Back to Long Tests report for BioC 3.22

This page was generated on 2025-10-18 23:55 -0400 (Sat, 18 Oct 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" 4887
lconwaymacOS 12.7.6 Montereyx86_644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4677
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 8/31HostnameOS / ArchCHECK
biodbNci 1.13.1  (landing page)
Pierrick Roger
Snapshot Date: 2025-10-18 09:55 -0400 (Sat, 18 Oct 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 12.7.6 Monterey / x86_64  ERROR  

CHECK results for biodbNci on nebbiolo2

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

raw results


Summary

Package: biodbNci
Version: 1.13.1
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: 2025-10-18 16:02:31 -0400 (Sat, 18 Oct 2025)
EndedAt: 2025-10-18 16:03:34 -0400 (Sat, 18 Oct 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 [2025-10-18 16:03:30.322][biodb::testContext]
biodb.INFO [2025-10-18 16:03:30.324][biodb::testContext] ********************************************************************************
biodb.INFO [2025-10-18 16:03:30.325][biodb::testContext] Test context - Generic long tests
biodb.INFO [2025-10-18 16:03:30.326][biodb::testContext] ********************************************************************************
biodb.INFO [2025-10-18 16:03:30.327][biodb::testContext]
biodb.INFO [2025-10-18 16:03:30.333][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.17.2.
biodb.DEBUG[2025-10-18 16:03:30.334][self$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.22-bioc/R/site-library/biodb/definitions.yml".
biodb.DEBUG[2025-10-18 16:03:30.341][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-10-18 16:03:30.342][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-10-18 16:03:30.343][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-10-18 16:03:30.344][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-18 16:03:30.345][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-18 16:03:30.346][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-18 16:03:30.347][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-10-18 16:03:30.364][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-10-18 16:03:30.365][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-18 16:03:30.373][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-18 16:03:30.374][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-18 16:03:30.375][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-10-18 16:03:30.376][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-10-18 16:03:30.377][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-18 16:03:30.378][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-18 16:03:30.378][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-18 16:03:30.379][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-10-18 16:03:30.380][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-10-18 16:03:30.381][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-10-18 16:03:30.382][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-18 16:03:30.383][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-18 16:03:30.384][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-18 16:03:30.385][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-10-18 16:03:30.385][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-10-18 16:03:30.386][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-10-18 16:03:30.387][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-18 16:03:30.388][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-18 16:03:30.389][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-18 16:03:30.390][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-10-18 16:03:30.391][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-10-18 16:03:30.392][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-18 16:03:30.392][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-18 16:03:30.393][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-18 16:03:30.394][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-10-18 16:03:30.395][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-10-18 16:03:30.396][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-10-18 16:03:30.397][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-18 16:03:30.398][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-18 16:03:30.398][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-18 16:03:30.399][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-10-18 16:03:30.400][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-10-18 16:03:30.401][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-18 16:03:30.402][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-18 16:03:30.403][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[2025-10-18 16:03:30.404][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-10-18 16:03:30.405][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-10-18 16:03:30.406][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-10-18 16:03:30.406][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-18 16:03:30.407][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-18 16:03:30.408][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-18 16:03:30.409][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-10-18 16:03:30.410][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-10-18 16:03:30.411][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-10-18 16:03:30.412][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-10-18 16:03:30.413][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-10-18 16:03:30.414][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-10-18 16:03:30.414][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-18 16:03:30.415][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-18 16:03:30.416][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[2025-10-18 16:03:30.417][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-10-18 16:03:30.418][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-10-18 16:03:30.419][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-18 16:03:30.420][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-18 16:03:30.420][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-18 16:03:30.421][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-10-18 16:03:30.422][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-10-18 16:03:30.423][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-18 16:03:30.424][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-18 16:03:30.425][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-18 16:03:30.426][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-10-18 16:03:30.426][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-10-18 16:03:30.427][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-18 16:03:30.428][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-18 16:03:30.429][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-18 16:03:30.430][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-10-18 16:03:30.431][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-10-18 16:03:30.432][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-10-18 16:03:30.433][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-18 16:03:30.433][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-18 16:03:30.434][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-18 16:03:30.435][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-10-18 16:03:30.436][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-10-18 16:03:30.440][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-10-18 16:03:30.441][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-18 16:03:30.442][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-18 16:03:30.442][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-18 16:03:30.443][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-10-18 16:03:30.444][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-10-18 16:03:30.445][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-10-18 16:03:30.446][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-18 16:03:30.447][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-18 16:03:30.448][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-18 16:03:30.451][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-10-18 16:03:30.482][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-10-18 16:03:30.496][self$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[2025-10-18 16:03:30.498][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-10-18 16:03:30.499][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-10-18 16:03:30.499][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-10-18 16:03:30.500][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-10-18 16:03:30.501][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-10-18 16:03:30.502][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-10-18 16:03:30.503][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-10-18 16:03:30.504][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-10-18 16:03:30.505][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-10-18 16:03:30.506][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-10-18 16:03:30.507][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-10-18 16:03:30.508][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-10-18 16:03:30.509][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-10-18 16:03:30.510][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-10-18 16:03:30.510][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-10-18 16:03:30.510][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-10-18 16:03:30.510][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-10-18 16:03:30.510][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-10-18 