Back to Long Tests report for BioC 3.22

This page was generated on 2025-09-27 23:55 -0400 (Sat, 27 Sep 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" 4832
lconwaymacOS 12.7.1 Montereyx86_644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4620
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 8/29HostnameOS / ArchCHECK
biodbNci 1.13.1  (landing page)
Pierrick Roger
Snapshot Date: 2025-09-27 09:55 -0400 (Sat, 27 Sep 2025)
git_url: https://git.bioconductor.org/packages/biodbNci
git_branch: devel
git_last_commit: 658b5cb
git_last_commit_date: 2025-07-24 10:46:27 -0400 (Thu, 24 Jul 2025)
nebbiolo2Linux (Ubuntu 24.04.3 LTS) / x86_64  ERROR  
lconwaymacOS 12.7.1 Monterey / x86_64  ERROR  

CHECK results for biodbNci on nebbiolo2

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

raw results


Summary

Package: biodbNci
Version: 1.13.1
Command: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --test-dir=longtests --no-stop-on-test-error --no-codoc --no-examples --no-manual --ignore-vignettes --check-subdirs=no biodbNci_1.13.1.tar.gz
StartedAt: 2025-09-27 16:02:34 -0400 (Sat, 27 Sep 2025)
EndedAt: 2025-09-27 16:03:37 -0400 (Sat, 27 Sep 2025)
EllapsedTime: 63.0 seconds
RetCode: 1
Status:   ERROR  
CheckDir: biodbNci.Rcheck
Warnings: NA

