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 merida1

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

raw results


Summary

Package: biodbNci
Version: 1.14.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --test-dir=longtests --no-stop-on-test-error --no-codoc --no-examples --no-manual --ignore-vignettes --check-subdirs=no biodbNci_1.14.0.tar.gz
StartedAt: 2026-02-21 16:01:21 -0500 (Sat, 21 Feb 2026)
EndedAt: 2026-02-21 16:02:49 -0500 (Sat, 21 Feb 2026)
EllapsedTime: 88.0 seconds
RetCode: 1
Status:   ERROR  
CheckDir: biodbNci.Rcheck
Warnings: NA

Tests output

biodbNci.Rcheck/tests/testthat.Rout.fail


R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> # 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 16:02:45.818][biodb::testContext]
biodb.INFO [2026-02-21 16:02:45.822][biodb::testContext] ********************************************************************************
biodb.INFO [2026-02-21 16:02:45.823][biodb::testContext] Test context - Generic long tests
biodb.INFO [2026-02-21 16:02:45.824][biodb::testContext] ********************************************************************************
biodb.INFO [2026-02-21 16:02:45.825][biodb::testContext]
biodb.INFO [2026-02-21 16:02:45.831][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.18.0.
biodb.DEBUG[2026-02-21 16:02:45.834][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2026-02-21 16:02:45.841][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2026-02-21 16:02:45.842][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2026-02-21 16:02:45.843][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2026-02-21 16:02:45.844][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:45.845][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:45.847][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-21 16:02:45.848][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2026-02-21 16:02:45.871][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2026-02-21 16:02:45.873][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:45.874][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:45.875][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:02:45.876][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2026-02-21 16:02:45.877][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2026-02-21 16:02:45.878][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:45.879][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:45.881][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-21 16:02:45.882][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2026-02-21 16:02:45.883][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2026-02-21 16:02:45.884][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2026-02-21 16:02:45.885][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:45.887][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:45.888][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:02:45.889][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2026-02-21 16:02:45.890][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2026-02-21 16:02:45.891][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2026-02-21 16:02:45.892][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:45.893][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:45.895][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-21 16:02:45.896][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2026-02-21 16:02:45.897][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2026-02-21 16:02:45.898][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:45.899][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:45.900][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-21 16:02:45.901][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2026-02-21 16:02:45.903][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2026-02-21 16:02:45.904][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2026-02-21 16:02:45.905][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:45.906][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:45.907][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-21 16:02:45.908][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2026-02-21 16:02:45.910][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2026-02-21 16:02:45.911][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:45.912][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:45.913][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-21 16:02:45.914][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2026-02-21 16:02:45.915][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2026-02-21 16:02:45.916][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2026-02-21 16:02:45.918][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:45.919][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:45.920][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-21 16:02:45.921][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2026-02-21 16:02:45.922][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2026-02-21 16:02:45.923][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2026-02-21 16:02:45.925][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2026-02-21 16:02:45.926][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2026-02-21 16:02:45.927][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2026-02-21 16:02:45.928][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:45.929][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:45.930][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:02:45.931][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2026-02-21 16:02:45.933][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2026-02-21 16:02:45.934][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:45.935][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:45.936][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-21 16:02:45.937][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2026-02-21 16:02:45.938][self$set] Set key entries.sep to "|".
biodb.DEBUG[2026-02-21 16:02:45.940][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:45.941][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:45.942][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:02:45.943][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2026-02-21 16:02:45.944][self$set] Set key offline to FALSE.
biodb.DEBUG[2026-02-21 16:02:45.945][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:45.946][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:45.947][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-21 16:02:45.949][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2026-02-21 16:02:45.950][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2026-02-21 16:02:45.951][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2026-02-21 16:02:45.952][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:45.953][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:45.954][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:02:45.956][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2026-02-21 16:02:45.957][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2026-02-21 16:02:45.967][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2026-02-21 16:02:45.969][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:45.970][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:45.971][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-21 16:02:45.972][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2026-02-21 16:02:45.974][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2026-02-21 16:02:45.975][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2026-02-21 16:02:45.976][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:45.977][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:45.978][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:02:45.982][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2026-02-21 16:02:46.028][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2026-02-21 16:02:46.056][self$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 16:02:46.058][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-02-21 16:02:46.059][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-02-21 16:02:46.060][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-02-21 16:02:46.062][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-02-21 16:02:46.063][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2026-02-21 16:02:46.064][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-02-21 16:02:46.065][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2026-02-21 16:02:46.067][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-02-21 16:02:46.068][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2026-02-21 16:02:46.069][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2026-02-21 16:02:46.070][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-02-21 16:02:46.072][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2026-02-21 16:02:46.073][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2026-02-21 16:02:46.074][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2026-02-21 16:02:46.074][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2026-02-21 16:02:46.074][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2026-02-21 16:02:46.074][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2026-02-21 16:02:46.074][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2026-02-21 16:02:46.075][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2026-02-21 16:02:46.077][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-02-21 16:02:46.078][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-02-21 16:02:46.079][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-02-21 16:02:46.080][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-02-21 16:02:46.082][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-02-21 16:02:46.083][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-02-21 16:02:46.084][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2026-02-21 16:02:46.085][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-02-21 16:02:46.086][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-02-21 16:02:46.088][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2026-02-21 16:02:46.089][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-02-21 16:02:46.090][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2026-02-21 16:02:46.092][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2026-02-21 16:02:46.094][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2026-02-21 16:02:46.095][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-02-21 16:02:46.096][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-02-21 16:02:46.097][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-02-21 16:02:46.098][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-02-21 16:02:46.100][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2026-02-21 16:02:46.101][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-02-21 16:02:46.102][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2026-02-21 16:02:46.103][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-02-21 16:02:46.105][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2026-02-21 16:02:46.106][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2026-02-21 16:02:46.107][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-02-21 16:02:46.108][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2026-02-21 16:02:46.110][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2026-02-21 16:02:46.111][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2026-02-21 16:02:46.111][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2026-02-21 16:02:46.111][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2026-02-21 16:02:46.111][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2026-02-21 16:02:46.111][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2026-02-21 16:02:46.112][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2026-02-21 16:02:46.113][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-02-21 16:02:46.114][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-02-21 16:02:46.115][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-02-21 16:02:46.117][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-02-21 16:02:46.118][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-02-21 16:02:46.119][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-02-21 16:02:46.120][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2026-02-21 16:02:46.121][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-02-21 16:02:46.122][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-02-21 16:02:46.123][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2026-02-21 16:02:46.125][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-02-21 16:02:46.126][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2026-02-21 16:02:46.128][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2026-02-21 16:02:46.129][self$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 16:02:46.131][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-02-21 16:02:46.132][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-02-21 16:02:46.133][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-02-21 16:02:46.134][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-02-21 16:02:46.136][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2026-02-21 16:02:46.137][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-02-21 16:02:46.138][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2026-02-21 16:02:46.139][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-02-21 16:02:46.140][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2026-02-21 16:02:46.142][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2026-02-21 16:02:46.143][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-02-21 16:02:46.144][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2026-02-21 16:02:46.145][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2026-02-21 16:02:46.146][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2026-02-21 16:02:46.148][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2026-02-21 16:02:46.149][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-02-21 16:02:46.150][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-02-21 16:02:46.151][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-02-21 16:02:46.152][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-02-21 16:02:46.153][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-02-21 16:02:46.154][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-02-21 16:02:46.156][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2026-02-21 16:02:46.157][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-02-21 16:02:46.158][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-02-21 16:02:46.159][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2026-02-21 16:02:46.160][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-02-21 16:02:46.162][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2026-02-21 16:02:46.164][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2026-02-21 16:02:46.166][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2026-02-21 16:02:46.167][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-02-21 16:02:46.168][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-02-21 16:02:46.170][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-02-21 16:02:46.171][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-02-21 16:02:46.172][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2026-02-21 16:02:46.173][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-02-21 16:02:46.175][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2026-02-21 16:02:46.176][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-02-21 16:02:46.177][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2026-02-21 16:02:46.178][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2026-02-21 16:02:46.180][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-02-21 16:02:46.181][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2026-02-21 16:02:46.182][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2026-02-21 16:02:46.183][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2026-02-21 16:02:46.185][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2026-02-21 16:02:46.186][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-02-21 16:02:46.187][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-02-21 16:02:46.188][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-02-21 16:02:46.189][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-02-21 16:02:46.191][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-02-21 16:02:46.192][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-02-21 16:02:46.193][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2026-02-21 16:02:46.194][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-02-21 16:02:46.195][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-02-21 16:02:46.197][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2026-02-21 16:02:46.198][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-02-21 16:02:46.202][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2026-02-21 16:02:46.203][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:46.204][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:02:46.205][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:46.207][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-21 16:02:46.208][FUN] 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 16:02:46.209][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:46.210][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:02:46.211][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:46.212][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-21 16:02:46.213][FUN] 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 16:02:46.214][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:46.216][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-21 16:02:46.217][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:46.218][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-21 16:02:46.219][FUN] 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 16:02:46.220][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:46.221][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:02:46.222][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:46.223][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-21 16:02:46.225][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-21 