718][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-21 16:03:21.718][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:03:21.719][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-21 16:03:21.720][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-21 16:03:21.721][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:03:21.722][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-21 16:03:21.723][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:03:21.724][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-21 16:03:21.724][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-21 16:03:21.725][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:03:21.726][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-21 16:03:21.727][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:03:21.728][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-21 16:03:21.729][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-21 16:03:21.729][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:03:21.730][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-21 16:03:21.731][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2026-02-21 16:03:21.733][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2026-02-21 16:03:21.734][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2026-02-21 16:03:21.735][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2026-02-21 16:03:21.737][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2026-02-21 16:03:21.738][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2026-02-21 16:03:21.739][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2026-02-21 16:03:21.741][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2026-02-21 16:03:21.742][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2026-02-21 16:03:21.743][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2026-02-21 16:03:21.745][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2026-02-21 16:03:21.746][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2026-02-21 16:03:21.747][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2026-02-21 16:03:21.748][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2026-02-21 16:03:21.750][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2026-02-21 16:03:21.751][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2026-02-21 16:03:21.752][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2026-02-21 16:03:21.754][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2026-02-21 16:03:21.755][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2026-02-21 16:03:21.756][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2026-02-21 16:03:21.758][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2026-02-21 16:03:21.759][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2026-02-21 16:03:21.760][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2026-02-21 16:03:21.762][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2026-02-21 16:03:21.763][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2026-02-21 16:03:21.764][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2026-02-21 16:03:21.766][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2026-02-21 16:03:21.767][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2026-02-21 16:03:21.768][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2026-02-21 16:03:21.770][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2026-02-21 16:03:21.771][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2026-02-21 16:03:21.772][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2026-02-21 16:03:21.774][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2026-02-21 16:03:21.775][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2026-02-21 16:03:21.776][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2026-02-21 16:03:21.777][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2026-02-21 16:03:21.779][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2026-02-21 16:03:21.780][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2026-02-21 16:03:21.781][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2026-02-21 16:03:21.783][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2026-02-21 16:03:21.784][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2026-02-21 16:03:21.785][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2026-02-21 16:03:21.787][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2026-02-21 16:03:21.788][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2026-02-21 16:03:21.789][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2026-02-21 16:03:21.791][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2026-02-21 16:03:21.792][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2026-02-21 16:03:21.793][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2026-02-21 16:03:21.795][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2026-02-21 16:03:21.796][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2026-02-21 16:03:21.797][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2026-02-21 16:03:21.798][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2026-02-21 16:03:21.800][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2026-02-21 16:03:21.801][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2026-02-21 16:03:21.802][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2026-02-21 16:03:21.804][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2026-02-21 16:03:21.805][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2026-02-21 16:03:21.806][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2026-02-21 16:03:21.808][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2026-02-21 16:03:21.809][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2026-02-21 16:03:21.810][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2026-02-21 16:03:21.812][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2026-02-21 16:03:21.813][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2026-02-21 16:03:21.814][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2026-02-21 16:03:21.815][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2026-02-21 16:03:21.817][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2026-02-21 16:03:21.818][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2026-02-21 16:03:21.819][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2026-02-21 16:03:21.821][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2026-02-21 16:03:21.822][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2026-02-21 16:03:21.823][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2026-02-21 16:03:21.825][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2026-02-21 16:03:21.826][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2026-02-21 16:03:21.827][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2026-02-21 16:03:21.828][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2026-02-21 16:03:21.830][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2026-02-21 16:03:21.831][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2026-02-21 16:03:21.837][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2026-02-21 16:03:21.838][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2026-02-21 16:03:21.839][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2026-02-21 16:03:21.840][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2026-02-21 16:03:21.842][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2026-02-21 16:03:21.843][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2026-02-21 16:03:21.844][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2026-02-21 16:03:21.846][initialize] This is biodb version 1.18.0.
biodb.DEBUG[2026-02-21 16:03:21.847][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2026-02-21 16:03:21.848][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2026-02-21 16:03:21.848][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-21 16:03:21.849][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:03:21.850][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[2026-02-21 16:03:21.851][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:03:21.852][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-21 16:03:21.853][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-21 16:03:21.853][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-21 16:03:21.854][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-21 16:03:21.855][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:03:21.856][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-21 16:03:21.857][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:03:21.858][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-21 16:03:21.859][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-21 16:03:21.859][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-21 16:03:21.860][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-21 16:03:21.861][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:03:21.862][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-21 16:03:21.863][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:03:21.864][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-21 16:03:21.864][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-21 16:03:21.865][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-21 16:03:21.866][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-21 16:03:21.867][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:03:21.868][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-21 16:03:21.869][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:03:21.870][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-21 16:03:21.870][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-21 16:03:21.871][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-21 16:03:21.872][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-21 16:03:21.873][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:03:21.874][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[2026-02-21 16:03:21.875][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:03:21.876][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-21 16:03:21.876][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-21 