Tests output

biodbNci.Rcheck/tests/testthat.Rout.fail


R version 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

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> # Script needed to run testthat automatically from ‘R CMD check’. See
> # testthat::test_dir documentation.
> library(testthat)
> library(biodbNci)
Warning message:
In fun(libname, pkgname) :
  Package 'biodbNci' is deprecated and will be removed from Bioconductor
  version 3.23
> Sys.setenv(TESTTHAT_REPORTER="summary")
> Sys.setenv(BIODB_LOG_DST="console")
> test_check("biodbNci")
biodb.INFO [2025-09-27 16:03:33.807][biodb::testContext]
biodb.INFO [2025-09-27 16:03:33.809][biodb::testContext] ********************************************************************************
biodb.INFO [2025-09-27 16:03:33.809][biodb::testContext] Test context - Generic long tests
biodb.INFO [2025-09-27 16:03:33.810][biodb::testContext] ********************************************************************************
biodb.INFO [2025-09-27 16:03:33.811][biodb::testContext]
biodb.INFO [2025-09-27 16:03:33.818][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.17.2.
biodb.DEBUG[2025-09-27 16:03:33.819][self$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.22-bioc/R/site-library/biodb/definitions.yml".
biodb.DEBUG[2025-09-27 16:03:33.826][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-09-27 16:03:33.827][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-09-27 16:03:33.828][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-09-27 16:03:33.829][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-27 16:03:33.830][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-27 16:03:33.831][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-27 16:03:33.832][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-09-27 16:03:33.849][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-09-27 16:03:33.850][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-27 16:03:33.851][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-27 16:03:33.852][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-27 16:03:33.853][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-09-27 16:03:33.854][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-09-27 16:03:33.855][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-27 16:03:33.855][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-27 16:03:33.865][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-27 16:03:33.866][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-09-27 16:03:33.867][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-09-27 16:03:33.868][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-09-27 16:03:33.868][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-27 16:03:33.869][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-27 16:03:33.870][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-27 16:03:33.871][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-09-27 16:03:33.872][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-09-27 16:03:33.873][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-09-27 16:03:33.874][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-27 16:03:33.874][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-27 16:03:33.875][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-27 16:03:33.876][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-09-27 16:03:33.877][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-09-27 16:03:33.878][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-27 16:03:33.879][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-27 16:03:33.880][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-27 16:03:33.881][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-09-27 16:03:33.881][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-09-27 16:03:33.882][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-09-27 16:03:33.883][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-27 16:03:33.884][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-27 16:03:33.885][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-27 16:03:33.886][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-09-27 16:03:33.887][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-09-27 16:03:33.888][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-27 16:03:33.888][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-27 16:03:33.889][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-27 16:03:33.890][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-09-27 16:03:33.891][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-09-27 16:03:33.892][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-09-27 16:03:33.893][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-27 16:03:33.894][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-27 16:03:33.894][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-27 16:03:33.895][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-09-27 16:03:33.896][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-09-27 16:03:33.897][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-09-27 16:03:33.898][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-09-27 16:03:33.899][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-09-27 16:03:33.900][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-09-27 16:03:33.901][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-27 16:03:33.902][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-27 16:03:33.902][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-27 16:03:33.903][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-09-27 16:03:33.904][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-09-27 16:03:33.905][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-27 16:03:33.906][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-27 16:03:33.907][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-27 16:03:33.908][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-09-27 16:03:33.909][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-09-27 16:03:33.909][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-27 16:03:33.910][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-27 16:03:33.911][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-27 16:03:33.912][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-09-27 16:03:33.913][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-09-27 16:03:33.914][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-27 16:03:33.914][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-27 16:03:33.915][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-27 16:03:33.916][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-09-27 16:03:33.917][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-09-27 16:03:33.918][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-09-27 16:03:33.919][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-27 16:03:33.920][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-27 16:03:33.921][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-27 16:03:33.921][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-09-27 16:03:33.922][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-09-27 16:03:33.926][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-09-27 16:03:33.927][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-27 16:03:33.928][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-27 16:03:33.928][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-27 16:03:33.930][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-09-27 16:03:33.930][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-09-27 16:03:33.931][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-09-27 16:03:33.932][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-27 16:03:33.933][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-27 16:03:33.934][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-27 16:03:33.937][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-09-27 16:03:33.967][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-09-27 16:03:33.982][self$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[2025-09-27 16:03:33.983][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-09-27 16:03:33.984][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-09-27 16:03:33.985][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-09-27 16:03:33.985][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-09-27 16:03:33.986][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-09-27 16:03:33.987][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-09-27 16:03:33.988][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-09-27 16:03:33.989][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-09-27 16:03:33.990][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-09-27 16:03:33.991][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-09-27 16:03:33.992][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-09-27 16:03:33.993][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-09-27 16:03:33.994][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-09-27 16:03:33.995][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-09-27 16:03:33.995][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-09-27 16:03:33.995][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-09-27 16:03:33.995][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-09-27 16:03:33.995][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-09-27 16:03:33.996][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-09-27 16:03:33.996][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-09-27 16:03:33.997][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-09-27 16:03:33.998][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-09-27 16:03:33.999][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-09-27 16:03:34.000][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-09-27 16:03:34.001][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-09-27 16:03:34.002][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-09-27 16:03:34.003][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-09-27 16:03:34.003][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-09-27 16:03:34.004][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-09-27 16:03:34.005][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-09-27 16:03:34.006][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-09-27 16:03:34.008][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-09-27 16:03:34.009][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-09-27 16:03:34.010][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-09-27 16:03:34.011][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-09-27 16:03:34.011][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-09-27 16:03:34.012][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-09-27 16:03:34.017][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-09-27 16:03:34.018][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-09-27 16:03:34.019][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-09-27 16:03:34.020][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-09-27 16:03:34.021][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-09-27 16:03:34.022][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-09-27 16:03:34.023][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-09-27 16:03:34.024][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-09-27 16:03:34.025][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-09-27 16:03:34.025][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-09-27 16:03:34.025][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-09-27 16:03:34.025][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-09-27 16:03:34.025][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-09-27 16:03:34.025][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-09-27 16:03:34.026][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-09-27 16:03:34.027][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-09-27 16:03:34.028][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-09-27 16:03:34.029][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-09-27 16:03:34.030][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-09-27 16:03:34.031][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-09-27 16:03:34.032][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-09-27 16:03:34.032][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-09-27 16:03:34.033][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-09-27 16:03:34.034][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-09-27 16:03:34.035][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-09-27 16:03:34.036][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-09-27 16:03:34.037][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-09-27 16:03:34.039][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-09-27 16:03:34.040][self$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[2025-09-27 16:03:34.041][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-09-27 16:03:34.041][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-09-27 16:03:34.042][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-09-27 16:03:34.043][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-09-27 16:03:34.044][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-09-27 16:03:34.045][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-09-27 16:03:34.046][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-09-27 16:03:34.047][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-09-27 16:03:34.048][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-09-27 16:03:34.049][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-09-27 16:03:34.050][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-09-27 16:03:34.051][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-09-27 16:03:34.051][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-09-27 16:03:34.052][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-09-27 16:03:34.053][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-09-27 16:03:34.054][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-09-27 16:03:34.055][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-09-27 16:03:34.056][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-09-27 16:03:34.057][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-09-27 16:03:34.058][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-09-27 16:03:34.058][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-09-27 16:03:34.059][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-09-27 16:03:34.060][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-09-27 16:03:34.061][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-09-27 16:03:34.062][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-09-27 16:03:34.063][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-09-27 16:03:34.064][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-09-27 16:03:34.066][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-09-27 16:03:34.066][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-09-27 16:03:34.067][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-09-27 16:03:34.068][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-09-27 16:03:34.069][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-09-27 16:03:34.070][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-09-27 16:03:34.071][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-09-27 16:03:34.072][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-09-27 16:03:34.073][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-09-27 16:03:34.074][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-09-27 16:03:34.075][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-09-27 16:03:34.076][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-09-27 16:03:34.077][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-09-27 16:03:34.077][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-09-27 16:03:34.078][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-09-27 16:03:34.079][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-09-27 16:03:34.080][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-09-27 16:03:34.081][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-09-27 16:03:34.082][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-09-27 16:03:34.083][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-09-27 16:03:34.084][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-09-27 16:03:34.084][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-09-27 16:03:34.085][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-09-27 16:03:34.086][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-09-27 16:03:34.087][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-09-27 16:03:34.088][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-09-27 16:03:34.089][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-09-27 16:03:34.090][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-09-27 16:03:34.093][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-09-27 16:03:34.094][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-09-27 16:03:34.095][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-27 16:03:34.096][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-27 16:03:34.096][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-27 16:03:34.097][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-27 16:03:34.098][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-27 16:03:34.099][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[2025-09-27 16:03:34.100][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-27 16:03:34.101][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-27 16:03:34.101][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-27 16:03:34.102][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-27 16:03:34.103][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-27 16:03:34.104][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-27 16:03:34.105][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-27 16:03:34.105][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-27 16:03:34.106][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-27 16:03:34.107][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-27 16:03:34.108][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-27 16:03:34.109][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-27 16:03:34.110][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-27 16:03:34.110][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-27 16:03:34.111][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-27 16:03:34.112][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-27 16:03:34.113][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-27 16:03:34.114][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-27 16:03:34.114][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-27 16:03:34.115][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-27 16:03:34.116][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-27 16:03:34.117][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-27 16:03:34.118][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-27 16:03:34.119][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-27 16:03:34.119][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-27 16:03:34.120][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-27 16:03:34.121][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-27 16:03:34.122][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-27 16:03:34.123][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-27 16:03:34.124][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-27 16:03:34.124][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-27 16:03:34.125][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-27 16:03:34.126][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-27 16:03:34.127][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-27 16:03:34.128][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[2025-09-27 16:03:34.128][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-27 16:03:34.129][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-27 16:03:34.130][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-27 16:03:34.131][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-27 16:03:34.132][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-27 16:03:34.133][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-27 16:03:34.133][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-27 16:03:34.134][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-27 16:03:34.135][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-27 16:03:34.136][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-27 16:03:34.137][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-27 16:03:34.137][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-27 16:03:34.138][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-27 16:03:34.139][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-27 16:03:34.140][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-27 16:03:34.141][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-27 16:03:34.142][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-27 16:03:34.142][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-27 16:03:34.143][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-27 16:03:34.144][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-27 16:03:34.145][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-27 16:03:34.146][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-27 16:03:34.146][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-27 16:03:34.147][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-27 