16:02:46.226][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:46.227][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-21 16:02:46.228][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:46.229][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-21 16:02:46.230][FUN] 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 16:02:46.231][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:46.232][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-21 16:02:46.234][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:46.235][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-21 16:02:46.236][FUN] 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 16:02:46.237][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:46.238][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:02:46.239][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:46.240][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-21 16:02:46.241][FUN] 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 16:02:46.243][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:46.244][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:02:46.245][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:46.246][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-21 16:02:46.247][FUN] 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 16:02:46.248][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:46.250][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:02:46.251][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:46.252][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-21 16:02:46.253][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-21 16:02:46.254][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:46.255][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-21 16:02:46.256][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:46.257][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-21 16:02:46.258][FUN] 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 16:02:46.259][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:46.261][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:02:46.262][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:46.263][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-21 16:02:46.264][FUN] 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 16:02:46.265][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:46.266][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:02:46.267][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:46.268][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-21 16:02:46.269][FUN] 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 16:02:46.271][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:46.272][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-21 16:02:46.273][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:46.274][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-21 16:02:46.275][FUN] 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 16:02:46.276][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:46.277][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:02:46.278][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:46.279][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-21 16:02:46.280][FUN] 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 16:02:46.282][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:46.283][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:02:46.284][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:46.285][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-21 16:02:46.286][FUN] 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 16:02:46.287][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:46.289][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:02:46.290][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:46.291][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-21 16:02:46.292][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-21 16:02:46.298][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:46.299][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:02:46.300][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2026-02-21 16:02:46.305][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2026-02-21 16:02:46.307][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2026-02-21 16:02:46.308][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2026-02-21 16:02:46.310][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2026-02-21 16:02:46.312][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2026-02-21 16:02:46.313][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2026-02-21 16:02:46.315][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2026-02-21 16:02:46.317][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2026-02-21 16:02:46.319][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2026-02-21 16:02:46.320][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2026-02-21 16:02:46.322][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2026-02-21 16:02:46.324][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2026-02-21 16:02:46.326][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2026-02-21 16:02:46.328][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2026-02-21 16:02:46.329][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2026-02-21 16:02:46.331][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2026-02-21 16:02:46.333][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2026-02-21 16:02:46.334][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2026-02-21 16:02:46.336][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2026-02-21 16:02:46.338][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2026-02-21 16:02:46.340][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2026-02-21 16:02:46.341][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2026-02-21 16:02:46.343][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2026-02-21 16:02:46.345][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2026-02-21 16:02:46.346][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2026-02-21 16:02:46.348][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2026-02-21 16:02:46.350][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2026-02-21 16:02:46.352][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2026-02-21 16:02:46.353][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2026-02-21 16:02:46.355][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2026-02-21 16:02:46.357][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2026-02-21 16:02:46.358][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2026-02-21 16:02:46.360][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2026-02-21 16:02:46.362][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2026-02-21 16:02:46.363][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2026-02-21 16:02:46.365][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2026-02-21 16:02:46.367][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2026-02-21 16:02:46.369][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2026-02-21 16:02:46.370][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2026-02-21 16:02:46.372][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2026-02-21 16:02:46.374][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2026-02-21 16:02:46.376][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2026-02-21 16:02:46.377][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2026-02-21 16:02:46.379][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2026-02-21 16:02:46.381][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2026-02-21 16:02:46.383][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2026-02-21 16:02:46.384][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2026-02-21 16:02:46.386][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2026-02-21 16:02:46.388][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2026-02-21 16:02:46.389][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2026-02-21 16:02:46.391][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2026-02-21 16:02:46.394][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2026-02-21 16:02:46.396][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2026-02-21 16:02:46.397][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2026-02-21 16:02:46.400][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2026-02-21 16:02:46.402][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2026-02-21 16:02:46.403][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2026-02-21 16:02:46.405][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2026-02-21 16:02:46.407][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2026-02-21 16:02:46.409][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2026-02-21 16:02:46.411][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2026-02-21 16:02:46.413][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2026-02-21 16:02:46.414][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2026-02-21 16:02:46.416][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2026-02-21 16:02:46.418][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2026-02-21 16:02:46.419][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2026-02-21 16:02:46.421][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2026-02-21 16:02:46.423][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2026-02-21 16:02:46.424][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2026-02-21 16:02:46.426][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2026-02-21 16:02:46.428][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2026-02-21 16:02:46.429][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2026-02-21 16:02:46.431][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2026-02-21 16:02:46.433][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2026-02-21 16:02:46.434][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2026-02-21 16:02:46.436][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2026-02-21 16:02:46.438][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2026-02-21 16:02:46.439][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2026-02-21 16:02:46.441][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2026-02-21 16:02:46.443][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2026-02-21 16:02:46.444][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2026-02-21 16:02:46.446][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2026-02-21 16:02:46.453][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2026-02-21 16:02:46.456][initialize] This is biodb version 1.18.0.
biodb.DEBUG[2026-02-21 16:02:46.459][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2026-02-21 16:02:46.460][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2026-02-21 16:02:46.461][FUN] 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 16:02:46.462][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:46.463][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:02:46.469][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:46.471][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-21 16:02:46.472][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-21 16:02:46.473][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-21 16:02:46.474][FUN] 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 16:02:46.476][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:46.477][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:02:46.478][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:46.479][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-21 16:02:46.480][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-21 16:02:46.481][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-21 16:02:46.482][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-21 16:02:46.483][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:46.484][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-21 16:02:46.486][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:46.487][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-21 16:02:46.488][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-21 16:02:46.489][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-21 16:02:46.490][FUN] 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 16:02:46.491][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:46.492][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:02:46.493][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:46.494][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-21 16:02:46.495][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-21 16:02:46.497][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-21 16:02:46.498][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-21 16:02:46.499][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:46.500][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 16:02:46.501][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:46.502][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-21 16:02:46.503][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-21 16:02:46.504][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-21 16:02:46.506][FUN] 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 16:02:46.507][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:46.508][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 16:02:46.509][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:46.510][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-21 16:02:46.511][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-21 16:02:46.512][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-21 16:02:46.513][FUN] 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 16:02:46.514][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:46.516][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-21 16:02:46.517][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:46.518][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-21 16:02:46.519][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-21 16:02:46.520][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-21 16:02:46.522][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 16:02:46.523][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:46.524][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.DEBUG[2026-02-21 16:02:46.525][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:46.526][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-21 16:02:46.527][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-21 16:02:46.528][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-21 16:02:46.529][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-21 16:02:46.530][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:46.532][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:02:46.533][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:46.534][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-21 16:02:46.535][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-21 16:02:46.536][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-21 16:02:46.537][FUN] 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 16:02:46.538][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:46.539][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 16:02:46.541][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:46.542][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-21 16:02:46.543][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-21 16:02:46.544][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-21 16:02:46.545][FUN] 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 16:02:46.546][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:46.547][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:02:46.548][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:46.555][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-21 16:02:46.556][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-21 16:02:46.557][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-21 16:02:46.558][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-21 16:02:46.559][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:46.560][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-21 16:02:46.561][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:46.562][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-21 16:02:46.564][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-21 16:02:46.565][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-21 16:02:46.566][FUN] 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 16:02:46.567][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:46.568][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:02:46.569][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:46.570][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-21 16:02:46.571][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-21 16:02:46.572][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-21 16:02:46.574][FUN] 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 16:02:46.575][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:46.576][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:02:46.577][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:46.578][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-21 16:02:46.579][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-21 16:02:46.580][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-21 16:02:46.581][FUN] 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 16:02:46.583][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:46.584][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:02:46.585][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:46.586][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-21 16:02:46.587][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-21 16:02:46.588][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-21 16:02:46.589][FUN] 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 16:02:46.590][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:46.592][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:02:46.593][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:46.594][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-21 16:02:46.595][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-21 16:02:46.596][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-21 16:02:46.597][FUN] 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 16:02:46.598][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:46.600][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:02:46.602][biodb$loadDefinitions] Load definitions from file "/Users/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNci.Rcheck/biodbNci/definitions.yml".