16:03:30.511][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-10-18 16:03:30.512][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-18 16:03:30.512][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-18 16:03:30.513][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-10-18 16:03:30.514][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-18 16:03:30.515][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-18 16:03:30.516][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-10-18 16:03:30.517][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-10-18 16:03:30.518][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-10-18 16:03:30.518][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-10-18 16:03:30.519][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-10-18 16:03:30.520][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-10-18 16:03:30.521][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-10-18 16:03:30.527][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-10-18 16:03:30.528][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-10-18 16:03:30.529][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-10-18 16:03:30.530][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-10-18 16:03:30.531][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-10-18 16:03:30.531][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-10-18 16:03:30.532][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-10-18 16:03:30.533][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-10-18 16:03:30.534][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-10-18 16:03:30.535][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-10-18 16:03:30.536][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-10-18 16:03:30.537][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-10-18 16:03:30.538][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-10-18 16:03:30.539][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-10-18 16:03:30.540][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-10-18 16:03:30.541][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-10-18 16:03:30.541][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-10-18 16:03:30.541][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-10-18 16:03:30.541][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-10-18 16:03:30.541][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-10-18 16:03:30.542][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-10-18 16:03:30.543][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-18 16:03:30.543][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-18 16:03:30.544][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-10-18 16:03:30.545][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-18 16:03:30.546][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-18 16:03:30.547][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-10-18 16:03:30.548][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-10-18 16:03:30.549][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-10-18 16:03:30.550][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-10-18 16:03:30.550][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-10-18 16:03:30.551][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-10-18 16:03:30.552][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-10-18 16:03:30.554][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-10-18 16:03:30.555][self$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[2025-10-18 16:03:30.556][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-10-18 16:03:30.557][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-10-18 16:03:30.558][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-10-18 16:03:30.559][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-10-18 16:03:30.560][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-10-18 16:03:30.560][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-10-18 16:03:30.561][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-10-18 16:03:30.562][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-10-18 16:03:30.563][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-10-18 16:03:30.564][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-10-18 16:03:30.565][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-10-18 16:03:30.566][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-10-18 16:03:30.567][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-10-18 16:03:30.568][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-10-18 16:03:30.569][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-10-18 16:03:30.570][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-18 16:03:30.570][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-18 16:03:30.571][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-10-18 16:03:30.572][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-18 16:03:30.573][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-18 16:03:30.574][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-10-18 16:03:30.575][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-10-18 16:03:30.576][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-10-18 16:03:30.576][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-10-18 16:03:30.577][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-10-18 16:03:30.578][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-10-18 16:03:30.579][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-10-18 16:03:30.581][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-10-18 16:03:30.582][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-10-18 16:03:30.583][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-10-18 16:03:30.584][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-10-18 16:03:30.585][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-10-18 16:03:30.586][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-10-18 16:03:30.586][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-10-18 16:03:30.587][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-10-18 16:03:30.588][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-10-18 16:03:30.589][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-10-18 16:03:30.590][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-10-18 16:03:30.591][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-10-18 16:03:30.592][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-10-18 16:03:30.593][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-10-18 16:03:30.594][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-10-18 16:03:30.595][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-10-18 16:03:30.596][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-10-18 16:03:30.597][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-18 16:03:30.597][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-18 16:03:30.598][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-10-18 16:03:30.599][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-18 16:03:30.600][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-18 16:03:30.601][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-10-18 16:03:30.602][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-10-18 16:03:30.603][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-10-18 16:03:30.603][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-10-18 16:03:30.604][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-10-18 16:03:30.605][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-10-18 16:03:30.609][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-10-18 16:03:30.610][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-10-18 16:03:30.610][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-18 16:03:30.611][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-18 16:03:30.612][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-18 16:03:30.613][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-18 16:03:30.614][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-18 16:03:30.614][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-18 16:03:30.615][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-18 16:03:30.616][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-18 16:03:30.617][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-18 16:03:30.618][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-18 16:03:30.619][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-18 16:03:30.619][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-18 16:03:30.620][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-18 16:03:30.621][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-18 16:03:30.622][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-18 16:03:30.623][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-18 16:03:30.624][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-18 16:03:30.624][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-18 16:03:30.625][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-18 16:03:30.626][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-18 16:03:30.627][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-18 16:03:30.628][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-18 16:03:30.628][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-18 16:03:30.629][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-18 16:03:30.630][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-18 16:03:30.631][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-18 16:03:30.632][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-18 16:03:30.633][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-18 16:03:30.633][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-18 16:03:30.634][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-18 