16:03:34.148][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-27 16:03:34.149][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-27 16:03:34.150][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-27 16:03:34.151][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-27 16:03:34.151][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-27 16:03:34.152][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-27 16:03:34.153][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-27 16:03:34.154][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-27 16:03:34.155][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-27 16:03:34.155][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-27 16:03:34.156][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-27 16:03:34.157][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-27 16:03:34.158][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-27 16:03:34.159][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-27 16:03:34.160][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-27 16:03:34.160][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-27 16:03:34.161][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-09-27 16:03:34.166][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-09-27 16:03:34.171][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-09-27 16:03:34.172][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-09-27 16:03:34.173][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-09-27 16:03:34.174][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-09-27 16:03:34.176][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-09-27 16:03:34.177][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-09-27 16:03:34.178][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-09-27 16:03:34.180][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-09-27 16:03:34.181][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-09-27 16:03:34.182][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-09-27 16:03:34.183][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-09-27 16:03:34.185][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-09-27 16:03:34.186][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-09-27 16:03:34.187][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-09-27 16:03:34.188][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-09-27 16:03:34.190][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-09-27 16:03:34.191][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-09-27 16:03:34.192][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-09-27 16:03:34.194][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-09-27 16:03:34.195][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-09-27 16:03:34.196][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-09-27 16:03:34.197][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-09-27 16:03:34.199][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-09-27 16:03:34.200][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-09-27 16:03:34.201][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-09-27 16:03:34.203][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-09-27 16:03:34.204][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-09-27 16:03:34.205][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-09-27 16:03:34.206][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-09-27 16:03:34.208][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-09-27 16:03:34.209][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-09-27 16:03:34.210][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-09-27 16:03:34.212][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-09-27 16:03:34.213][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-09-27 16:03:34.214][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-09-27 16:03:34.215][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-09-27 16:03:34.217][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-09-27 16:03:34.218][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-09-27 16:03:34.219][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-09-27 16:03:34.220][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-09-27 16:03:34.222][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-09-27 16:03:34.223][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-09-27 16:03:34.224][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-09-27 16:03:34.226][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-09-27 16:03:34.227][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-09-27 16:03:34.228][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-09-27 16:03:34.229][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-09-27 16:03:34.231][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-09-27 16:03:34.232][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-09-27 16:03:34.233][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-09-27 16:03:34.235][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-09-27 16:03:34.236][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-09-27 16:03:34.237][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-09-27 16:03:34.238][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-09-27 16:03:34.240][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-09-27 16:03:34.241][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-09-27 16:03:34.242][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-09-27 16:03:34.243][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-09-27 16:03:34.245][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-09-27 16:03:34.246][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-09-27 16:03:34.247][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-09-27 16:03:34.249][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-09-27 16:03:34.250][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-09-27 16:03:34.251][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-09-27 16:03:34.252][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-09-27 16:03:34.254][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-09-27 16:03:34.255][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-09-27 16:03:34.256][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-09-27 16:03:34.257][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-09-27 16:03:34.259][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-09-27 16:03:34.260][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-09-27 16:03:34.261][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-09-27 16:03:34.263][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-09-27 16:03:34.264][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-09-27 16:03:34.265][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-09-27 16:03:34.266][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-09-27 16:03:34.268][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-09-27 16:03:34.269][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-09-27 16:03:34.270][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-09-27 16:03:34.272][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-09-27 16:03:34.273][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-09-27 16:03:34.287][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-09-27 16:03:34.289][initialize] This is biodb version 1.17.2.
biodb.DEBUG[2025-09-27 16:03:34.293][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-09-27 16:03:34.294][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-09-27 16:03:34.295][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-27 16:03:34.296][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-09-27 16:03:34.297][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-27 16:03:34.302][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-27 16:03:34.303][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-27 16:03:34.304][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-27 16:03:34.304][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-27 16:03:34.305][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-27 16:03:34.306][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-27 16:03:34.307][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-27 16:03:34.308][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-27 16:03:34.309][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-27 16:03:34.310][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-27 16:03:34.311][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-27 16:03:34.312][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-27 16:03:34.313][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-27 16:03:34.314][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-27 16:03:34.315][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-27 16:03:34.316][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-27 16:03:34.316][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-27 16:03:34.317][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-27 16:03:34.318][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-27 16:03:34.319][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-27 16:03:34.320][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-27 16:03:34.321][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-27 16:03:34.322][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-27 16:03:34.323][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-27 16:03:34.324][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-27 16:03:34.325][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-27 16:03:34.326][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-27 16:03:34.340][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-27 16:03:34.341][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-27 16:03:34.342][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-27 16:03:34.343][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-27 16:03:34.344][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-27 16:03:34.345][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-27 16:03:34.346][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-27 16:03:34.347][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-27 16:03:34.348][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-27 16:03:34.349][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-27 16:03:34.350][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-27 16:03:34.351][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-27 16:03:34.351][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-27 16:03:34.352][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-27 16:03:34.353][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-27 16:03:34.354][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-27 16:03:34.355][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-27 16:03:34.356][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-27 16:03:34.357][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-27 16:03:34.358][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-27 16:03:34.359][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-27 16:03:34.360][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-27 16:03:34.361][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-27 16:03:34.361][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-27 16:03:34.362][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-27 16:03:34.363][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-27 16:03:34.364][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-27 16:03:34.365][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-27 16:03:34.366][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-27 16:03:34.367][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-27 16:03:34.368][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-27 16:03:34.369][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-27 16:03:34.370][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-27 16:03:34.370][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-27 16:03:34.371][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-27 16:03:34.372][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-27 16:03:34.373][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-27 16:03:34.374][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-27 16:03:34.375][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-27 16:03:34.376][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-27 16:03:34.377][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-27 16:03:34.378][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-27 16:03:34.379][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-27 16:03:34.379][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-27 16:03:34.380][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-27 16:03:34.381][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-27 16:03:34.382][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-27 16:03:34.383][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-27 16:03:34.384][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-27 16:03:34.385][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-27 16:03:34.386][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-27 16:03:34.387][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-27 16:03:34.387][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-27 16:03:34.388][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-27 16:03:34.389][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-27 16:03:34.390][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-27 16:03:34.391][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-27 16:03:34.392][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-27 16:03:34.393][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-27 16:03:34.394][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-27 16:03:34.394][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-27 16:03:34.395][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-27 16:03:34.396][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-27 16:03:34.397][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-27 16:03:34.398][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-27 16:03:34.399][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-27 16:03:34.400][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-27 16:03:34.401][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-27 16:03:34.402][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-27 16:03:34.403][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-27 16:03:34.403][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-27 16:03:34.404][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-27 16:03:34.405][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-27 16:03:34.406][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-27 16:03:34.407][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-27 16:03:34.408][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-27 16:03:34.409][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-27 16:03:34.410][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-27 16:03:34.410][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-27 16:03:34.411][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-27 16:03:34.412][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-27 16:03:34.413][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-27 16:03:34.414][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-27 16:03:34.415][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-27 16:03:34.416][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-27 16:03:34.418][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNci.Rcheck/biodbNci/definitions.yml".
biodb.DEBUG[2025-09-27 16:03:34.427][self$getDbsInfo()$define] Define connector nci.cactus.
biodb.DEBUG[2025-09-27 16:03:34.429][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-09-27 16:03:34.430][self$setPropertyValue] Setting property "description" to "National Cancer Institute (USA) CACTUS Database.".
biodb.DEBUG[2025-09-27 16:03:34.431][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-09-27 16:03:34.432][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-09-27 16:03:34.433][self$setPropertyValue] Setting property "downloadable" to "TRUE".
biodb.DEBUG[2025-09-27 16:03:34.434][self$setPropertyValue] Setting property "dwnld.ext" to "gz".
biodb.DEBUG[2025-09-27 16:03:34.435][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-09-27 16:03:34.436][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-09-27 16:03:34.437][self$setPropertyValue] Setting property "entry.content.type" to "sdf".
biodb.DEBUG[2025-09-27 16:03:34.438][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-09-27 16:03:34.439][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-09-27 16:03:34.440][self$setPropertyValue] Setting property "name" to "NCI CACTUS".
biodb.DEBUG[2025-09-27 16:03:34.441][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-09-27 16:03:34.442][self$setPropertyValue] Setting property "parsing.expr" to "NSC".
biodb.DEBUG[2025-09-27 16:03:34.442][self$setPropertyValue] Setting property "parsing.expr" to "DTP names".
biodb.DEBUG[2025-09-27 16:03:34.442][self$setPropertyValue] Setting property "parsing.expr" to "Standard InChI".
biodb.DEBUG[2025-09-27 16:03:34.442][self$setPropertyValue] Setting property "parsing.expr" to "c("Standard InChIKey", "^InChIKey=(.*)$")".
biodb.DEBUG[2025-09-27 16:03:34.442][self$setPropertyValue] Setting property "parsing.expr" to "Formula".
biodb.DEBUG[2025-09-27 16:03:34.442][self$setPropertyValue] Setting property "parsing.expr" to "Molecular Weight".
biodb.DEBUG[2025-09-27 16:03:34.442][self$setPropertyValue] Setting property "parsing.expr" to "CAS".
biodb.DEBUG[2025-09-27 16:03:34.443][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-09-27 16:03:34.444][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-09-27 16:03:34.445][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-09-27 16:03:34.446][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-09-27 16:03:34.447][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-09-27 16:03:34.448][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-09-27 16:03:34.449][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-09-27 16:03:34.450][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-09-27 16:03:34.451][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-09-27 16:03:34.452][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/".
biodb.DEBUG[2025-09-27 16:03:34.452][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/".
biodb.DEBUG[2025-09-27 16:03:34.452][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/download/nci/".
biodb.DEBUG[2025-09-27 16:03:34.452][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/download/nci/NCI-Open_2012-05-01.sdf.gz".
biodb.DEBUG[2025-09-27 16:03:34.453][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-09-27 16:03:34.454][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-09-27 16:03:34.454][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-09-27 16:03:34.455][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-09-27 16:03:34.461][self$getEntryFields()$define] Define field nci.cactus.id.
biodb.DEBUG[2025-09-27 16:03:34.482][super$initialize] Initialize connector nci.cactus.
biodb.DEBUG[2025-09-27 16:03:34.496][biodb$getFactory()$createConn] Creating new connector nci.cactus for database class nci.cactus .
biodb.INFO [2025-09-27 16:03:34.505][biodb::testThat]
biodb.INFO [2025-09-27 16:03:34.511][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2025-09-27 16:03:34.512][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-09-27 16:03:34.513][biodb::testThat]
biodb.TRACE[2025-09-27 16:03:34.516][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNci.Rcheck/biodbNci/testref/entry-nci.cactus-749674-content.sdf".
biodb.DEBUG[2025-09-27 16:03:34.517][biodb$getFactory()$createEntryFromCo ...] Creating NCI CACTUS entries from 1 content(s).
biodb.DEBUG[2025-09-27 16:03:34.520][biodb$getFactory()$createEntryFromCo ...] Parsing 1 NCI CACTUS entries.