biodb.DEBUG[2026-02-21 16:02:46.616][self$getDbsInfo()$define] Define connector nci.cactus.
biodb.DEBUG[2026-02-21 16:02:46.618][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2026-02-21 16:02:46.620][self$setPropertyValue] Setting property "description" to "National Cancer Institute (USA) CACTUS Database.".
biodb.DEBUG[2026-02-21 16:02:46.621][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-02-21 16:02:46.622][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-02-21 16:02:46.624][self$setPropertyValue] Setting property "downloadable" to "TRUE".
biodb.DEBUG[2026-02-21 16:02:46.625][self$setPropertyValue] Setting property "dwnld.ext" to "gz".
biodb.DEBUG[2026-02-21 16:02:46.626][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2026-02-21 16:02:46.628][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-02-21 16:02:46.629][self$setPropertyValue] Setting property "entry.content.type" to "sdf".
biodb.DEBUG[2026-02-21 16:02:46.630][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-02-21 16:02:46.632][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2026-02-21 16:02:46.633][self$setPropertyValue] Setting property "name" to "NCI CACTUS".
biodb.DEBUG[2026-02-21 16:02:46.634][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-02-21 16:02:46.635][self$setPropertyValue] Setting property "parsing.expr" to "NSC".
biodb.DEBUG[2026-02-21 16:02:46.635][self$setPropertyValue] Setting property "parsing.expr" to "DTP names".
biodb.DEBUG[2026-02-21 16:02:46.635][self$setPropertyValue] Setting property "parsing.expr" to "Standard InChI".
biodb.DEBUG[2026-02-21 16:02:46.635][self$setPropertyValue] Setting property "parsing.expr" to "c("Standard InChIKey", "^InChIKey=(.*)$")".
biodb.DEBUG[2026-02-21 16:02:46.635][self$setPropertyValue] Setting property "parsing.expr" to "Formula".
biodb.DEBUG[2026-02-21 16:02:46.635][self$setPropertyValue] Setting property "parsing.expr" to "Molecular Weight".
biodb.DEBUG[2026-02-21 16:02:46.635][self$setPropertyValue] Setting property "parsing.expr" to "CAS".
biodb.DEBUG[2026-02-21 16:02:46.637][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2026-02-21 16:02:46.638][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2026-02-21 16:02:46.639][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2026-02-21 16:02:46.641][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-02-21 16:02:46.642][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-02-21 16:02:46.643][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-02-21 16:02:46.644][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-02-21 16:02:46.645][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-02-21 16:02:46.647][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-02-21 16:02:46.648][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/".
biodb.DEBUG[2026-02-21 16:02:46.648][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/".
biodb.DEBUG[2026-02-21 16:02:46.648][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/download/nci/".
biodb.DEBUG[2026-02-21 16:02:46.648][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/download/nci/NCI-Open_2012-05-01.sdf.gz".
biodb.DEBUG[2026-02-21 16:02:46.649][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-02-21 16:02:46.650][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-02-21 16:02:46.651][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2026-02-21 16:02:46.653][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-02-21 16:02:46.661][self$getEntryFields()$define] Define field nci.cactus.id.
biodb.DEBUG[2026-02-21 16:02:46.684][super$initialize] Initialize connector nci.cactus.
biodb.DEBUG[2026-02-21 16:02:46.701][biodb$getFactory()$createConn] Creating new connector nci.cactus for database class nci.cactus .
biodb.INFO [2026-02-21 16:02:46.711][biodb::testThat]
biodb.INFO [2026-02-21 16:02:46.712][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2026-02-21 16:02:46.713][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-02-21 16:02:46.715][biodb::testThat]
biodb.TRACE[2026-02-21 16:02:46.719][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNci.Rcheck/biodbNci/testref/entry-nci.cactus-749674-content.sdf".
biodb.DEBUG[2026-02-21 16:02:46.721][biodb$getFactory()$createEntryFromCo ...] Creating NCI CACTUS entries from 1 content(s).
biodb.DEBUG[2026-02-21 16:02:46.725][biodb$getFactory()$createEntryFromCo ...] Parsing 1 NCI CACTUS entries.
biodb.DEBUG[2026-02-21 16:02:46.734][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2026-02-21 16:02:46.735][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-21 16:02:46.736][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-21 16:02:46.752][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2026-02-21 16:02:46.753][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-21 16:02:46.754][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:46.756][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2026-02-21 16:02:46.778][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-21 16:02:46.779][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-21 16:02:46.781][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:46.782][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:46.783][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-21 16:02:46.801][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-21 16:02:46.802][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:46.804][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:46.808][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2026-02-21 16:02:46.809][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2026-02-21 16:02:46.810][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:46.812][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:46.857][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2026-02-21 16:02:46.859][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2026-02-21 16:02:46.860][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:46.861][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:46.863][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2026-02-21 16:02:46.865][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2026-02-21 16:02:46.866][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:46.867][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:46.869][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2026-02-21 16:02:46.870][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2026-02-21 16:02:46.871][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:46.873][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:46.876][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2026-02-21 16:02:46.877][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2026-02-21 16:02:46.879][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:46.880][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:46.881][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2026-02-21 16:02:46.882][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2026-02-21 16:02:46.884][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:46.885][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:46.887][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-02-21 16:02:46.888][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-02-21 16:02:46.889][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:46.891][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:46.892][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-02-21 16:02:46.893][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-02-21 16:02:46.895][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:46.896][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:46.899][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2026-02-21 16:02:46.900][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2026-02-21 16:02:46.901][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:46.902][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:46.904][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2026-02-21 16:02:46.905][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2026-02-21 16:02:46.906][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:46.908][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:46.909][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-21 16:02:46.910][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-21 16:02:46.912][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:46.913][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:46.914][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2026-02-21 16:02:46.916][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2026-02-21 16:02:46.917][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:46.918][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:46.920][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-21 16:02:46.921][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-21 16:02:46.922][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:46.923][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:46.925][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-21 16:02:46.926][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-21 16:02:46.927][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:46.929][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:46.930][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-21 16:02:46.931][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-21 16:02:46.933][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:46.934][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:46.980][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-21 16:02:46.982][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-21 16:02:46.983][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:46.984][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:46.985][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-21 16:02:46.987][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-21 16:02:46.988][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:46.989][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:46.990][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-21 16:02:46.992][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-21 16:02:46.993][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:46.994][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2026-02-21 16:02:46.995][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 749674.
biodb.TRACE[2026-02-21 16:02:46.998][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2026-02-21 16:02:47.000][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2026-02-21 16:02:47.001][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:47.002][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:47.003][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2026-02-21 16:02:47.005][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2026-02-21 16:02:47.006][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:47.007][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:47.008][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2026-02-21 16:02:47.010][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2026-02-21 16:02:47.011][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:47.012][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:47.013][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2026-02-21 16:02:47.015][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2026-02-21 16:02:47.016][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:47.017][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:47.020][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-21 16:02:47.022][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-21 16:02:47.023][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:47.024][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:47.042][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2026-02-21 16:02:47.043][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2026-02-21 16:02:47.044][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:47.050][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:47.057][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-21 16:02:47.058][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-21 16:02:47.059][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:47.061][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:47.062][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-21 16:02:47.063][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-21 16:02:47.064][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:47.066][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:47.067][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-21 16:02:47.068][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-21 16:02:47.069][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:47.071][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:47.074][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-21 16:02:47.076][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-21 16:02:47.077][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:47.078][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:47.080][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-21 16:02:47.081][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-21 16:02:47.082][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:47.083][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:47.085][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-21 16:02:47.086][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-21 16:02:47.087][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:47.089][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:47.091][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2026-02-21 16:02:47.092][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2026-02-21 16:02:47.093][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:47.094][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:47.096][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2026-02-21 16:02:47.097][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2026-02-21 16:02:47.098][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:47.100][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:47.101][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2026-02-21 16:02:47.102][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2026-02-21 16:02:47.103][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:47.105][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:47.115][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-21 16:02:47.116][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-21 16:02:47.118][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:47.119][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:47.120][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-21 16:02:47.121][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-21 16:02:47.123][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:47.124][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:47.125][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-21 16:02:47.126][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-21 16:02:47.128][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:47.129][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:47.130][ef$get] Asked field names are: accession.
biodb.TRACE[2026-02-21 16:02:47.132][ef$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-21 16:02:47.133][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:47.134][ef$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:47.135][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-21 16:02:47.137][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-21 16:02:47.138][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:47.139][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:47.152][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2026-02-21 16:02:47.153][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2026-02-21 16:02:47.154][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:47.156][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:47.157][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2026-02-21 16:02:47.158][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2026-02-21 16:02:47.159][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:47.161][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:47.162][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2026-02-21 16:02:47.163][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2026-02-21 16:02:47.164][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:47.166][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:47.167][ef$get] Asked field names are: formula.
biodb.TRACE[2026-02-21 16:02:47.168][ef$get] Realnames of fields are: formula.
biodb.TRACE[2026-02-21 16:02:47.170][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:47.171][ef$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:47.172][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2026-02-21 16:02:47.173][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2026-02-21 16:02:47.175][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:47.176][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:47.188][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2026-02-21 16:02:47.190][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2026-02-21 16:02:47.191][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:47.192][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:47.193][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2026-02-21 16:02:47.195][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2026-02-21 16:02:47.196][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:47.197][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:47.199][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2026-02-21 16:02:47.200][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2026-02-21 16:02:47.201][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:47.203][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:47.204][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2026-02-21 16:02:47.205][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2026-02-21 16:02:47.207][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:47.208][ef$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:47.209][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2026-02-21 16:02:47.211][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2026-02-21 16:02:47.212][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:47.213][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:47.226][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2026-02-21 16:02:47.228][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2026-02-21 16:02:47.229][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:47.231][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:47.232][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2026-02-21 16:02:47.233][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2026-02-21 16:02:47.234][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:47.236][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:47.237][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2026-02-21 16:02:47.238][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2026-02-21 16:02:47.240][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:47.241][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:47.242][ef$get] Asked field names are: inchi.