16:03:30.635][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-18 16:03:30.636][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-18 16:03:30.637][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-18 16:03:30.637][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-18 16:03:30.638][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-18 16:03:30.639][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-18 16:03:30.640][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-18 16:03:30.641][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-18 16:03:30.642][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-18 16:03:30.642][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-18 16:03:30.643][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-18 16:03:30.644][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-18 16:03:30.645][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-18 16:03:30.646][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-18 16:03:30.647][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-18 16:03:30.647][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-18 16:03:30.648][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-18 16:03:30.649][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-18 16:03:30.650][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-18 16:03:30.651][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-18 16:03:30.651][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-18 16:03:30.652][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-18 16:03:30.653][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-18 16:03:30.654][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-18 16:03:30.655][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-18 16:03:30.656][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-18 16:03:30.656][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-18 16:03:30.657][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-18 16:03:30.658][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-18 16:03:30.659][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-18 16:03:30.660][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-18 16:03:30.660][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-18 16:03:30.661][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-18 16:03:30.662][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-18 16:03:30.663][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-18 16:03:30.664][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-18 16:03:30.665][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-18 16:03:30.665][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-18 16:03:30.666][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-18 16:03:30.667][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-18 16:03:30.668][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-18 16:03:30.669][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-18 16:03:30.669][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-18 16:03:30.670][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-18 16:03:30.671][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-18 16:03:30.672][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-18 16:03:30.673][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-18 16:03:30.674][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-18 16:03:30.678][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-18 16:03:30.679][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-18 16:03:30.680][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-18 16:03:30.680][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-10-18 16:03:30.685][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-10-18 16:03:30.686][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-10-18 16:03:30.687][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-10-18 16:03:30.689][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-10-18 16:03:30.690][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-10-18 16:03:30.691][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-10-18 16:03:30.692][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-10-18 16:03:30.694][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-10-18 16:03:30.695][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-10-18 16:03:30.696][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-10-18 16:03:30.698][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-10-18 16:03:30.699][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-10-18 16:03:30.700][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-10-18 16:03:30.701][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-10-18 16:03:30.703][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-10-18 16:03:30.704][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-10-18 16:03:30.705][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-10-18 16:03:30.707][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-10-18 16:03:30.708][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-10-18 16:03:30.709][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-10-18 16:03:30.711][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-10-18 16:03:30.712][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-10-18 16:03:30.713][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-10-18 16:03:30.714][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-10-18 16:03:30.716][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-10-18 16:03:30.717][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-10-18 16:03:30.718][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-10-18 16:03:30.720][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-10-18 16:03:30.721][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-10-18 16:03:30.722][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-10-18 16:03:30.723][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-10-18 16:03:30.725][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-10-18 16:03:30.726][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-10-18 16:03:30.727][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-10-18 16:03:30.728][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-10-18 16:03:30.730][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-10-18 16:03:30.731][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-10-18 16:03:30.732][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-10-18 16:03:30.734][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-10-18 16:03:30.735][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-10-18 16:03:30.736][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-10-18 16:03:30.737][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-10-18 16:03:30.739][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-10-18 16:03:30.740][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-10-18 16:03:30.741][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-10-18 16:03:30.743][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-10-18 16:03:30.744][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-10-18 16:03:30.745][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-10-18 16:03:30.746][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-10-18 16:03:30.748][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-10-18 16:03:30.749][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-10-18 16:03:30.750][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-10-18 16:03:30.752][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-10-18 16:03:30.753][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-10-18 16:03:30.754][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-10-18 16:03:30.755][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-10-18 16:03:30.757][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-10-18 16:03:30.758][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-10-18 16:03:30.759][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-10-18 16:03:30.760][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-10-18 16:03:30.762][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-10-18 16:03:30.763][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-10-18 16:03:30.764][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-10-18 16:03:30.766][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-10-18 16:03:30.767][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-10-18 16:03:30.768][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-10-18 16:03:30.769][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-10-18 16:03:30.771][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-10-18 16:03:30.772][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-10-18 16:03:30.773][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-10-18 16:03:30.781][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-10-18 16:03:30.783][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-10-18 16:03:30.785][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-10-18 16:03:30.786][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-10-18 16:03:30.788][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-10-18 16:03:30.789][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-10-18 16:03:30.791][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-10-18 16:03:30.792][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-10-18 16:03:30.794][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-10-18 16:03:30.795][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-10-18 16:03:30.797][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-10-18 16:03:30.798][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-10-18 16:03:30.805][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-10-18 16:03:30.807][initialize] This is biodb version 1.17.2.