biodb.DEBUG[2025-09-27 16:03:34.528][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-09-27 16:03:34.528][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-27 16:03:34.529][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-27 16:03:34.540][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-09-27 16:03:34.541][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-27 16:03:34.542][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-09-27 16:03:34.543][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-09-27 16:03:34.558][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-27 16:03:34.559][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-27 16:03:34.560][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:03:34.561][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:03:34.562][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-27 16:03:34.573][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-27 16:03:34.574][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:03:34.575][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:03:34.577][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-09-27 16:03:34.578][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-09-27 16:03:34.579][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:03:34.580][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:03:34.604][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-09-27 16:03:34.605][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-09-27 16:03:34.606][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:03:34.606][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:03:34.608][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-09-27 16:03:34.609][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-27 16:03:34.610][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:03:34.611][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:03:34.611][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-09-27 16:03:34.612][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-27 16:03:34.613][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:03:34.614][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:03:34.616][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-09-27 16:03:34.617][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-09-27 16:03:34.618][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:03:34.619][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:03:34.620][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-09-27 16:03:34.621][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-09-27 16:03:34.621][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:03:34.622][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:03:34.624][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-09-27 16:03:34.625][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-09-27 16:03:34.626][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:03:34.626][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:03:34.627][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-09-27 16:03:34.628][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-09-27 16:03:34.629][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:03:34.630][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:03:34.632][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-09-27 16:03:34.633][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-09-27 16:03:34.634][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:03:34.634][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:03:34.635][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-09-27 16:03:34.636][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-09-27 16:03:34.637][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:03:34.638][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:03:34.645][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-27 16:03:34.646][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-27 16:03:34.647][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:03:34.647][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:03:34.648][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-09-27 16:03:34.649][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-09-27 16:03:34.650][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:03:34.651][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:03:34.652][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-27 16:03:34.653][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-27 16:03:34.654][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:03:34.655][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:03:34.656][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-27 16:03:34.657][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-27 16:03:34.658][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:03:34.658][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:03:34.659][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-27 16:03:34.660][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-27 16:03:34.661][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:03:34.662][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:03:34.693][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-27 16:03:34.694][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-27 16:03:34.695][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:03:34.695][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:03:34.696][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-27 16:03:34.697][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-27 16:03:34.698][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:03:34.699][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:03:34.700][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-27 16:03:34.701][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-27 16:03:34.702][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:03:34.703][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-09-27 16:03:34.704][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 749674.
biodb.TRACE[2025-09-27 16:03:34.706][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-09-27 16:03:34.707][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-09-27 16:03:34.708][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:03:34.708][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:03:34.709][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-09-27 16:03:34.710][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-09-27 16:03:34.711][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:03:34.712][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:03:34.713][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-09-27 16:03:34.714][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-09-27 16:03:34.715][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:03:34.716][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:03:34.717][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-09-27 16:03:34.718][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-09-27 16:03:34.719][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:03:34.719][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:03:34.721][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-27 16:03:34.722][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-27 16:03:34.723][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:03:34.724][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:03:34.736][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-09-27 16:03:34.737][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-09-27 16:03:34.738][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:03:34.739][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:03:34.743][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-27 16:03:34.744][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-27 16:03:34.744][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:03:34.745][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:03:34.746][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-27 16:03:34.747][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-27 16:03:34.787][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:03:34.788][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:03:34.789][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-27 16:03:34.790][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-27 16:03:34.790][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:03:34.791][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:03:34.794][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-27 16:03:34.795][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-27 16:03:34.795][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:03:34.796][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:03:34.797][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-27 16:03:34.798][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-27 16:03:34.799][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:03:34.800][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:03:34.801][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-27 16:03:34.802][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-27 16:03:34.803][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:03:34.804][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:03:34.805][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-09-27 16:03:34.806][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-09-27 16:03:34.807][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:03:34.808][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:03:34.808][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-09-27 16:03:34.809][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-09-27 16:03:34.810][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:03:34.811][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:03:34.812][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-09-27 16:03:34.813][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-09-27 16:03:34.814][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:03:34.815][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:03:34.821][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-27 16:03:34.822][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-27 16:03:34.823][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:03:34.824][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:03:34.825][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-27 16:03:34.826][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-27 16:03:34.827][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:03:34.828][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:03:34.829][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-27 16:03:34.829][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-27 16:03:34.830][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:03:34.831][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:03:34.832][ef$get] Asked field names are: accession.
biodb.TRACE[2025-09-27 16:03:34.833][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-27 16:03:34.834][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:03:34.835][ef$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:03:34.836][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-27 16:03:34.837][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-27 16:03:34.838][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:03:34.839][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:03:34.846][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-09-27 16:03:34.847][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-09-27 16:03:34.848][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:03:34.849][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:03:34.850][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-09-27 16:03:34.851][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-09-27 16:03:34.851][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:03:34.852][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:03:34.853][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-09-27 16:03:34.854][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-09-27 16:03:34.855][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:03:34.856][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:03:34.857][ef$get] Asked field names are: formula.
biodb.TRACE[2025-09-27 16:03:34.858][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-09-27 16:03:34.859][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:03:34.860][ef$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:03:34.861][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-09-27 16:03:34.862][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-09-27 16:03:34.862][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:03:34.863][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:03:34.870][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-09-27 16:03:34.871][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-27 16:03:34.872][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:03:34.873][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:03:34.874][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-09-27 16:03:34.875][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-27 16:03:34.876][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:03:34.877][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:03:34.878][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-09-27 16:03:34.879][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-27 16:03:34.880][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:03:34.880][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:03:34.881][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-09-27 16:03:34.882][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-27 16:03:34.883][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:03:34.884][ef$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:03:34.885][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-09-27 16:03:34.886][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-27 16:03:34.887][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:03:34.888][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:03:34.895][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-09-27 16:03:34.896][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-09-27 16:03:34.897][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:03:34.898][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:03:34.899][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-09-27 16:03:34.900][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-09-27 16:03:34.904][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:03:34.905][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:03:34.906][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-09-27 16:03:34.907][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-09-27 16:03:34.908][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:03:34.909][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:03:34.910][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-09-27 16:03:34.911][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-09-27 16:03:34.912][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:03:34.912][ef$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:03:34.913][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-09-27 16:03:34.914][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-09-27 16:03:34.915][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:03:34.916][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:03:34.923][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-09-27 16:03:34.924][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-09-27 16:03:34.925][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:03:34.926][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:03:34.927][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-09-27 16:03:34.928][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-09-27 16:03:34.929][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:03:34.930][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:03:34.931][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-09-27 16:03:34.932][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-09-27 16:03:34.933][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:03:34.934][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:03:34.935][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-09-27 16:03:34.936][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-09-27 16:03:34.937][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:03:34.937][ef$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:03:34.938][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-09-27 16:03:34.939][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-09-27 16:03:34.940][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:03:34.941][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:03:34.948][ef$get] Asked field names are: accession.
biodb.TRACE[2025-09-27 16:03:34.949][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-27 16:03:34.950][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:03:34.951][ef$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:03:34.954][ef$get] Asked field names are: formula.
biodb.TRACE[2025-09-27 16:03:34.955][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-09-27 16:03:34.956][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:03:34.957][ef$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:03:34.961][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-09-27 16:03:34.962][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-09-27 16:03:34.963][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:03:34.964][ef$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:03:34.967][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-09-27 16:03:34.968][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-09-27 16:03:34.969][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:03:34.970][ef$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:03:34.974][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-09-27 16:03:34.975][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-27 16:03:34.976][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:03:34.976][ef$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:03:34.992][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNci.Rcheck/biodbNci/testref/entry-nci.cactus-750690-content.sdf".
biodb.DEBUG[2025-09-27 16:03:35.028][biodb$getFactory()$createEntryFromCo ...] Creating NCI CACTUS entries from 1 content(s).
biodb.DEBUG[2025-09-27 16:03:35.029][biodb$getFactory()$createEntryFromCo ...] Parsing 1 NCI CACTUS entries.
biodb.DEBUG[2025-09-27 16:03:35.030][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-09-27 16:03:35.031][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-27 16:03:35.032][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-27 16:03:35.036][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-09-27 16:03:35.036][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-27 16:03:35.037][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-09-27 16:03:35.038][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-09-27 16:03:35.047][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-27 16:03:35.047][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-27 16:03:35.048][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:03:35.049][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:03:35.050][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-27 16:03:35.051][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-27 16:03:35.052][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:03:35.053][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:03:35.070][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-09-27 16:03:35.071][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-09-27 16:03:35.072][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:03:35.072][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:03:35.073][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-09-27 16:03:35.074][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-09-27 16:03:35.075][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:03:35.076][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:03:35.078][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-09-27 16:03:35.079][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-09-27 16:03:35.079][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:03:35.080][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:03:35.081][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-09-27 16:03:35.082][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-09-27 16:03:35.083][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:03:35.084][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:03:35.085][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-09-27 16:03:35.086][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-27 16:03:35.087][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:03:35.088][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:03:35.089][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-09-27 16:03:35.090][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-27 16:03:35.091][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:03:35.092][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:03:35.093][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-09-27 16:03:35.094][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-09-27 16:03:35.095][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:03:35.096][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:03:35.096][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-09-27 16:03:35.097][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-09-27 16:03:35.098][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:03:35.099][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:03:35.100][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-09-27 16:03:35.101][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-09-27 16:03:35.102][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:03:35.103][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:03:35.104][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-09-27 16:03:35.105][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-09-27 16:03:35.106][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:03:35.107][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:03:35.108][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-09-27 16:03:35.109][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-09-27 16:03:35.110][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:03:35.110][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:03:35.111][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-09-27 16:03:35.112][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-09-27 16:03:35.113][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:03:35.114][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:03:35.115][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-09-27 16:03:35.116][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-09-27 16:03:35.117][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:03:35.121][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:03:35.123][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-09-27 