biodb.TRACE[2026-02-21 16:02:47.244][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2026-02-21 16:02:47.245][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:47.246][ef$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:47.247][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2026-02-21 16:02:47.249][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2026-02-21 16:02:47.250][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:47.251][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:47.263][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-02-21 16:02:47.264][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-02-21 16:02:47.266][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:47.267][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:47.268][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-02-21 16:02:47.269][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-02-21 16:02:47.271][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:47.272][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:47.273][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-02-21 16:02:47.274][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-02-21 16:02:47.276][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:47.281][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:47.283][ef$get] Asked field names are: inchikey.
biodb.TRACE[2026-02-21 16:02:47.284][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-02-21 16:02:47.285][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:47.287][ef$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:47.288][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-02-21 16:02:47.289][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-02-21 16:02:47.290][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:47.291][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:47.303][ef$get] Asked field names are: accession.
biodb.TRACE[2026-02-21 16:02:47.305][ef$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-21 16:02:47.306][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:47.308][ef$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:47.314][ef$get] Asked field names are: formula.
biodb.TRACE[2026-02-21 16:02:47.316][ef$get] Realnames of fields are: formula.
biodb.TRACE[2026-02-21 16:02:47.317][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:47.318][ef$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:47.325][ef$get] Asked field names are: inchi.
biodb.TRACE[2026-02-21 16:02:47.326][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2026-02-21 16:02:47.328][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:47.329][ef$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:47.335][ef$get] Asked field names are: inchikey.
biodb.TRACE[2026-02-21 16:02:47.337][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-02-21 16:02:47.338][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:47.339][ef$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:47.346][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2026-02-21 16:02:47.347][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2026-02-21 16:02:47.348][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:47.349][ef$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:47.373][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNci.Rcheck/biodbNci/testref/entry-nci.cactus-750690-content.sdf".
biodb.DEBUG[2026-02-21 16:02:47.421][biodb$getFactory()$createEntryFromCo ...] Creating NCI CACTUS entries from 1 content(s).
biodb.DEBUG[2026-02-21 16:02:47.423][biodb$getFactory()$createEntryFromCo ...] Parsing 1 NCI CACTUS entries.
biodb.DEBUG[2026-02-21 16:02:47.425][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2026-02-21 16:02:47.426][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-21 16:02:47.427][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-21 16:02:47.434][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2026-02-21 16:02:47.435][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-21 16:02:47.437][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:47.438][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2026-02-21 16:02:47.454][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-21 16:02:47.455][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-21 16:02:47.457][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:47.458][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:47.459][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-21 16:02:47.460][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-21 16:02:47.462][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:47.463][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:47.489][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2026-02-21 16:02:47.490][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2026-02-21 16:02:47.525][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:47.527][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:47.528][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2026-02-21 16:02:47.529][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2026-02-21 16:02:47.531][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:47.532][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:47.534][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2026-02-21 16:02:47.536][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2026-02-21 16:02:47.537][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:47.538][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:47.539][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2026-02-21 16:02:47.541][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2026-02-21 16:02:47.542][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:47.543][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:47.545][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2026-02-21 16:02:47.546][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2026-02-21 16:02:47.548][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:47.549][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:47.550][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2026-02-21 16:02:47.552][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2026-02-21 16:02:47.553][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:47.554][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:47.556][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-02-21 16:02:47.557][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-02-21 16:02:47.558][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:47.560][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:47.561][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-02-21 16:02:47.562][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-02-21 16:02:47.563][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:47.565][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:47.566][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-02-21 16:02:47.568][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-02-21 16:02:47.569][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:47.570][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:47.571][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-02-21 16:02:47.573][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-02-21 16:02:47.574][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:47.575][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:47.576][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-02-21 16:02:47.578][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-02-21 16:02:47.579][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:47.580][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:47.581][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-02-21 16:02:47.583][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-02-21 16:02:47.584][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:47.585][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:47.586][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-02-21 16:02:47.588][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-02-21 16:02:47.589][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:47.590][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:47.593][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2026-02-21 16:02:47.594][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2026-02-21 16:02:47.595][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:47.596][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:47.598][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2026-02-21 16:02:47.599][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2026-02-21 16:02:47.600][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:47.601][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:47.603][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-02-21 16:02:47.605][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-02-21 16:02:47.606][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:47.607][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:47.608][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-02-21 16:02:47.609][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-02-21 16:02:47.611][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:47.612][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:47.614][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2026-02-21 16:02:47.616][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2026-02-21 16:02:47.617][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:47.618][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:47.619][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2026-02-21 16:02:47.620][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2026-02-21 16:02:47.622][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:47.623][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:47.624][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-21 16:02:47.625][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-21 16:02:47.627][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:47.628][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:47.629][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2026-02-21 16:02:47.630][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2026-02-21 16:02:47.632][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:47.633][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:47.634][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-21 16:02:47.635][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-21 16:02:47.637][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:47.638][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:47.639][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-21 16:02:47.640][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-21 16:02:47.641][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:47.643][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:47.644][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-21 16:02:47.645][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-21 16:02:47.646][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:47.648][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:47.649][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-21 16:02:47.650][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-21 16:02:47.652][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:47.653][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:47.654][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-21 16:02:47.655][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-21 16:02:47.657][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:47.658][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:47.659][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-21 16:02:47.660][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-21 16:02:47.661][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:47.663][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2026-02-21 16:02:47.664][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 750690.
biodb.TRACE[2026-02-21 16:02:47.691][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2026-02-21 16:02:47.693][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2026-02-21 16:02:47.694][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:47.695][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:47.696][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2026-02-21 16:02:47.698][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2026-02-21 16:02:47.699][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:47.700][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:47.701][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2026-02-21 16:02:47.703][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2026-02-21 16:02:47.704][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:47.705][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:47.706][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2026-02-21 16:02:47.708][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2026-02-21 16:02:47.709][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:47.710][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:47.713][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-21 16:02:47.714][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-21 16:02:47.715][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:47.716][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:47.723][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2026-02-21 16:02:47.724][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2026-02-21 16:02:47.725][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:47.726][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:47.733][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-21 16:02:47.734][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-21 16:02:47.735][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:47.740][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:47.742][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-21 16:02:47.743][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-21 16:02:47.744][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:47.745][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:47.747][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-21 16:02:47.748][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-21 16:02:47.749][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:47.750][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:47.754][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-21 16:02:47.755][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-21 16:02:47.756][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:47.757][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:47.759][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-21 16:02:47.760][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-21 16:02:47.761][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:47.762][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:47.764][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-21 16:02:47.765][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-21 16:02:47.766][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:47.767][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:47.769][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2026-02-21 16:02:47.770][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2026-02-21 16:02:47.771][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:47.773][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:47.774][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2026-02-21 16:02:47.775][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2026-02-21 16:02:47.776][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:47.778][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:47.779][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2026-02-21 16:02:47.780][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2026-02-21 16:02:47.781][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:47.783][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:47.806][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-21 16:02:47.808][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-21 16:02:47.809][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:47.810][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:47.811][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-21 16:02:47.813][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-21 16:02:47.814][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:47.815][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:47.817][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-21 16:02:47.818][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-21 16:02:47.819][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:47.821][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:47.822][ef$get] Asked field names are: accession.