biodb.DEBUG[2025-10-18 16:03:30.811][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-10-18 16:03:30.812][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-10-18 16:03:30.812][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-18 16:03:30.813][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-10-18 16:03:30.814][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-18 16:03:30.819][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-18 16:03:30.820][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-18 16:03:30.821][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-18 16:03:30.822][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-18 16:03:30.823][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-18 16:03:30.824][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-18 16:03:30.825][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-18 16:03:30.826][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-18 16:03:30.827][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-18 16:03:30.827][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-18 16:03:30.828][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-18 16:03:30.829][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-18 16:03:30.830][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-18 16:03:30.831][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[2025-10-18 16:03:30.832][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-18 16:03:30.833][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-18 16:03:30.834][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-18 16:03:30.835][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-18 16:03:30.836][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-18 16:03:30.851][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-18 16:03:30.852][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[2025-10-18 16:03:30.853][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-18 16:03:30.854][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-18 16:03:30.855][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-18 16:03:30.855][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-18 16:03:30.856][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-18 16:03:30.857][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-18 16:03:30.858][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-18 16:03:30.859][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-18 16:03:30.860][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-18 16:03:30.861][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-18 16:03:30.862][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-18 16:03:30.863][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-18 16:03:30.864][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-18 16:03:30.865][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[2025-10-18 16:03:30.865][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-18 16:03:30.866][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-18 16:03:30.867][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-18 16:03:30.868][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-18 16:03:30.869][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-18 16:03:30.870][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-18 16:03:30.871][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-18 16:03:30.872][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-18 16:03:30.873][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-18 16:03:30.874][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-18 16:03:30.874][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-18 16:03:30.875][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-18 16:03:30.876][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-18 16:03:30.877][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-18 16:03:30.878][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-18 16:03:30.879][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-18 16:03:30.880][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-18 16:03:30.881][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-18 16:03:30.882][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-18 16:03:30.883][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-18 16:03:30.883][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-18 16:03:30.884][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-18 16:03:30.885][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-18 16:03:30.886][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-18 16:03:30.887][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-18 16:03:30.888][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-18 16:03:30.889][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-18 16:03:30.890][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-18 16:03:30.891][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-18 16:03:30.891][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-18 16:03:30.892][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-18 16:03:30.893][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-18 16:03:30.894][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-18 16:03:30.895][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-18 16:03:30.896][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-18 16:03:30.897][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-18 16:03:30.898][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-18 16:03:30.899][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-18 16:03:30.899][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-18 16:03:30.900][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-18 16:03:30.901][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-18 16:03:30.902][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[2025-10-18 16:03:30.903][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-18 16:03:30.904][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-18 16:03:30.905][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-18 16:03:30.906][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-18 16:03:30.906][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-18 16:03:30.907][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-18 16:03:30.908][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-18 16:03:30.909][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-18 16:03:30.910][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-18 16:03:30.911][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-18 16:03:30.912][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-18 16:03:30.913][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-18 16:03:30.914][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-18 16:03:30.915][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[2025-10-18 16:03:30.915][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-18 16:03:30.916][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-18 16:03:30.917][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-18 16:03:30.918][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-18 16:03:30.919][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-18 16:03:30.920][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-18 16:03:30.921][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[2025-10-18 16:03:30.922][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-18 16:03:30.922][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-18 16:03:30.923][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-18 16:03:30.924][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-18 16:03:30.925][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-18 16:03:30.926][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-18 16:03:30.927][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-18 16:03:30.928][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-18 16:03:30.929][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-18 16:03:30.930][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-18 16:03:30.930][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-18 16:03:30.931][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-18 16:03:30.932][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-18 16:03:30.933][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-18 16:03:30.935][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNci.Rcheck/biodbNci/definitions.yml".
biodb.DEBUG[2025-10-18 16:03:30.944][self$getDbsInfo()$define] Define connector nci.cactus.
biodb.DEBUG[2025-10-18 16:03:30.946][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-10-18 16:03:30.947][self$setPropertyValue] Setting property "description" to "National Cancer Institute (USA) CACTUS Database.".
biodb.DEBUG[2025-10-18 16:03:30.948][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-10-18 16:03:30.949][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-10-18 16:03:30.950][self$setPropertyValue] Setting property "downloadable" to "TRUE".
biodb.DEBUG[2025-10-18 16:03:30.951][self$setPropertyValue] Setting property "dwnld.ext" to "gz".
biodb.DEBUG[2025-10-18 16:03:30.952][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-10-18 16:03:30.953][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-10-18 16:03:30.954][self$setPropertyValue] Setting property "entry.content.type" to "sdf".
biodb.DEBUG[2025-10-18 16:03:30.955][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-10-18 16:03:30.956][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-10-18 16:03:30.957][self$setPropertyValue] Setting property "name" to "NCI CACTUS".
biodb.DEBUG[2025-10-18 16:03:30.958][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-10-18 16:03:30.959][self$setPropertyValue] Setting property "parsing.expr" to "NSC".
biodb.DEBUG[2025-10-18 16:03:30.959][self$setPropertyValue] Setting property "parsing.expr" to "DTP names".
biodb.DEBUG[2025-10-18 16:03:30.959][self$setPropertyValue] Setting property "parsing.expr" to "Standard InChI".