16:03:35.124][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-09-27 16:03:35.124][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:03:35.125][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:03:35.126][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-09-27 16:03:35.127][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-09-27 16:03:35.128][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:03:35.129][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:03:35.130][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-09-27 16:03:35.131][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-09-27 16:03:35.132][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:03:35.133][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:03:35.134][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-09-27 16:03:35.135][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-09-27 16:03:35.136][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:03:35.137][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:03:35.138][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-09-27 16:03:35.139][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-09-27 16:03:35.140][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:03:35.141][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:03:35.142][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-09-27 16:03:35.143][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-09-27 16:03:35.144][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:03:35.145][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:03:35.145][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-27 16:03:35.146][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-27 16:03:35.147][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:03:35.148][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:03:35.149][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-09-27 16:03:35.150][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-09-27 16:03:35.151][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:03:35.152][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:03:35.153][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-27 16:03:35.154][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-27 16:03:35.155][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:03:35.156][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:03:35.156][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-27 16:03:35.157][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-27 16:03:35.158][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:03:35.159][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:03:35.160][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-27 16:03:35.161][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-27 16:03:35.162][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:03:35.163][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:03:35.164][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-27 16:03:35.165][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-27 16:03:35.166][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:03:35.167][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:03:35.167][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-27 16:03:35.168][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-27 16:03:35.169][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:03:35.170][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:03:35.171][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-27 16:03:35.172][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-27 16:03:35.173][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:03:35.174][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-09-27 16:03:35.175][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 750690.
biodb.TRACE[2025-09-27 16:03:35.193][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-09-27 16:03:35.194][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-09-27 16:03:35.195][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:03:35.196][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:03:35.197][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-09-27 16:03:35.198][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-09-27 16:03:35.199][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:03:35.200][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:03:35.201][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-09-27 16:03:35.202][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-09-27 16:03:35.202][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:03:35.203][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:03:35.204][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-09-27 16:03:35.205][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-09-27 16:03:35.206][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:03:35.207][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:03:35.209][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-27 16:03:35.210][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-27 16:03:35.210][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:03:35.211][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:03:35.215][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-09-27 16:03:35.216][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-09-27 16:03:35.217][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:03:35.218][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:03:35.222][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-27 16:03:35.223][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-27 16:03:35.224][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:03:35.225][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:03:35.226][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-27 16:03:35.227][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-27 16:03:35.227][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:03:35.228][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:03:35.232][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-27 16:03:35.233][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-27 16:03:35.234][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:03:35.235][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:03:35.237][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-27 16:03:35.238][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-27 16:03:35.239][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:03:35.240][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:03:35.241][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-27 16:03:35.242][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-27 16:03:35.243][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:03:35.244][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:03:35.245][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-27 16:03:35.246][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-27 16:03:35.246][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:03:35.247][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:03:35.248][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-09-27 16:03:35.249][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-09-27 16:03:35.250][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:03:35.251][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:03:35.252][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-09-27 16:03:35.253][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-09-27 16:03:35.254][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:03:35.255][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:03:35.256][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-09-27 16:03:35.257][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-09-27 16:03:35.258][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:03:35.258][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:03:35.273][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-27 16:03:35.274][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-27 16:03:35.275][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:03:35.276][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:03:35.277][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-27 16:03:35.278][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-27 16:03:35.278][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:03:35.279][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:03:35.280][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-27 16:03:35.281][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-27 16:03:35.282][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:03:35.283][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:03:35.284][ef$get] Asked field names are: accession.
biodb.TRACE[2025-09-27 16:03:35.285][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-27 16:03:35.286][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:03:35.287][ef$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:03:35.288][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-27 16:03:35.288][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-27 16:03:35.289][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:03:35.290][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:03:35.297][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-09-27 16:03:35.298][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-09-27 16:03:35.299][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:03:35.300][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:03:35.301][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-09-27 16:03:35.302][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-09-27 16:03:35.303][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:03:35.304][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:03:35.304][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-09-27 16:03:35.305][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-09-27 16:03:35.306][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:03:35.307][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:03:35.308][ef$get] Asked field names are: cas.id.
biodb.TRACE[2025-09-27 16:03:35.309][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-09-27 16:03:35.310][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:03:35.311][ef$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:03:35.312][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-09-27 16:03:35.313][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-09-27 16:03:35.314][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:03:35.314][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:03:35.321][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-09-27 16:03:35.322][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-09-27 16:03:35.323][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:03:35.324][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:03:35.325][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-09-27 16:03:35.326][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-09-27 16:03:35.327][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:03:35.328][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:03:35.329][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-09-27 16:03:35.330][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-09-27 16:03:35.331][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:03:35.331][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:03:35.332][ef$get] Asked field names are: name.
biodb.TRACE[2025-09-27 16:03:35.333][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-09-27 16:03:35.334][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:03:35.335][ef$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:03:35.336][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-09-27 16:03:35.337][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-09-27 16:03:35.338][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:03:35.339][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:03:35.350][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-09-27 16:03:35.351][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-09-27 16:03:35.352][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:03:35.352][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:03:35.353][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-09-27 16:03:35.354][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-09-27 16:03:35.355][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:03:35.356][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:03:35.357][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-09-27 16:03:35.358][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-09-27 16:03:35.359][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:03:35.360][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:03:35.361][ef$get] Asked field names are: formula.
biodb.TRACE[2025-09-27 16:03:35.362][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-09-27 16:03:35.363][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:03:35.364][ef$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:03:35.365][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-09-27 16:03:35.366][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-09-27 16:03:35.366][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:03:35.367][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:03:35.374][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-09-27 16:03:35.375][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-27 16:03:35.376][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:03:35.377][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:03:35.378][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-09-27 16:03:35.379][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-27 16:03:35.380][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:03:35.381][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:03:35.382][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-09-27 16:03:35.383][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-27 16:03:35.384][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:03:35.385][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:03:35.386][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-09-27 16:03:35.387][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-27 16:03:35.387][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:03:35.388][ef$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:03:35.389][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-09-27 16:03:35.390][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-27 16:03:35.391][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:03:35.392][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:03:35.399][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-09-27 16:03:35.400][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-09-27 16:03:35.401][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:03:35.402][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:03:35.403][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-09-27 16:03:35.404][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-09-27 16:03:35.405][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:03:35.405][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:03:35.406][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-09-27 16:03:35.407][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-09-27 16:03:35.408][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:03:35.409][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:03:35.410][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-09-27 16:03:35.411][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-09-27 16:03:35.412][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:03:35.413][ef$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:03:35.414][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-09-27 16:03:35.415][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-09-27 16:03:35.416][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:03:35.416][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:03:35.423][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-09-27 16:03:35.424][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-09-27 16:03:35.425][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:03:35.426][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:03:35.427][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-09-27 16:03:35.428][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-09-27 16:03:35.429][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:03:35.430][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:03:35.431][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-09-27 16:03:35.432][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-09-27 16:03:35.433][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:03:35.433][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:03:35.434][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-09-27 16:03:35.435][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-09-27 16:03:35.436][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:03:35.437][ef$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:03:35.438][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-09-27 16:03:35.439][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-09-27 16:03:35.440][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:03:35.441][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:03:35.448][ef$get] Asked field names are: accession.
biodb.TRACE[2025-09-27 16:03:35.449][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-27 16:03:35.450][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:03:35.451][ef$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:03:35.454][ef$get] Asked field names are: cas.id.
biodb.TRACE[2025-09-27 16:03:35.455][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-09-27 16:03:35.460][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:03:35.461][ef$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:03:35.464][ef$get] Asked field names are: formula.
biodb.TRACE[2025-09-27 16:03:35.465][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-09-27 16:03:35.466][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:03:35.467][ef$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:03:35.471][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-09-27 16:03:35.472][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-09-27 16:03:35.473][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:03:35.474][ef$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:03:35.477][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-09-27 16:03:35.478][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-09-27 16:03:35.479][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:03:35.480][ef$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:03:35.484][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-09-27 16:03:35.485][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-27 16:03:35.486][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:03:35.487][ef$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:03:35.490][ef$get] Asked field names are: name.
biodb.TRACE[2025-09-27 16:03:35.491][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-09-27 16:03:35.492][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:03:35.493][ef$get] fields variable is a list.
biodb.INFO [2025-09-27 16:03:35.499][biodb::testThat]
biodb.INFO [2025-09-27 16:03:35.500][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2025-09-27 16:03:35.501][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-09-27 16:03:35.502][biodb::testThat]
biodb.DEBUG[2025-09-27 16:03:35.504][private$loadEntries] Creating entries from ids [2]: "749674, 750690".
biodb.DEBUG[2025-09-27 16:03:35.506][conn$getEntryContent] Get NCI CACTUS entry content(s) for 2 id(s)...
biodb.DEBUG[2025-09-27 16:03:35.508][self$isDownloaded] Database nci.cactus has already been downloaded.
biodb.DEBUG[2025-09-27 16:03:35.536][self$isDownloaded] Database nci.cactus has already been downloaded.
biodb.INFO [2025-09-27 16:03:35.537][self$download] Extract whole database of nci.cactus.
biodb.INFO [2025-09-27 16:03:35.538][private$doExtractDownload] Extracting content of downloaded biodbNci, a library for connecting to the National Cancer Institute (USA) CACTUS Database....
biodb.INFO [2025-09-27 16:03:35.579][biodb::testThat]
biodb.INFO [2025-09-27 16:03:35.580][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2025-09-27 16:03:35.581][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-09-27 16:03:35.582][biodb::testThat]
biodb.INFO [2025-09-27 16:03:35.587][biodb::testThat]
biodb.INFO [2025-09-27 16:03:35.588][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2025-09-27 16:03:35.588][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-09-27 16:03:35.589][biodb::testThat]
biodb.WARN [2025-09-27 16:03:35.607][self$searchForEntries] This database is not searchable by field "name".
biodb.WARN [2025-09-27 16:03:35.625][self$searchForEntries] This database is not searchable by field "name".
biodb.INFO [2025-09-27 16:03:35.632][biodb::testThat]
biodb.INFO [2025-09-27 16:03:35.633][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2025-09-27 16:03:35.634][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-09-27 16:03:35.634][biodb::testThat]
biodb.DEBUG[2025-09-27 16:03:35.650][private$loadEntries] Creating entries from ids [1]: "749674".
biodb.DEBUG[2025-09-27 16:03:35.698][conn$getEntryContent] Get NCI CACTUS entry content(s) for 1 id(s)...