biodb.TRACE[2026-02-21 16:02:47.823][ef$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-21 16:02:47.825][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:47.826][ef$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:47.827][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-21 16:02:47.828][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-21 16:02:47.830][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:47.831][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:47.843][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2026-02-21 16:02:47.845][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2026-02-21 16:02:47.846][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:47.848][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:47.849][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2026-02-21 16:02:47.850][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2026-02-21 16:02:47.851][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:47.853][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:47.854][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2026-02-21 16:02:47.855][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2026-02-21 16:02:47.856][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:47.858][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:47.859][ef$get] Asked field names are: cas.id.
biodb.TRACE[2026-02-21 16:02:47.860][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2026-02-21 16:02:47.862][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:47.863][ef$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:47.864][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2026-02-21 16:02:47.866][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2026-02-21 16:02:47.867][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:47.868][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:47.882][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-02-21 16:02:47.883][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-02-21 16:02:47.885][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:47.886][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:47.887][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-02-21 16:02:47.889][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-02-21 16:02:47.890][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:47.891][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:47.893][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-02-21 16:02:47.894][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-02-21 16:02:47.896][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:47.897][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:47.898][ef$get] Asked field names are: name.
biodb.TRACE[2026-02-21 16:02:47.900][ef$get] Realnames of fields are: name.
biodb.TRACE[2026-02-21 16:02:47.901][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:47.902][ef$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:47.903][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-02-21 16:02:47.905][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-02-21 16:02:47.906][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:47.907][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:47.919][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2026-02-21 16:02:47.921][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2026-02-21 16:02:47.922][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:47.923][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:47.925][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2026-02-21 16:02:47.926][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2026-02-21 16:02:47.927][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:47.928][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:47.929][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2026-02-21 16:02:47.931][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2026-02-21 16:02:47.932][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:47.933][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:47.935][ef$get] Asked field names are: formula.
biodb.TRACE[2026-02-21 16:02:47.936][ef$get] Realnames of fields are: formula.
biodb.TRACE[2026-02-21 16:02:47.937][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:47.938][ef$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:47.939][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2026-02-21 16:02:47.941][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2026-02-21 16:02:47.942][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:47.943][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:47.955][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2026-02-21 16:02:47.956][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2026-02-21 16:02:47.958][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:47.959][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:47.960][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2026-02-21 16:02:47.965][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2026-02-21 16:02:47.967][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:47.968][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:47.969][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2026-02-21 16:02:47.971][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2026-02-21 16:02:47.972][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:47.973][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:47.974][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2026-02-21 16:02:47.976][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2026-02-21 16:02:47.977][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:47.978][ef$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:47.979][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2026-02-21 16:02:47.981][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2026-02-21 16:02:47.982][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:47.983][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:47.994][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2026-02-21 16:02:47.996][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2026-02-21 16:02:47.997][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:47.998][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:48.000][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2026-02-21 16:02:48.001][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2026-02-21 16:02:48.002][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:48.004][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:48.005][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2026-02-21 16:02:48.006][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2026-02-21 16:02:48.007][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:48.009][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:48.010][ef$get] Asked field names are: inchi.
biodb.TRACE[2026-02-21 16:02:48.011][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2026-02-21 16:02:48.012][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:48.014][ef$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:48.015][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2026-02-21 16:02:48.016][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2026-02-21 16:02:48.017][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:48.018][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:48.030][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-02-21 16:02:48.032][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-02-21 16:02:48.033][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:48.034][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:48.035][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-02-21 16:02:48.037][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-02-21 16:02:48.038][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:48.039][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:48.040][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-02-21 16:02:48.042][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-02-21 16:02:48.043][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:48.044][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:48.045][ef$get] Asked field names are: inchikey.
biodb.TRACE[2026-02-21 16:02:48.047][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-02-21 16:02:48.048][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:48.049][ef$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:48.050][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-02-21 16:02:48.052][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-02-21 16:02:48.053][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:48.054][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:48.066][ef$get] Asked field names are: accession.
biodb.TRACE[2026-02-21 16:02:48.067][ef$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-21 16:02:48.068][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:48.070][ef$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:48.076][ef$get] Asked field names are: cas.id.
biodb.TRACE[2026-02-21 16:02:48.078][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2026-02-21 16:02:48.079][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:48.080][ef$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:48.087][ef$get] Asked field names are: formula.
biodb.TRACE[2026-02-21 16:02:48.088][ef$get] Realnames of fields are: formula.
biodb.TRACE[2026-02-21 16:02:48.089][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:48.090][ef$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:48.097][ef$get] Asked field names are: inchi.
biodb.TRACE[2026-02-21 16:02:48.098][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2026-02-21 16:02:48.099][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:48.101][ef$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:48.107][ef$get] Asked field names are: inchikey.
biodb.TRACE[2026-02-21 16:02:48.108][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-02-21 16:02:48.109][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:48.111][ef$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:48.117][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2026-02-21 16:02:48.119][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2026-02-21 16:02:48.120][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:48.121][ef$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:48.127][ef$get] Asked field names are: name.
biodb.TRACE[2026-02-21 16:02:48.129][ef$get] Realnames of fields are: name.
biodb.TRACE[2026-02-21 16:02:48.130][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:48.131][ef$get] fields variable is a list.
biodb.INFO [2026-02-21 16:02:48.142][biodb::testThat]
biodb.INFO [2026-02-21 16:02:48.143][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2026-02-21 16:02:48.145][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-02-21 16:02:48.146][biodb::testThat]
biodb.DEBUG[2026-02-21 16:02:48.149][private$loadEntries] Creating entries from ids [2]: "749674, 750690".
biodb.DEBUG[2026-02-21 16:02:48.153][conn$getEntryContent] Get NCI CACTUS entry content(s) for 2 id(s)...
biodb.DEBUG[2026-02-21 16:02:48.157][self$isDownloaded] Database nci.cactus has already been downloaded.
biodb.DEBUG[2026-02-21 16:02:48.202][self$isDownloaded] Database nci.cactus has already been downloaded.
biodb.INFO [2026-02-21 16:02:48.204][self$download] Extract whole database of nci.cactus.
biodb.INFO [2026-02-21 16:02:48.205][private$doExtractDownload] Extracting content of downloaded biodbNci, a library for connecting to the National Cancer Institute (USA) CACTUS Database....
Saving _problems/test_long_100_generic-38.R
biodb.INFO [2026-02-21 16:02:48.380][biodb::testThat]
biodb.INFO [2026-02-21 16:02:48.382][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2026-02-21 16:02:48.383][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-02-21 16:02:48.384][biodb::testThat]
biodb.INFO [2026-02-21 16:02:48.400][biodb::testThat]
biodb.INFO [2026-02-21 16:02:48.402][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2026-02-21 16:02:48.403][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-02-21 16:02:48.404][biodb::testThat]
biodb.WARN [2026-02-21 16:02:48.427][self$searchForEntries] This database is not searchable by field "name".
biodb.WARN [2026-02-21 16:02:48.453][self$searchForEntries] This database is not searchable by field "name".
biodb.INFO [2026-02-21 16:02:48.464][biodb::testThat]
biodb.INFO [2026-02-21 16:02:48.466][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2026-02-21 16:02:48.467][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-02-21 16:02:48.468][biodb::testThat]
biodb.DEBUG[2026-02-21 16:02:48.492][private$loadEntries] Creating entries from ids [1]: "749674".
biodb.DEBUG[2026-02-21 16:02:48.558][conn$getEntryContent] Get NCI CACTUS entry content(s) for 1 id(s)...
biodb.DEBUG[2026-02-21 16:02:48.560][self$isDownloaded] Database nci.cactus has already been downloaded.
biodb.DEBUG[2026-02-21 16:02:48.562][self$isDownloaded] Database nci.cactus has already been downloaded.
biodb.INFO [2026-02-21 16:02:48.564][self$download] Extract whole database of nci.cactus.
biodb.INFO [2026-02-21 16:02:48.587][private$doExtractDownload] Extracting content of downloaded biodbNci, a library for connecting to the National Cancer Institute (USA) CACTUS Database....
Saving _problems/test_long_100_generic-38.R
biodb.INFO [2026-02-21 16:02:48.661][biodb::testThat]
biodb.INFO [2026-02-21 16:02:48.663][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2026-02-21 16:02:48.664][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-02-21 16:02:48.665][biodb::testThat]
biodb.INFO [2026-02-21 16:02:48.675][biodb::testThat]
biodb.INFO [2026-02-21 16:02:48.677][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2026-02-21 16:02:48.678][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-02-21 16:02:48.679][biodb::testThat]
biodb.INFO [2026-02-21 16:02:48.689][biodb::testThat]
biodb.INFO [2026-02-21 16:02:48.691][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2026-02-21 16:02:48.692][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-02-21 16:02:48.693][biodb::testThat]
biodb.INFO [2026-02-21 16:02:48.703][biodb::testThat]
biodb.INFO [2026-02-21 16:02:48.704][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2026-02-21 16:02:48.705][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-02-21 16:02:48.706][biodb::testThat]
biodb.INFO [2026-02-21 16:02:48.715][biodb$terminate] Closing BiodbMain instance...
biodb.INFO [2026-02-21 16:02:48.717][self$deleteConn] Connector "nci.cactus" deleted.
biodb.DEBUG[2026-02-21 16:02:48.718][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2026-02-21 16:02:48.720][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-21 16:02:48.721][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-21 16:02:48.722][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-21 16:02:48.723][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-21 16:02:48.724][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:48.726][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2026-02-21 16:02:48.739][biodb::testContext]
biodb.INFO [2026-02-21 16:02:48.741][biodb::testContext] ********************************************************************************
biodb.INFO [2026-02-21 16:02:48.742][biodb::testContext] Test context - Example long tests
biodb.INFO [2026-02-21 16:02:48.743][biodb::testContext] ********************************************************************************
biodb.INFO [2026-02-21 16:02:48.745][biodb::testContext]
biodb.INFO [2026-02-21 16:02:48.747][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.18.0.
biodb.DEBUG[2026-02-21 16:02:48.749][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2026-02-21 16:02:48.754][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2026-02-21 16:02:48.756][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2026-02-21 16:02:48.757][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2026-02-21 16:02:48.758][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:48.759][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:48.761][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-21 16:02:48.762][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2026-02-21 16:02:48.763][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2026-02-21 16:02:48.765][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:48.766][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:48.767][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-21 16:02:48.768][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2026-02-21 16:02:48.770][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2026-02-21 16:02:48.771][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:48.772][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:48.773][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:02:48.774][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2026-02-21 16:02:48.776][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2026-02-21 16:02:48.777][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2026-02-21 16:02:48.778][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:48.779][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:48.780][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-21 16:02:48.781][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2026-02-21 16:02:48.783][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2026-02-21 16:02:48.789][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2026-02-21 16:02:48.790][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:48.791][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:48.792][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-21 16:02:48.794][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2026-02-21 16:02:48.795][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2026-02-21 16:02:48.796][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:48.797][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:48.798][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-21 16:02:48.799][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2026-02-21 16:02:48.801][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2026-02-21 16:02:48.802][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2026-02-21 16:02:48.803][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:48.804][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:48.805][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:02:48.807][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2026-02-21 16:02:48.808][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2026-02-21 16:02:48.809][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:48.810][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:48.811][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-21 16:02:48.813][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2026-02-21 16:02:48.814][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2026-02-21 16:02:48.815][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2026-02-21 16:02:48.816][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:48.817][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:48.819][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:02:48.820][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2026-02-21 16:02:48.821][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2026-02-21 16:02:48.822][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2026-02-21 16:02:48.824][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2026-02-21 16:02:48.825][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2026-02-21 16:02:48.826][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2026-02-21 16:02:48.827][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:48.829][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:48.830][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-21 16:02:48.831][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2026-02-21 16:02:48.832][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2026-02-21 16:02:48.833][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:48.834][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:48.836][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:02:48.837][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2026-02-21 16:02:48.838][self$set] Set key entries.sep to "|".