biodb.DEBUG[2025-10-18 16:03:30.959][self$setPropertyValue] Setting property "parsing.expr" to "c("Standard InChIKey", "^InChIKey=(.*)$")".
biodb.DEBUG[2025-10-18 16:03:30.959][self$setPropertyValue] Setting property "parsing.expr" to "Formula".
biodb.DEBUG[2025-10-18 16:03:30.959][self$setPropertyValue] Setting property "parsing.expr" to "Molecular Weight".
biodb.DEBUG[2025-10-18 16:03:30.959][self$setPropertyValue] Setting property "parsing.expr" to "CAS".
biodb.DEBUG[2025-10-18 16:03:30.960][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-10-18 16:03:30.961][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-10-18 16:03:30.961][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-10-18 16:03:30.962][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-18 16:03:30.963][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-18 16:03:30.964][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-10-18 16:03:30.965][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-18 16:03:30.966][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-18 16:03:30.967][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-10-18 16:03:30.968][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/".
biodb.DEBUG[2025-10-18 16:03:30.968][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/".
biodb.DEBUG[2025-10-18 16:03:30.968][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/download/nci/".
biodb.DEBUG[2025-10-18 16:03:30.968][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/download/nci/NCI-Open_2012-05-01.sdf.gz".
biodb.DEBUG[2025-10-18 16:03:30.969][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-10-18 16:03:30.969][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-10-18 16:03:30.970][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-10-18 16:03:30.971][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-10-18 16:03:30.977][self$getEntryFields()$define] Define field nci.cactus.id.
biodb.DEBUG[2025-10-18 16:03:30.997][super$initialize] Initialize connector nci.cactus.
biodb.DEBUG[2025-10-18 16:03:31.017][biodb$getFactory()$createConn] Creating new connector nci.cactus for database class nci.cactus .
biodb.INFO [2025-10-18 16:03:31.025][biodb::testThat]
biodb.INFO [2025-10-18 16:03:31.025][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2025-10-18 16:03:31.026][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-10-18 16:03:31.027][biodb::testThat]
biodb.TRACE[2025-10-18 16:03:31.030][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNci.Rcheck/biodbNci/testref/entry-nci.cactus-749674-content.sdf".
biodb.DEBUG[2025-10-18 16:03:31.032][biodb$getFactory()$createEntryFromCo ...] Creating NCI CACTUS entries from 1 content(s).
biodb.DEBUG[2025-10-18 16:03:31.035][biodb$getFactory()$createEntryFromCo ...] Parsing 1 NCI CACTUS entries.
biodb.DEBUG[2025-10-18 16:03:31.042][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-10-18 16:03:31.043][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-18 16:03:31.043][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-18 16:03:31.054][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-10-18 16:03:31.055][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-18 16:03:31.056][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-10-18 16:03:31.057][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-10-18 16:03:31.073][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-18 16:03:31.074][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-18 16:03:31.075][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:03:31.076][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:03:31.077][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-18 16:03:31.088][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-18 16:03:31.089][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:03:31.090][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:03:31.092][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-10-18 16:03:31.093][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-10-18 16:03:31.094][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:03:31.095][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:03:31.118][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-10-18 16:03:31.119][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-10-18 16:03:31.120][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:03:31.121][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:03:31.122][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-10-18 16:03:31.123][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-10-18 16:03:31.124][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:03:31.125][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:03:31.126][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-10-18 16:03:31.127][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-10-18 16:03:31.128][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:03:31.129][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:03:31.131][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-10-18 16:03:31.132][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-10-18 16:03:31.133][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:03:31.133][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:03:31.134][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-10-18 16:03:31.135][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-10-18 16:03:31.136][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:03:31.137][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:03:31.139][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-10-18 16:03:31.140][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-10-18 16:03:31.140][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:03:31.141][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:03:31.142][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-10-18 16:03:31.143][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-10-18 16:03:31.144][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:03:31.145][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:03:31.147][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-10-18 16:03:31.154][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-10-18 16:03:31.155][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:03:31.156][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:03:31.157][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-10-18 16:03:31.158][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-10-18 16:03:31.159][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:03:31.160][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:03:31.160][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-18 16:03:31.161][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-18 16:03:31.162][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:03:31.163][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:03:31.164][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-10-18 16:03:31.165][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-10-18 16:03:31.166][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:03:31.167][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:03:31.168][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-18 16:03:31.169][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-18 16:03:31.170][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:03:31.171][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:03:31.172][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-18 16:03:31.173][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-18 16:03:31.173][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:03:31.174][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:03:31.175][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-18 16:03:31.176][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-18 16:03:31.177][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:03:31.178][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:03:31.209][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-18 16:03:31.210][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-18 16:03:31.211][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:03:31.212][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:03:31.213][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-18 16:03:31.214][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-18 16:03:31.214][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:03:31.215][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:03:31.216][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-18 16:03:31.217][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-18 16:03:31.218][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:03:31.219][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-10-18 16:03:31.220][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 749674.