biodb.DEBUG[2025-09-27 16:03:35.699][self$isDownloaded] Database nci.cactus has already been downloaded.
biodb.DEBUG[2025-09-27 16:03:35.700][self$isDownloaded] Database nci.cactus has already been downloaded.
biodb.INFO [2025-09-27 16:03:35.701][self$download] Extract whole database of nci.cactus.
biodb.INFO [2025-09-27 16:03:35.713][private$doExtractDownload] Extracting content of downloaded biodbNci, a library for connecting to the National Cancer Institute (USA) CACTUS Database....
biodb.INFO [2025-09-27 16:03:35.735][biodb::testThat]
biodb.INFO [2025-09-27 16:03:35.736][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2025-09-27 16:03:35.737][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-09-27 16:03:35.738][biodb::testThat]
biodb.INFO [2025-09-27 16:03:35.744][biodb::testThat]
biodb.INFO [2025-09-27 16:03:35.745][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2025-09-27 16:03:35.746][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-09-27 16:03:35.747][biodb::testThat]
biodb.INFO [2025-09-27 16:03:35.753][biodb::testThat]
biodb.INFO [2025-09-27 16:03:35.754][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2025-09-27 16:03:35.755][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-09-27 16:03:35.755][biodb::testThat]
biodb.INFO [2025-09-27 16:03:35.761][biodb::testThat]
biodb.INFO [2025-09-27 16:03:35.761][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2025-09-27 16:03:35.762][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-09-27 16:03:35.763][biodb::testThat]
biodb.INFO [2025-09-27 16:03:35.772][biodb$terminate] Closing BiodbMain instance...
biodb.INFO [2025-09-27 16:03:35.773][self$deleteConn] Connector "nci.cactus" deleted.
biodb.DEBUG[2025-09-27 16:03:35.774][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-09-27 16:03:35.774][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-27 16:03:35.775][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-27 16:03:35.776][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-27 16:03:35.777][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-27 16:03:35.778][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-09-27 16:03:35.779][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2025-09-27 16:03:35.787][biodb::testContext]
biodb.INFO [2025-09-27 16:03:35.788][biodb::testContext] ********************************************************************************
biodb.INFO [2025-09-27 16:03:35.789][biodb::testContext] Test context - Example long tests
biodb.INFO [2025-09-27 16:03:35.790][biodb::testContext] ********************************************************************************
biodb.INFO [2025-09-27 16:03:35.791][biodb::testContext]
biodb.INFO [2025-09-27 16:03:35.793][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.17.2.
biodb.DEBUG[2025-09-27 16:03:35.794][self$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.22-bioc/R/site-library/biodb/definitions.yml".
biodb.DEBUG[2025-09-27 16:03:35.798][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-09-27 16:03:35.799][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-09-27 16:03:35.800][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-09-27 16:03:35.800][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-27 16:03:35.801][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-27 16:03:35.802][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-27 16:03:35.803][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-09-27 16:03:35.804][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-09-27 16:03:35.805][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-27 16:03:35.806][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-27 16:03:35.806][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-27 16:03:35.807][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-09-27 16:03:35.808][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-09-27 16:03:35.809][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-27 16:03:35.810][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-27 16:03:35.811][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[2025-09-27 16:03:35.812][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-09-27 16:03:35.813][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-09-27 16:03:35.813][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-09-27 16:03:35.814][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-27 16:03:35.815][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-27 16:03:35.816][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-27 16:03:35.817][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-09-27 16:03:35.818][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-09-27 16:03:35.819][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-09-27 16:03:35.820][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-27 16:03:35.820][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-27 16:03:35.821][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-27 16:03:35.822][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-09-27 16:03:35.823][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-09-27 16:03:35.824][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-27 16:03:35.825][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-27 16:03:35.826][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-27 16:03:35.826][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-09-27 16:03:35.827][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-09-27 16:03:35.828][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-09-27 16:03:35.829][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-27 16:03:35.830][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-27 16:03:35.831][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-27 16:03:35.832][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-09-27 16:03:35.833][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-09-27 16:03:35.834][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-27 16:03:35.834][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-27 16:03:35.835][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-27 16:03:35.836][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-09-27 16:03:35.837][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-09-27 16:03:35.838][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-09-27 16:03:35.839][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-27 16:03:35.840][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-27 16:03:35.840][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-27 16:03:35.841][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-09-27 16:03:35.842][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-09-27 16:03:35.843][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-09-27 16:03:35.844][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-09-27 16:03:35.845][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-09-27 16:03:35.846][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-09-27 16:03:35.847][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-27 16:03:35.848][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-27 16:03:35.848][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-27 16:03:35.849][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-09-27 16:03:35.850][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-09-27 16:03:35.851][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-27 16:03:35.852][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-27 16:03:35.853][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-27 16:03:35.854][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-09-27 16:03:35.855][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-09-27 16:03:35.855][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-27 16:03:35.856][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-27 16:03:35.857][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-27 16:03:35.858][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-09-27 16:03:35.859][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-09-27 16:03:35.860][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-27 16:03:35.861][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-27 16:03:35.861][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-27 16:03:35.862][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-09-27 16:03:35.863][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-09-27 16:03:35.864][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-09-27 16:03:35.865][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-27 16:03:35.866][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-27 16:03:35.867][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-27 16:03:35.868][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-09-27 16:03:35.869][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-09-27 16:03:35.873][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-09-27 16:03:35.874][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-27 16:03:35.875][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-27 16:03:35.876][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-27 16:03:35.877][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-09-27 16:03:35.882][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-09-27 16:03:35.883][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-09-27 16:03:35.884][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-27 16:03:35.885][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-27 16:03:35.886][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-27 16:03:35.887][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-09-27 16:03:35.889][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-09-27 16:03:35.890][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2025-09-27 16:03:35.891][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-09-27 16:03:35.892][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-09-27 16:03:35.893][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-09-27 16:03:35.894][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-09-27 16:03:35.894][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-09-27 16:03:35.895][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-09-27 16:03:35.896][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-09-27 16:03:35.897][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-09-27 16:03:35.898][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-09-27 16:03:35.899][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-09-27 16:03:35.900][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-09-27 16:03:35.901][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-09-27 16:03:35.902][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-09-27 16:03:35.903][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-09-27 16:03:35.903][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-09-27 16:03:35.903][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-09-27 16:03:35.903][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-09-27 16:03:35.903][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-09-27 16:03:35.904][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-09-27 16:03:35.905][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-09-27 16:03:35.906][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-09-27 16:03:35.907][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-09-27 16:03:35.908][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-09-27 16:03:35.908][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-09-27 16:03:35.909][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-09-27 16:03:35.910][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-09-27 16:03:35.911][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-09-27 16:03:35.912][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-09-27 16:03:35.913][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-09-27 16:03:35.914][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-09-27 16:03:35.915][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-09-27 16:03:35.916][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-09-27 16:03:35.917][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-09-27 16:03:35.918][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-09-27 16:03:35.919][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-09-27 16:03:35.920][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-09-27 16:03:35.921][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-09-27 16:03:35.922][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-09-27 16:03:35.923][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-09-27 16:03:35.924][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-09-27 16:03:35.925][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-09-27 16:03:35.926][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-09-27 16:03:35.927][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-09-27 16:03:35.928][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-09-27 16:03:35.929][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-09-27 16:03:35.930][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-09-27 16:03:35.931][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-09-27 16:03:35.931][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-09-27 16:03:35.931][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-09-27 16:03:35.931][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-09-27 16:03:35.931][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-09-27 16:03:35.931][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-09-27 16:03:35.932][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-09-27 16:03:35.933][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-09-27 16:03:35.934][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-09-27 16:03:35.935][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-09-27 16:03:35.936][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-09-27 16:03:35.937][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-09-27 16:03:35.938][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-09-27 16:03:35.939][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-09-27 16:03:35.939][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-09-27 16:03:35.940][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-09-27 16:03:35.941][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-09-27 16:03:35.942][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-09-27 16:03:35.944][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-09-27 16:03:35.945][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2025-09-27 16:03:35.946][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-09-27 16:03:35.947][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-09-27 16:03:35.948][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-09-27 16:03:35.948][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-09-27 16:03:35.949][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-09-27 16:03:35.950][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-09-27 16:03:35.951][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-09-27 16:03:35.952][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-09-27 16:03:35.953][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-09-27 16:03:35.954][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-09-27 16:03:35.955][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-09-27 16:03:35.956][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-09-27 16:03:35.957][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-09-27 16:03:35.958][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-09-27 16:03:35.959][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-09-27 16:03:35.959][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-09-27 16:03:35.960][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-09-27 16:03:35.961][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-09-27 16:03:35.962][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-09-27 16:03:35.963][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-09-27 16:03:35.964][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-09-27 16:03:35.965][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-09-27 16:03:35.966][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-09-27 16:03:35.966][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-09-27 16:03:35.967][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-09-27 16:03:35.968][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-09-27 16:03:35.969][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-09-27 16:03:35.971][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-09-27 16:03:35.972][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-09-27 16:03:35.973][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-09-27 16:03:35.974][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-09-27 16:03:35.975][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-09-27 16:03:35.976][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-09-27 16:03:35.976][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-09-27 16:03:35.977][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-09-27 16:03:35.978][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-09-27 16:03:35.979][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-09-27 16:03:35.980][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-09-27 16:03:35.981][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-09-27 16:03:35.982][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-09-27 16:03:35.983][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-09-27 16:03:35.984][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-09-27 16:03:35.985][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-09-27 16:03:35.986][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-09-27 16:03:35.987][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-09-27 16:03:35.988][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-09-27 16:03:35.992][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-09-27 16:03:35.993][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-09-27 16:03:35.994][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-09-27 16:03:35.995][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-09-27 16:03:35.995][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-09-27 16:03:35.996][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-09-27 16:03:35.997][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-09-27 16:03:35.998][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-09-27 16:03:35.999][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-09-27 16:03:36.000][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-09-27 16:03:36.001][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-09-27 16:03:36.002][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-27 16:03:36.003][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-27 16:03:36.003][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-27 16:03:36.004][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-27 16:03:36.005][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-27 16:03:36.006][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-27 16:03:36.007][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-27 16:03:36.008][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-27 16:03:36.008][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-27 16:03:36.009][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-27 16:03:36.010][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-27 16:03:36.011][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-27 16:03:36.012][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-27 16:03:36.013][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-27 16:03:36.013][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-27 16:03:36.014][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-27 16:03:36.015][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-27 16:03:36.016][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-27 16:03:36.017][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-27 16:03:36.018][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-27 16:03:36.018][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-27 16:03:36.019][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-27 16:03:36.020][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-27 16:03:36.021][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-27 16:03:36.022][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-27 16:03:36.023][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-27 16:03:36.023][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-27 16:03:36.024][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-27 16:03:36.025][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-27 16:03:36.026][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-27 16:03:36.027][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-27 16:03:36.027][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-27 16:03:36.028][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-27 16:03:36.029][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-27 16:03:36.030][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-27 16:03:36.031][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-27 16:03:36.032][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-27 16:03:36.032][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-27 16:03:36.033][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-27 16:03:36.034][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-27 16:03:36.035][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-27 16:03:36.036][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-27 