biodb.DEBUG[2026-02-21 16:02:48.840][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:48.841][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:48.842][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-21 16:02:48.843][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2026-02-21 16:02:48.845][self$set] Set key offline to FALSE.
biodb.DEBUG[2026-02-21 16:02:48.846][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:48.847][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:48.848][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 16:02:48.849][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2026-02-21 16:02:48.851][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2026-02-21 16:02:48.852][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2026-02-21 16:02:48.853][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:48.854][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:48.855][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-21 16:02:48.857][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2026-02-21 16:02:48.858][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2026-02-21 16:02:48.868][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2026-02-21 16:02:48.869][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:48.871][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:48.872][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 16:02:48.873][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2026-02-21 16:02:48.874][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2026-02-21 16:02:48.875][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2026-02-21 16:02:48.877][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:48.878][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:48.879][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-21 16:02:48.880][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2026-02-21 16:02:48.883][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2026-02-21 16:02:48.884][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2026-02-21 16:02:48.885][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-02-21 16:02:48.887][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-02-21 16:02:48.888][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-02-21 16:02:48.889][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-02-21 16:02:48.891][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2026-02-21 16:02:48.892][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-02-21 16:02:48.893][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2026-02-21 16:02:48.894][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-02-21 16:02:48.896][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2026-02-21 16:02:48.897][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2026-02-21 16:02:48.899][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-02-21 16:02:48.900][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2026-02-21 16:02:48.901][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2026-02-21 16:02:48.902][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2026-02-21 16:02:48.902][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2026-02-21 16:02:48.902][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2026-02-21 16:02:48.902][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2026-02-21 16:02:48.902][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2026-02-21 16:02:48.904][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2026-02-21 16:02:48.905][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-02-21 16:02:48.906][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-02-21 16:02:48.907][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-02-21 16:02:48.908][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-02-21 16:02:48.910][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-02-21 16:02:48.911][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-02-21 16:02:48.912][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2026-02-21 16:02:48.913][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-02-21 16:02:48.914][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-02-21 16:02:48.915][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2026-02-21 16:02:48.917][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-02-21 16:02:48.918][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2026-02-21 16:02:48.920][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2026-02-21 16:02:48.922][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2026-02-21 16:02:48.923][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-02-21 16:02:48.924][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-02-21 16:02:48.925][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-02-21 16:02:48.927][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-02-21 16:02:48.928][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2026-02-21 16:02:48.929][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-02-21 16:02:48.930][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2026-02-21 16:02:48.932][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-02-21 16:02:48.933][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2026-02-21 16:02:48.934][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2026-02-21 16:02:48.935][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-02-21 16:02:48.937][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2026-02-21 16:02:48.938][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2026-02-21 16:02:48.939][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2026-02-21 16:02:48.939][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2026-02-21 16:02:48.939][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2026-02-21 16:02:48.939][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2026-02-21 16:02:48.939][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2026-02-21 16:02:48.940][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2026-02-21 16:02:48.942][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-02-21 16:02:48.943][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-02-21 16:02:48.944][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-02-21 16:02:48.945][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-02-21 16:02:48.946][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-02-21 16:02:48.947][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-02-21 16:02:48.949][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2026-02-21 16:02:48.950][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-02-21 16:02:48.951][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-02-21 16:02:48.952][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2026-02-21 16:02:48.953][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-02-21 16:02:48.955][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2026-02-21 16:02:48.957][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2026-02-21 16:02:48.958][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2026-02-21 16:02:48.959][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-02-21 16:02:48.961][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-02-21 16:02:48.962][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-02-21 16:02:48.963][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-02-21 16:02:48.964][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2026-02-21 16:02:48.966][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-02-21 16:02:48.967][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2026-02-21 16:02:48.968][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-02-21 16:02:48.970][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2026-02-21 16:02:48.971][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2026-02-21 16:02:48.972][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-02-21 16:02:48.973][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2026-02-21 16:02:48.974][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2026-02-21 16:02:48.976][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2026-02-21 16:02:48.977][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2026-02-21 16:02:48.978][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-02-21 16:02:48.979][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-02-21 16:02:48.980][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-02-21 16:02:48.982][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-02-21 16:02:48.983][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-02-21 16:02:48.984][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-02-21 16:02:48.985][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2026-02-21 16:02:48.986][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-02-21 16:02:48.988][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-02-21 16:02:48.989][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2026-02-21 16:02:48.990][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-02-21 16:02:48.996][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2026-02-21 16:02:48.998][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2026-02-21 16:02:48.999][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2026-02-21 16:02:49.001][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-02-21 16:02:49.002][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-02-21 16:02:49.003][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-02-21 16:02:49.004][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-02-21 16:02:49.006][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2026-02-21 16:02:49.007][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-02-21 16:02:49.008][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2026-02-21 16:02:49.009][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-02-21 16:02:49.011][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2026-02-21 16:02:49.012][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2026-02-21 16:02:49.013][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-02-21 16:02:49.014][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2026-02-21 16:02:49.016][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2026-02-21 16:02:49.017][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2026-02-21 16:02:49.018][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2026-02-21 16:02:49.019][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-02-21 16:02:49.020][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-02-21 16:02:49.022][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-02-21 16:02:49.023][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-02-21 16:02:49.024][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-02-21 16:02:49.025][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-02-21 16:02:49.026][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2026-02-21 16:02:49.028][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-02-21 16:02:49.029][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-02-21 16:02:49.030][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2026-02-21 16:02:49.032][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-02-21 16:02:49.033][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2026-02-21 16:02:49.035][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:49.036][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:02:49.037][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:49.038][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-21 16:02:49.039][FUN] 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 16:02:49.040][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:49.042][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-21 16:02:49.043][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:49.044][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-21 16:02:49.045][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-21 16:02:49.046][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:49.047][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:02:49.048][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:49.049][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-21 16:02:49.051][FUN] 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 16:02:49.052][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:49.053][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-21 16:02:49.054][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:49.055][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-21 16:02:49.056][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-21 16:02:49.057][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:49.059][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-21 16:02:49.060][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:49.061][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-21 16:02:49.062][FUN] 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 16:02:49.063][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:49.064][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:02:49.065][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:49.066][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-21 16:02:49.067][FUN] 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 16:02:49.069][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:49.070][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:02:49.071][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:49.072][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-21 16:02:49.073][FUN] 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 16:02:49.074][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:49.075][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:02:49.077][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:49.078][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-21 16:02:49.079][FUN] 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 16:02:49.080][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:49.081][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:02:49.082][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:49.083][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-21 16:02:49.085][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-21 16:02:49.086][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:49.087][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:02:49.088][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:49.089][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-21 16:02:49.091][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-21 16:02:49.092][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:49.093][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-21 16:02:49.094][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:49.095][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-21 16:02:49.097][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-21 16:02:49.098][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:49.099][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-21 16:02:49.100][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:49.101][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-21 16:02:49.102][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-21 16:02:49.103][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:49.104][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:02:49.105][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:49.107][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-21 16:02:49.108][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-21 16:02:49.109][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:49.110][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-21 16:02:49.111][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:49.112][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-21 16:02:49.114][FUN] 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 16:02:49.115][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:49.116][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-21 16:02:49.117][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:49.118][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-21 16:02:49.120][FUN] 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 16:02:49.121][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:49.122][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:02:49.123][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:49.124][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-21 16:02:49.125][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-21 16:02:49.127][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:49.128][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:02:49.129][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2026-02-21 16:02:49.131][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2026-02-21 16:02:49.133][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2026-02-21 16:02:49.135][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2026-02-21 16:02:49.137][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2026-02-21 16:02:49.139][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2026-02-21 16:02:49.140][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2026-02-21 