16:03:21.877][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-21 16:03:21.878][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-21 16:03:21.879][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:03:21.880][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-21 16:03:21.881][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:03:21.881][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-21 16:03:21.882][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-21 16:03:21.883][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-21 16:03:21.884][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-21 16:03:21.885][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:03:21.886][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-21 16:03:21.887][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:03:21.887][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-21 16:03:21.888][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-21 16:03:21.889][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-21 16:03:21.890][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-21 16:03:21.891][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:03:21.892][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[2026-02-21 16:03:21.893][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:03:21.893][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-21 16:03:21.894][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-21 16:03:21.895][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-21 16:03:21.896][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-21 16:03:21.897][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:03:21.898][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-21 16:03:21.898][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:03:21.899][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-21 16:03:21.900][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-21 16:03:21.901][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-21 16:03:21.902][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-21 16:03:21.903][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:03:21.904][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-21 16:03:21.904][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:03:21.905][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-21 16:03:21.906][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-21 16:03:21.907][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-21 16:03:21.908][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-21 16:03:21.909][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:03:21.909][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-21 16:03:21.910][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:03:21.911][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-21 16:03:21.912][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-21 16:03:21.913][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-21 16:03:21.914][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-21 16:03:21.915][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:03:21.915][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-21 16:03:21.916][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:03:21.917][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-21 16:03:21.918][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-21 16:03:21.919][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-21 16:03:21.920][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-21 16:03:21.920][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:03:21.921][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-21 16:03:21.922][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:03:21.923][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-21 16:03:21.924][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-21 16:03:21.925][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-21 16:03:21.926][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-21 16:03:21.926][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:03:21.927][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[2026-02-21 16:03:21.928][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:03:21.929][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-21 16:03:21.930][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-21 16:03:21.931][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-21 16:03:21.932][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-21 16:03:21.932][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:03:21.933][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-21 16:03:21.934][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:03:21.935][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-21 16:03:21.936][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-21 16:03:21.937][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-21 16:03:21.937][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-21 16:03:21.938][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:03:21.939][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-21 16:03:21.940][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:03:21.941][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-21 16:03:21.942][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-21 16:03:21.943][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-21 16:03:21.943][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-21 16:03:21.944][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:03:21.945][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-21 16:03:21.947][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNci.Rcheck/biodbNci/definitions.yml".
biodb.DEBUG[2026-02-21 16:03:21.948][self$getDbsInfo()$define] Define connector nci.cactus.
biodb.DEBUG[2026-02-21 16:03:21.950][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2026-02-21 16:03:21.951][self$setPropertyValue] Setting property "description" to "National Cancer Institute (USA) CACTUS Database.".
biodb.DEBUG[2026-02-21 16:03:21.952][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-02-21 16:03:21.953][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-02-21 16:03:21.954][self$setPropertyValue] Setting property "downloadable" to "TRUE".
biodb.DEBUG[2026-02-21 16:03:21.955][self$setPropertyValue] Setting property "dwnld.ext" to "gz".
biodb.DEBUG[2026-02-21 16:03:21.956][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2026-02-21 16:03:21.957][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-02-21 16:03:21.958][self$setPropertyValue] Setting property "entry.content.type" to "sdf".
biodb.DEBUG[2026-02-21 16:03:21.959][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-02-21 16:03:21.960][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2026-02-21 16:03:21.961][self$setPropertyValue] Setting property "name" to "NCI CACTUS".
biodb.DEBUG[2026-02-21 16:03:21.961][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-02-21 16:03:21.962][self$setPropertyValue] Setting property "parsing.expr" to "NSC".
biodb.DEBUG[2026-02-21 16:03:21.962][self$setPropertyValue] Setting property "parsing.expr" to "DTP names".
biodb.DEBUG[2026-02-21 16:03:21.962][self$setPropertyValue] Setting property "parsing.expr" to "Standard InChI".
biodb.DEBUG[2026-02-21 16:03:21.962][self$setPropertyValue] Setting property "parsing.expr" to "c("Standard InChIKey", "^InChIKey=(.*)$")".
biodb.DEBUG[2026-02-21 16:03:21.962][self$setPropertyValue] Setting property "parsing.expr" to "Formula".
biodb.DEBUG[2026-02-21 16:03:21.962][self$setPropertyValue] Setting property "parsing.expr" to "Molecular Weight".
biodb.DEBUG[2026-02-21 16:03:21.962][self$setPropertyValue] Setting property "parsing.expr" to "CAS".
biodb.DEBUG[2026-02-21 16:03:21.963][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2026-02-21 16:03:21.964][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2026-02-21 16:03:21.965][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2026-02-21 16:03:21.966][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-02-21 16:03:21.967][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-02-21 16:03:21.968][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-02-21 16:03:21.969][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-02-21 16:03:21.970][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-02-21 16:03:21.971][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-02-21 16:03:21.972][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/".
biodb.DEBUG[2026-02-21 16:03:21.972][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/".
biodb.DEBUG[2026-02-21 16:03:21.972][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/download/nci/".
biodb.DEBUG[2026-02-21 16:03:21.972][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/download/nci/NCI-Open_2012-05-01.sdf.gz".
biodb.DEBUG[2026-02-21 16:03:21.973][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-02-21 16:03:21.974][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-02-21 16:03:21.974][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2026-02-21 16:03:21.975][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-02-21 16:03:21.977][self$getEntryFields()$define] Define field nci.cactus.id.
biodb.DEBUG[2026-02-21 16:03:21.980][super$initialize] Initialize connector nci.cactus.
biodb.DEBUG[2026-02-21 16:03:21.987][biodb$getFactory()$createConn] Creating new connector nci.cactus for database class nci.cactus .
biodb.INFO [2026-02-21 16:03:21.988][biodb$terminate] Closing BiodbMain instance...
biodb.INFO [2026-02-21 16:03:21.989][self$deleteConn] Connector "nci.cactus" deleted.
biodb.DEBUG[2026-02-21 16:03:21.989][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2026-02-21 16:03:21.990][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-21 16:03:21.991][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-21 16:03:21.992][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-21 16:03:21.993][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-21 16:03:21.993][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:03:21.994][FUN] Functions in observer 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)