16:03:36.037][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-27 16:03:36.037][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-27 16:03:36.038][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-27 16:03:36.039][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-27 16:03:36.040][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-27 16:03:36.041][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-27 16:03:36.041][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-27 16:03:36.042][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-27 16:03:36.043][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-27 16:03:36.044][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-27 16:03:36.045][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-27 16:03:36.046][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-27 16:03:36.046][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-27 16:03:36.047][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[2025-09-27 16:03:36.048][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-27 16:03:36.049][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-27 16:03:36.050][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-27 16:03:36.051][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-27 16:03:36.051][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-27 16:03:36.052][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-27 16:03:36.053][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-27 16:03:36.054][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-27 16:03:36.055][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-27 16:03:36.055][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-27 16:03:36.056][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-27 16:03:36.057][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-27 16:03:36.058][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-27 16:03:36.059][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-27 16:03:36.060][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-27 16:03:36.060][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-27 16:03:36.061][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-27 16:03:36.062][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-27 16:03:36.063][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-27 16:03:36.064][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[2025-09-27 16:03:36.064][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-27 16:03:36.065][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-27 16:03:36.066][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-27 16:03:36.067][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-27 16:03:36.068][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-27 16:03:36.069][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-09-27 16:03:36.070][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-09-27 16:03:36.071][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-09-27 16:03:36.073][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-09-27 16:03:36.074][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-09-27 16:03:36.075][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-09-27 16:03:36.076][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-09-27 16:03:36.078][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-09-27 16:03:36.079][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-09-27 16:03:36.080][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-09-27 16:03:36.082][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-09-27 16:03:36.083][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-09-27 16:03:36.084][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-09-27 16:03:36.085][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-09-27 16:03:36.087][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-09-27 16:03:36.088][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-09-27 16:03:36.089][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-09-27 16:03:36.091][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-09-27 16:03:36.092][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-09-27 16:03:36.093][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-09-27 16:03:36.098][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-09-27 16:03:36.099][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-09-27 16:03:36.101][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-09-27 16:03:36.102][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-09-27 16:03:36.103][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-09-27 16:03:36.104][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-09-27 16:03:36.106][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-09-27 16:03:36.107][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-09-27 16:03:36.108][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-09-27 16:03:36.109][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-09-27 16:03:36.111][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-09-27 16:03:36.112][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-09-27 16:03:36.113][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-09-27 16:03:36.115][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-09-27 16:03:36.116][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-09-27 16:03:36.117][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-09-27 16:03:36.118][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-09-27 16:03:36.120][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-09-27 16:03:36.121][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-09-27 16:03:36.122][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-09-27 16:03:36.124][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-09-27 16:03:36.125][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-09-27 16:03:36.126][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-09-27 16:03:36.127][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-09-27 16:03:36.129][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-09-27 16:03:36.130][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-09-27 16:03:36.131][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-09-27 16:03:36.133][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-09-27 16:03:36.134][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-09-27 16:03:36.135][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-09-27 16:03:36.136][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-09-27 16:03:36.138][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-09-27 16:03:36.139][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-09-27 16:03:36.140][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-09-27 16:03:36.142][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-09-27 16:03:36.143][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-09-27 16:03:36.144][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-09-27 16:03:36.145][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-09-27 16:03:36.147][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-09-27 16:03:36.148][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-09-27 16:03:36.149][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-09-27 16:03:36.150][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-09-27 16:03:36.152][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-09-27 16:03:36.153][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-09-27 16:03:36.154][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-09-27 16:03:36.156][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-09-27 16:03:36.157][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-09-27 16:03:36.158][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-09-27 16:03:36.159][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-09-27 16:03:36.161][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-09-27 16:03:36.162][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-09-27 16:03:36.163][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-09-27 16:03:36.164][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-09-27 16:03:36.166][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-09-27 16:03:36.167][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-09-27 16:03:36.168][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-09-27 16:03:36.170][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-09-27 16:03:36.171][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-09-27 16:03:36.172][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-09-27 16:03:36.173][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-09-27 16:03:36.175][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-09-27 16:03:36.176][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-09-27 16:03:36.177][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-09-27 16:03:36.179][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-09-27 16:03:36.180][initialize] This is biodb version 1.17.2.
biodb.DEBUG[2025-09-27 16:03:36.181][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-09-27 16:03:36.182][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-09-27 16:03:36.183][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-27 16:03:36.183][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-09-27 16:03:36.184][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-27 16:03:36.185][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-27 16:03:36.186][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-27 16:03:36.187][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-27 16:03:36.188][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-27 16:03:36.188][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-27 16:03:36.189][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-27 16:03:36.190][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-27 16:03:36.191][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-27 16:03:36.192][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-27 16:03:36.193][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-27 16:03:36.193][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-27 16:03:36.194][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-27 16:03:36.195][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-27 16:03:36.196][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-27 16:03:36.197][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-27 16:03:36.198][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-27 16:03:36.198][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-27 16:03:36.199][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-27 16:03:36.204][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-27 16:03:36.205][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-27 16:03:36.206][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-27 16:03:36.206][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-27 16:03:36.207][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-27 16:03:36.208][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-27 16:03:36.209][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-27 16:03:36.210][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-27 16:03:36.211][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-27 16:03:36.211][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-27 16:03:36.212][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-27 16:03:36.213][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-27 16:03:36.214][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-27 16:03:36.215][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-27 16:03:36.215][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-27 16:03:36.216][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-27 16:03:36.217][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-27 16:03:36.218][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-27 16:03:36.219][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-27 16:03:36.220][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-27 16:03:36.220][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-27 16:03:36.221][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-27 16:03:36.222][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-27 16:03:36.223][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-27 16:03:36.224][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-27 16:03:36.225][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-27 16:03:36.225][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-27 16:03:36.226][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-27 16:03:36.227][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-27 16:03:36.228][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-27 16:03:36.229][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-27 16:03:36.229][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-27 16:03:36.230][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-27 16:03:36.231][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-27 16:03:36.232][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-27 16:03:36.233][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-27 16:03:36.234][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-27 16:03:36.234][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-27 16:03:36.235][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-27 16:03:36.236][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-27 16:03:36.237][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-27 16:03:36.238][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-27 16:03:36.238][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-27 16:03:36.239][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-27 16:03:36.240][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-27 16:03:36.241][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-27 16:03:36.242][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-27 16:03:36.243][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-27 16:03:36.243][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-27 16:03:36.244][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-27 16:03:36.245][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-27 16:03:36.246][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-27 16:03:36.247][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-27 16:03:36.247][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-27 16:03:36.248][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-27 16:03:36.249][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-27 16:03:36.250][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-27 16:03:36.251][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-27 16:03:36.252][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-27 16:03:36.252][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-27 16:03:36.253][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-27 16:03:36.254][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-27 16:03:36.255][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-27 16:03:36.256][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-27 16:03:36.256][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-27 16:03:36.257][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-27 16:03:36.258][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-27 16:03:36.259][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-27 16:03:36.260][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-27 16:03:36.261][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-27 16:03:36.261][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-27 16:03:36.262][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-27 16:03:36.263][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-27 16:03:36.264][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-27 16:03:36.265][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-27 16:03:36.265][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-27 16:03:36.266][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-27 16:03:36.267][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-27 16:03:36.268][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-27 16:03:36.269][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-27 16:03:36.270][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-27 16:03:36.270][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-27 16:03:36.271][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-27 16:03:36.272][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-27 16:03:36.273][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-27 16:03:36.274][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-27 16:03:36.274][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-27 16:03:36.275][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-27 16:03:36.276][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-27 16:03:36.277][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-27 16:03:36.278][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-27 16:03:36.279][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-27 16:03:36.279][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-27 16:03:36.280][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-27 16:03:36.282][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNci.Rcheck/biodbNci/definitions.yml".
biodb.DEBUG[2025-09-27 16:03:36.283][self$getDbsInfo()$define] Define connector nci.cactus.
biodb.DEBUG[2025-09-27 16:03:36.285][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-09-27 16:03:36.286][self$setPropertyValue] Setting property "description" to "National Cancer Institute (USA) CACTUS Database.".
biodb.DEBUG[2025-09-27 16:03:36.287][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-09-27 16:03:36.287][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-09-27 16:03:36.288][self$setPropertyValue] Setting property "downloadable" to "TRUE".
biodb.DEBUG[2025-09-27 16:03:36.289][self$setPropertyValue] Setting property "dwnld.ext" to "gz".
biodb.DEBUG[2025-09-27 16:03:36.290][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-09-27 16:03:36.291][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-09-27 16:03:36.292][self$setPropertyValue] Setting property "entry.content.type" to "sdf".
biodb.DEBUG[2025-09-27 16:03:36.293][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-09-27 16:03:36.294][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-09-27 16:03:36.295][self$setPropertyValue] Setting property "name" to "NCI CACTUS".
biodb.DEBUG[2025-09-27 16:03:36.296][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-09-27 16:03:36.297][self$setPropertyValue] Setting property "parsing.expr" to "NSC".
biodb.DEBUG[2025-09-27 16:03:36.297][self$setPropertyValue] Setting property "parsing.expr" to "DTP names".
biodb.DEBUG[2025-09-27 16:03:36.297][self$setPropertyValue] Setting property "parsing.expr" to "Standard InChI".
biodb.DEBUG[2025-09-27 16:03:36.297][self$setPropertyValue] Setting property "parsing.expr" to "c("Standard InChIKey", "^InChIKey=(.*)$")".
biodb.DEBUG[2025-09-27 16:03:36.297][self$setPropertyValue] Setting property "parsing.expr" to "Formula".
biodb.DEBUG[2025-09-27 16:03:36.297][self$setPropertyValue] Setting property "parsing.expr" to "Molecular Weight".
biodb.DEBUG[2025-09-27 16:03:36.297][self$setPropertyValue] Setting property "parsing.expr" to "CAS".
biodb.DEBUG[2025-09-27 16:03:36.298][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-09-27 16:03:36.299][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-09-27 16:03:36.300][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-09-27 16:03:36.300][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-09-27 16:03:36.301][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-09-27 16:03:36.302][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-09-27 16:03:36.303][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-09-27 16:03:36.304][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-09-27 16:03:36.305][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-09-27 16:03:36.309][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/".
biodb.DEBUG[2025-09-27 16:03:36.309][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/".
biodb.DEBUG[2025-09-27 16:03:36.309][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/download/nci/".
biodb.DEBUG[2025-09-27 16:03:36.309][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/download/nci/NCI-Open_2012-05-01.sdf.gz".
biodb.DEBUG[2025-09-27 16:03:36.310][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-09-27 16:03:36.311][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-09-27 16:03:36.312][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-09-27 16:03:36.313][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-09-27 16:03:36.314][self$getEntryFields()$define] Define field nci.cactus.id.
biodb.DEBUG[2025-09-27 16:03:36.317][super$initialize] Initialize connector nci.cactus.
biodb.DEBUG[2025-09-27 16:03:36.320][biodb$getFactory()$createConn] Creating new connector nci.cactus for database class nci.cactus .
biodb.INFO [2025-09-27 16:03:36.321][biodb$terminate] Closing BiodbMain instance...
biodb.INFO [2025-09-27 16:03:36.322][self$deleteConn] Connector "nci.cactus" deleted.
biodb.DEBUG[2025-09-27 16:03:36.323][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-09-27 16:03:36.323][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-27 16:03:36.324][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-27 16:03:36.325][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-27 16:03:36.326][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-27 16:03:36.327][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-09-27 16:03:36.328][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
[ FAIL 2 | WARN 0 | SKIP 0 | PASS 85 ]