16:02:49.142][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2026-02-21 16:02:49.144][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2026-02-21 16:02:49.146][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2026-02-21 16:02:49.147][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2026-02-21 16:02:49.149][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2026-02-21 16:02:49.151][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2026-02-21 16:02:49.153][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2026-02-21 16:02:49.154][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2026-02-21 16:02:49.156][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2026-02-21 16:02:49.158][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2026-02-21 16:02:49.160][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2026-02-21 16:02:49.161][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2026-02-21 16:02:49.163][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2026-02-21 16:02:49.165][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2026-02-21 16:02:49.167][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2026-02-21 16:02:49.169][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2026-02-21 16:02:49.170][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2026-02-21 16:02:49.172][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2026-02-21 16:02:49.174][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2026-02-21 16:02:49.175][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2026-02-21 16:02:49.177][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2026-02-21 16:02:49.179][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2026-02-21 16:02:49.180][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2026-02-21 16:02:49.182][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2026-02-21 16:02:49.184][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2026-02-21 16:02:49.186][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2026-02-21 16:02:49.191][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2026-02-21 16:02:49.193][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2026-02-21 16:02:49.195][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2026-02-21 16:02:49.197][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2026-02-21 16:02:49.198][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2026-02-21 16:02:49.200][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2026-02-21 16:02:49.202][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2026-02-21 16:02:49.203][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2026-02-21 16:02:49.205][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2026-02-21 16:02:49.207][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2026-02-21 16:02:49.208][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2026-02-21 16:02:49.210][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2026-02-21 16:02:49.212][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2026-02-21 16:02:49.213][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2026-02-21 16:02:49.215][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2026-02-21 16:02:49.217][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2026-02-21 16:02:49.219][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2026-02-21 16:02:49.220][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2026-02-21 16:02:49.222][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2026-02-21 16:02:49.224][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2026-02-21 16:02:49.226][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2026-02-21 16:02:49.227][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2026-02-21 16:02:49.229][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2026-02-21 16:02:49.231][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2026-02-21 16:02:49.233][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2026-02-21 16:02:49.234][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2026-02-21 16:02:49.236][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2026-02-21 16:02:49.238][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2026-02-21 16:02:49.240][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2026-02-21 16:02:49.241][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2026-02-21 16:02:49.243][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2026-02-21 16:02:49.245][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2026-02-21 16:02:49.247][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2026-02-21 16:02:49.249][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2026-02-21 16:02:49.250][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2026-02-21 16:02:49.252][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2026-02-21 16:02:49.254][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2026-02-21 16:02:49.255][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2026-02-21 16:02:49.257][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2026-02-21 16:02:49.259][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2026-02-21 16:02:49.261][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2026-02-21 16:02:49.262][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2026-02-21 16:02:49.264][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2026-02-21 16:02:49.266][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2026-02-21 16:02:49.267][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2026-02-21 16:02:49.269][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2026-02-21 16:02:49.271][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2026-02-21 16:02:49.273][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2026-02-21 16:02:49.274][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2026-02-21 16:02:49.276][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2026-02-21 16:02:49.278][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2026-02-21 16:02:49.280][initialize] This is biodb version 1.18.0.
biodb.DEBUG[2026-02-21 16:02:49.281][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2026-02-21 16:02:49.282][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2026-02-21 16:02:49.283][FUN] 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 16:02:49.284][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:49.286][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-21 16:02:49.287][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:49.288][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-21 16:02:49.289][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-21 16:02:49.290][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-21 16:02:49.291][FUN] 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 16:02:49.292][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:49.294][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-21 16:02:49.295][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:49.296][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-21 16:02:49.297][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-21 16:02:49.298][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-21 16:02:49.299][FUN] 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 16:02:49.300][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:49.301][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:02:49.303][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:49.304][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-21 16:02:49.305][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-21 16:02:49.306][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-21 16:02:49.307][FUN] 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 16:02:49.308][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:49.309][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-21 16:02:49.311][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:49.312][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-21 16:02:49.313][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-21 16:02:49.314][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-21 16:02:49.315][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-21 16:02:49.316][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:49.317][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:02:49.319][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:49.320][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-21 16:02:49.321][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-21 16:02:49.322][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-21 16:02:49.323][FUN] 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 16:02:49.324][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:49.325][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:02:49.326][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:49.328][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-21 16:02:49.329][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-21 16:02:49.330][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-21 16:02:49.331][FUN] 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 16:02:49.332][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:49.333][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:02:49.334][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:49.336][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-21 16:02:49.337][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-21 16:02:49.338][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-21 16:02:49.339][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-21 16:02:49.340][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:49.341][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-21 16:02:49.343][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:49.344][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-21 16:02:49.345][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-21 16:02:49.346][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-21 16:02:49.347][FUN] 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 16:02:49.348][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:49.349][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:02:49.351][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:49.352][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-21 16:02:49.353][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-21 16:02:49.354][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-21 16:02:49.355][FUN] 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 16:02:49.356][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:49.357][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:02:49.358][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:49.360][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-21 16:02:49.361][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-21 16:02:49.362][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-21 16:02:49.363][FUN] 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 16:02:49.364][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:49.365][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 16:02:49.366][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:49.368][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-21 16:02:49.369][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-21 16:02:49.370][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-21 16:02:49.371][FUN] 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 16:02:49.372][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:49.373][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:02:49.374][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:49.376][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-21 16:02:49.377][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-21 16:02:49.378][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-21 16:02:49.379][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-21 16:02:49.385][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:49.386][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-21 16:02:49.387][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:49.388][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-21 16:02:49.389][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-21 16:02:49.390][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-21 16:02:49.391][FUN] 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 16:02:49.392][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:49.393][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 16:02:49.395][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:49.396][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-21 16:02:49.397][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-21 16:02:49.398][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-21 16:02:49.399][FUN] 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 16:02:49.400][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:49.401][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 16:02:49.402][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:49.403][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-21 16:02:49.405][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-21 16:02:49.406][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-21 16:02:49.407][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-21 16:02:49.408][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:49.409][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-21 16:02:49.410][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:49.411][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-21 16:02:49.412][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-21 16:02:49.413][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-21 16:02:49.415][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-21 16:02:49.416][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:49.417][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-21 16:02:49.419][biodb$loadDefinitions] Load definitions from file "/Users/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNci.Rcheck/biodbNci/definitions.yml".
biodb.DEBUG[2026-02-21 16:02:49.421][self$getDbsInfo()$define] Define connector nci.cactus.
biodb.DEBUG[2026-02-21 16:02:49.424][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2026-02-21 16:02:49.425][self$setPropertyValue] Setting property "description" to "National Cancer Institute (USA) CACTUS Database.".
biodb.DEBUG[2026-02-21 16:02:49.426][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-02-21 16:02:49.427][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-02-21 16:02:49.429][self$setPropertyValue] Setting property "downloadable" to "TRUE".
biodb.DEBUG[2026-02-21 16:02:49.430][self$setPropertyValue] Setting property "dwnld.ext" to "gz".
biodb.DEBUG[2026-02-21 16:02:49.431][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2026-02-21 16:02:49.432][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-02-21 16:02:49.434][self$setPropertyValue] Setting property "entry.content.type" to "sdf".
biodb.DEBUG[2026-02-21 16:02:49.435][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-02-21 16:02:49.436][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2026-02-21 16:02:49.437][self$setPropertyValue] Setting property "name" to "NCI CACTUS".
biodb.DEBUG[2026-02-21 16:02:49.439][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-02-21 16:02:49.440][self$setPropertyValue] Setting property "parsing.expr" to "NSC".
biodb.DEBUG[2026-02-21 16:02:49.440][self$setPropertyValue] Setting property "parsing.expr" to "DTP names".
biodb.DEBUG[2026-02-21 16:02:49.440][self$setPropertyValue] Setting property "parsing.expr" to "Standard InChI".
biodb.DEBUG[2026-02-21 16:02:49.440][self$setPropertyValue] Setting property "parsing.expr" to "c("Standard InChIKey", "^InChIKey=(.*)$")".
biodb.DEBUG[2026-02-21 16:02:49.440][self$setPropertyValue] Setting property "parsing.expr" to "Formula".
biodb.DEBUG[2026-02-21 16:02:49.440][self$setPropertyValue] Setting property "parsing.expr" to "Molecular Weight".
biodb.DEBUG[2026-02-21 16:02:49.440][self$setPropertyValue] Setting property "parsing.expr" to "CAS".
biodb.DEBUG[2026-02-21 16:02:49.441][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2026-02-21 16:02:49.443][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2026-02-21 16:02:49.444][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2026-02-21 16:02:49.445][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-02-21 16:02:49.446][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-02-21 16:02:49.448][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-02-21 16:02:49.449][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-02-21 16:02:49.450][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-02-21 16:02:49.451][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-02-21 16:02:49.452][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/".
biodb.DEBUG[2026-02-21 16:02:49.452][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/".
biodb.DEBUG[2026-02-21 16:02:49.452][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/download/nci/".
biodb.DEBUG[2026-02-21 16:02:49.452][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/download/nci/NCI-Open_2012-05-01.sdf.gz".
biodb.DEBUG[2026-02-21 16:02:49.454][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-02-21 16:02:49.455][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-02-21 16:02:49.456][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2026-02-21 16:02:49.457][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-02-21 16:02:49.459][self$getEntryFields()$define] Define field nci.cactus.id.
biodb.DEBUG[2026-02-21 16:02:49.463][super$initialize] Initialize connector nci.cactus.
biodb.DEBUG[2026-02-21 16:02:49.467][biodb$getFactory()$createConn] Creating new connector nci.cactus for database class nci.cactus .
biodb.INFO [2026-02-21 16:02:49.468][biodb$terminate] Closing BiodbMain instance...
biodb.INFO [2026-02-21 16:02:49.470][self$deleteConn] Connector "nci.cactus" deleted.
biodb.DEBUG[2026-02-21 16:02:49.471][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2026-02-21 16:02:49.472][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-21 16:02:49.473][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-21 16:02:49.474][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-21 16:02:49.475][FUN] 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 16:02:49.476][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:49.478][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
[ FAIL 2 | WARN 0 | SKIP 2 | PASS 85 ]