biodb.TRACE[2025-10-18 16:03:31.222][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-10-18 16:03:31.223][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-10-18 16:03:31.224][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:03:31.225][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:03:31.226][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-10-18 16:03:31.227][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-10-18 16:03:31.228][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:03:31.229][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:03:31.230][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-10-18 16:03:31.231][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-10-18 16:03:31.231][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:03:31.232][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:03:31.233][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-10-18 16:03:31.234][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-10-18 16:03:31.235][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:03:31.236][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:03:31.238][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-18 16:03:31.239][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-18 16:03:31.240][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:03:31.241][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:03:31.253][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-10-18 16:03:31.254][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-10-18 16:03:31.255][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:03:31.256][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:03:31.302][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-18 16:03:31.303][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-18 16:03:31.304][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:03:31.305][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:03:31.306][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-18 16:03:31.307][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-18 16:03:31.308][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:03:31.308][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:03:31.309][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-18 16:03:31.310][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-18 16:03:31.311][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:03:31.312][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:03:31.315][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-18 16:03:31.316][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-18 16:03:31.317][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:03:31.317][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:03:31.318][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-18 16:03:31.319][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-18 16:03:31.320][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:03:31.321][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:03:31.322][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-18 16:03:31.323][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-18 16:03:31.324][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:03:31.325][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:03:31.326][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-10-18 16:03:31.327][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-10-18 16:03:31.328][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:03:31.329][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:03:31.330][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-10-18 16:03:31.331][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-10-18 16:03:31.332][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:03:31.333][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:03:31.333][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-10-18 16:03:31.334][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-10-18 16:03:31.335][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:03:31.336][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:03:31.343][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-18 16:03:31.344][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-18 16:03:31.345][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:03:31.346][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:03:31.346][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-18 16:03:31.347][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-18 16:03:31.348][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:03:31.349][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:03:31.350][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-18 16:03:31.351][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-18 16:03:31.352][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:03:31.353][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:03:31.354][ef$get] Asked field names are: accession.
biodb.TRACE[2025-10-18 16:03:31.355][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-18 16:03:31.356][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:03:31.357][ef$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:03:31.357][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-18 16:03:31.358][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-18 16:03:31.359][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:03:31.360][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:03:31.368][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-10-18 16:03:31.369][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-10-18 16:03:31.369][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:03:31.370][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:03:31.371][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-10-18 16:03:31.372][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-10-18 16:03:31.373][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:03:31.374][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:03:31.375][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-10-18 16:03:31.376][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-10-18 16:03:31.377][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:03:31.378][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:03:31.379][ef$get] Asked field names are: formula.
biodb.TRACE[2025-10-18 16:03:31.380][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-10-18 16:03:31.380][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:03:31.381][ef$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:03:31.382][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-10-18 16:03:31.383][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-10-18 16:03:31.384][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:03:31.385][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:03:31.392][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-10-18 16:03:31.393][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-10-18 16:03:31.394][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:03:31.395][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:03:31.396][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-10-18 16:03:31.397][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-10-18 16:03:31.397][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:03:31.398][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:03:31.399][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-10-18 16:03:31.400][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-10-18 16:03:31.401][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:03:31.402][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:03:31.403][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-10-18 16:03:31.404][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-10-18 16:03:31.405][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:03:31.406][ef$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:03:31.407][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-10-18 16:03:31.408][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-10-18 16:03:31.408][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:03:31.409][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:03:31.420][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-10-18 16:03:31.421][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-10-18 16:03:31.422][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:03:31.423][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:03:31.424][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-10-18 16:03:31.425][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-10-18 16:03:31.426][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:03:31.426][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:03:31.427][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-10-18 16:03:31.428][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-10-18 16:03:31.429][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:03:31.430][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:03:31.431][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-10-18 16:03:31.432][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-10-18 16:03:31.433][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:03:31.434][ef$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:03:31.435][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-10-18 16:03:31.436][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-10-18 16:03:31.437][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:03:31.437][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:03:31.445][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-10-18 16:03:31.446][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-10-18 16:03:31.446][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:03:31.447][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:03:31.448][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-10-18 16:03:31.449][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-10-18 16:03:31.450][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:03:31.451][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:03:31.452][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-10-18 16:03:31.453][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-10-18 16:03:31.454][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:03:31.455][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:03:31.455][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-10-18 16:03:31.456][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-10-18 16:03:31.457][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:03:31.458][ef$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:03:31.459][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-10-18 16:03:31.460][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-10-18 16:03:31.461][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:03:31.462][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:03:31.469][ef$get] Asked field names are: accession.
biodb.TRACE[2025-10-18 16:03:31.470][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-18 16:03:31.471][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:03:31.472][ef$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:03:31.475][ef$get] Asked field names are: formula.