══ 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 0 | PASS 85 ]
Error: Test failures
Execution halted

'R CMD check' output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --test-dir=longtests --no-stop-on-test-error --no-codoc --no-examples --no-manual --ignore-vignettes --check-subdirs=no biodbNci_1.13.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNci.Rcheck’
* using R version 4.5.1 Patched (2025-08-23 r88802)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* using options ‘--no-codoc --no-examples --no-manual --ignore-vignettes --no-stop-on-test-error’
* checking for file ‘biodbNci/DESCRIPTION’ ... OK
* this is package ‘biodbNci’ version ‘1.13.1’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘biodbNci’ can be installed ... OK
* used C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
* checking installed package size ... INFO
  installed size is  6.1Mb
  sub-directories of 1Mb or more:
    libs   5.8Mb
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking whether startup messages can be suppressed ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  NciCactusConn.Rd: BiodbConn
  NciCactusEntry.Rd: BiodbSdfEntry
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... SKIPPED
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... OK
* checking files in ‘vignettes’ ... SKIPPED
* checking examples ... SKIPPED
* checking for unstated dependencies in ‘longtests’ ... OK
* checking tests in ‘longtests’ ...
  Running ‘testthat.R’
 ERROR
Running the tests in ‘longtests/testthat.R’ failed.
Last 13 lines of output:
  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 0 | PASS 85 ]
  Error: Test failures
  Execution halted
* DONE

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

Installation output

biodbNci.Rcheck/00install.out

* installing *source* package ‘biodbNci’ ...
** this is package ‘biodbNci’ version ‘1.13.1’
** using staged installation
** libs
using C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/testthat/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/testthat/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c extractEntries.cpp -o extractEntries.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/testthat/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c test-100-example.cpp -o test-100-example.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/testthat/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c test-runner.cpp -o test-runner.o
g++ -std=gnu++17 -shared -L/home/biocbuild/bbs-3.22-bioc/R/lib -L/usr/local/lib -o biodbNci.so RcppExports.o extractEntries.o test-100-example.o test-runner.o -L/home/biocbuild/bbs-3.22-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNci.Rcheck/00LOCK-biodbNci/00new/biodbNci/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning in fun(libname, pkgname) :
  Package 'biodbNci' is deprecated and will be removed from Bioconductor
  version 3.23
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
Warning in fun(libname, pkgname) :
  Package 'biodbNci' is deprecated and will be removed from Bioconductor
  version 3.23
** testing if installed package keeps a record of temporary installation path
* DONE (biodbNci)