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

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

[ FAIL 2 | WARN 0 | SKIP 2 | PASS 85 ]
Error:
! Test failures.
Execution halted

'R CMD check' output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --test-dir=longtests --no-stop-on-test-error --no-codoc --no-examples --no-manual --ignore-vignettes --check-subdirs=no biodbNci_1.14.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNci.Rcheck’
* using R version 4.5.2 (2025-10-31)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using options ‘--no-codoc --no-examples --no-manual --ignore-vignettes --no-stop-on-test-error’
* checking for file ‘biodbNci/DESCRIPTION’ ... OK
* this is package ‘biodbNci’ version ‘1.14.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘biodbNci’ can be installed ... OK
* used C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
* used SDK: ‘MacOSX11.3.1.sdk’
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking whether startup messages can be suppressed ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  NciCactusConn.Rd: BiodbConn
  NciCactusEntry.Rd: BiodbSdfEntry
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... SKIPPED
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... OK
* checking files in ‘vignettes’ ... SKIPPED
* checking examples ... SKIPPED
* checking for unstated dependencies in ‘longtests’ ... OK
* checking tests in ‘longtests’ ...
  Running ‘testthat.R’
 ERROR
Running the tests in ‘longtests/testthat.R’ failed.
Last 13 lines of output:
      ▆
   1. ├─base::do.call(fct, params)
   2. └─biodb (local) `<fn>`(conn = `<NcCctsCn>`, opt = `<named list>`)
   3.   └─opt$refEntries$getRealEntry(id)
   4.     └─self$getRealEntries(ids = id)
   5.       └─private$bdb$getFactory()$getEntry(...)
   6.         └─private$loadEntries(conn$getId(), missing.ids, drop = FALSE)
   7.           └─conn$getEntryContent(ids)
   8.             └─self$download()
   9.               └─private$doExtractDownload()
  
  [ FAIL 2 | WARN 0 | SKIP 2 | PASS 85 ]
  Error:
  ! Test failures.
  Execution halted
* DONE

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

Installation output

biodbNci.Rcheck/00install.out

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