biodb.TRACE[2025-10-18 16:03:31.476][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-10-18 16:03:31.477][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:03:31.478][ef$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:03:31.482][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-10-18 16:03:31.483][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-10-18 16:03:31.484][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:03:31.485][ef$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:03:31.488][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-10-18 16:03:31.489][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-10-18 16:03:31.490][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:03:31.491][ef$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:03:31.495][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-10-18 16:03:31.496][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-10-18 16:03:31.496][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:03:31.497][ef$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:03:31.513][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNci.Rcheck/biodbNci/testref/entry-nci.cactus-750690-content.sdf".
biodb.DEBUG[2025-10-18 16:03:31.549][biodb$getFactory()$createEntryFromCo ...] Creating NCI CACTUS entries from 1 content(s).
biodb.DEBUG[2025-10-18 16:03:31.550][biodb$getFactory()$createEntryFromCo ...] Parsing 1 NCI CACTUS entries.
biodb.DEBUG[2025-10-18 16:03:31.552][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-10-18 16:03:31.553][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-18 16:03:31.553][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-18 16:03:31.557][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-10-18 16:03:31.558][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-18 16:03:31.559][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-10-18 16:03:31.560][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-10-18 16:03:31.569][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-18 16:03:31.570][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-18 16:03:31.570][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:03:31.571][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:03:31.572][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-18 16:03:31.573][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-18 16:03:31.574][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:03:31.575][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:03:31.592][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-10-18 16:03:31.593][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-10-18 16:03:31.594][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:03:31.595][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:03:31.596][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-10-18 16:03:31.597][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-10-18 16:03:31.598][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:03:31.598][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:03:31.600][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-10-18 16:03:31.601][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-10-18 16:03:31.602][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:03:31.603][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:03:31.604][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-10-18 16:03:31.605][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-10-18 16:03:31.605][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:03:31.606][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:03:31.608][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-10-18 16:03:31.609][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-10-18 16:03:31.609][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:03:31.610][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:03:31.611][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-10-18 16:03:31.612][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-10-18 16:03:31.613][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:03:31.614][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:03:31.615][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-10-18 16:03:31.616][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-10-18 16:03:31.617][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:03:31.618][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:03:31.619][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-10-18 16:03:31.620][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-10-18 16:03:31.621][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:03:31.622][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:03:31.623][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-10-18 16:03:31.624][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-10-18 16:03:31.625][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:03:31.626][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:03:31.627][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-10-18 16:03:31.628][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-10-18 16:03:31.632][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:03:31.633][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:03:31.634][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-10-18 16:03:31.635][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-10-18 16:03:31.636][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:03:31.637][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:03:31.637][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-10-18 16:03:31.638][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-10-18 16:03:31.639][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:03:31.640][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:03:31.641][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-10-18 16:03:31.642][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-10-18 16:03:31.643][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:03:31.644][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:03:31.646][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-10-18 16:03:31.647][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-10-18 16:03:31.647][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:03:31.648][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:03:31.649][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-10-18 16:03:31.650][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-10-18 16:03:31.651][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:03:31.652][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:03:31.653][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-10-18 16:03:31.654][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-10-18 16:03:31.655][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:03:31.656][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:03:31.657][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-10-18 16:03:31.658][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-10-18 16:03:31.659][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:03:31.660][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:03:31.661][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-10-18 16:03:31.662][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-10-18 16:03:31.663][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:03:31.664][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:03:31.665][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-10-18 16:03:31.666][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-10-18 16:03:31.667][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:03:31.668][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:03:31.669][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-18 16:03:31.670][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-18 16:03:31.670][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:03:31.671][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:03:31.672][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-10-18 16:03:31.673][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-10-18 16:03:31.674][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:03:31.675][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:03:31.676][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-18 16:03:31.677][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-18 16:03:31.678][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:03:31.679][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:03:31.680][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-18 16:03:31.681][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-18 16:03:31.681][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:03:31.682][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:03:31.683][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-18 16:03:31.684][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-18 16:03:31.685][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:03:31.686][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:03:31.687][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-18 16:03:31.688][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-18 16:03:31.689][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:03:31.690][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:03:31.691][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-18 16:03:31.692][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-18 16:03:31.693][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:03:31.693][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:03:31.694][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-18 16:03:31.695][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-18 16:03:31.696][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:03:31.697][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-10-18 16:03:31.698][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 750690.
biodb.TRACE[2025-10-18 16:03:31.717][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-10-18 16:03:31.718][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-10-18 16:03:31.719][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:03:31.720][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:03:31.721][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-10-18 16:03:31.722][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-10-18 16:03:31.723][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:03:31.724][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:03:31.725][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-10-18 16:03:31.726][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-10-18 16:03:31.726][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:03:31.727][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:03:31.728][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-10-18 16:03:31.729][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-10-18 16:03:31.730][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:03:31.731][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:03:31.733][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-18 16:03:31.734][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-18 16:03:31.734][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:03:31.735][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:03:31.740][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-10-18 16:03:31.744][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-10-18 16:03:31.745][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:03:31.746][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:03:31.750][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-18 16:03:31.751][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-18 16:03:31.752][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:03:31.753][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:03:31.753][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-18 16:03:31.754][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-18 16:03:31.755][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:03:31.756][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:03:31.757][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-18 16:03:31.758][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-18 16:03:31.759][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:03:31.760][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:03:31.762][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-18 16:03:31.763][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-18 16:03:31.764][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:03:31.765][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:03:31.766][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-18 16:03:31.767][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-18 16:03:31.768][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:03:31.768][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:03:31.769][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-18 16:03:31.770][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-18 16:03:31.771][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:03:31.772][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:03:31.773][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-10-18 16:03:31.774][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-10-18 16:03:31.775][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:03:31.776][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:03:31.777][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-10-18 16:03:31.778][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-10-18 16:03:31.779][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:03:31.780][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:03:31.781][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-10-18 16:03:31.782][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-10-18 16:03:31.782][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:03:31.783][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:03:31.798][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-18 16:03:31.799][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-18 16:03:31.800][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:03:31.801][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:03:31.802][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-18 16:03:31.803][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-18 16:03:31.804][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:03:31.805][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:03:31.805][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-18 16:03:31.806][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-18 16:03:31.807][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:03:31.808][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:03:31.809][ef$get] Asked field names are: accession.
biodb.TRACE[2025-10-18 16:03:31.810][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-18 16:03:31.811][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:03:31.812][ef$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:03:31.813][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-18 16:03:31.814][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-18 16:03:31.815][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:03:31.815][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:03:31.823][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-10-18 16:03:31.824][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-10-18 16:03:31.824][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:03:31.825][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:03:31.826][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-10-18 16:03:31.827][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-10-18 16:03:31.828][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:03:31.829][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:03:31.830][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-10-18 16:03:31.831][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-10-18 16:03:31.832][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:03:31.833][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:03:31.834][ef$get] Asked field names are: cas.id.
biodb.TRACE[2025-10-18 16:03:31.834][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-10-18 16:03:31.835][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:03:31.836][ef$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:03:31.837][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-10-18 16:03:31.838][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-10-18 16:03:31.839][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:03:31.840][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:03:31.847][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-10-18 16:03:31.848][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-10-18 16:03:31.849][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:03:31.850][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:03:31.851][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-10-18 16:03:31.856][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-10-18 16:03:31.857][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:03:31.858][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:03:31.858][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-10-18 16:03:31.859][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-10-18 16:03:31.860][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:03:31.861][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:03:31.862][ef$get] Asked field names are: name.
biodb.TRACE[2025-10-18 16:03:31.863][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-10-18 16:03:31.864][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:03:31.865][ef$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:03:31.866][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-10-18 16:03:31.867][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-10-18 16:03:31.868][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:03:31.869][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:03:31.876][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-10-18 16:03:31.877][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-10-18 16:03:31.878][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:03:31.879][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:03:31.880][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-10-18 16:03:31.881][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-10-18 16:03:31.881][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:03:31.882][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:03:31.883][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-10-18 16:03:31.884][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-10-18 16:03:31.885][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:03:31.886][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:03:31.887][ef$get] Asked field names are: formula.
biodb.TRACE[2025-10-18 16:03:31.888][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-10-18 16:03:31.889][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:03:31.890][ef$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:03:31.891][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-10-18 16:03:31.892][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-10-18 16:03:31.892][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:03:31.893][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:03:31.900][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-10-18 16:03:31.901][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-10-18 16:03:31.902][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:03:31.903][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:03:31.904][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-10-18 16:03:31.905][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-10-18 16:03:31.906][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:03:31.907][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:03:31.908][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-10-18 16:03:31.909][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-10-18 16:03:31.910][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:03:31.910][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:03:31.911][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-10-18 16:03:31.912][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-10-18 16:03:31.913][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:03:31.914][ef$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:03:31.915][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-10-18 16:03:31.916][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-10-18 16:03:31.917][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:03:31.918][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:03:31.925][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-10-18 16:03:31.926][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-10-18 16:03:31.927][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:03:31.928][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:03:31.929][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-10-18 16:03:31.929][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-10-18 16:03:31.930][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:03:31.931][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:03:31.932][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-10-18 16:03:31.933][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-10-18 16:03:31.934][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:03:31.935][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:03:31.936][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-10-18 16:03:31.937][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-10-18 16:03:31.938][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:03:31.939][ef$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:03:31.939][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-10-18 16:03:31.940][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-10-18 16:03:31.941][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:03:31.942][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:03:31.949][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-10-18 16:03:31.950][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-10-18 16:03:31.951][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:03:31.952][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:03:31.953][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-10-18 16:03:31.954][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-10-18 16:03:31.955][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:03:31.956][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:03:31.957][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-10-18 16:03:31.958][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-10-18 16:03:31.958][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:03:31.959][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:03:31.960][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-10-18 16:03:31.961][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-10-18 16:03:31.962][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:03:31.963][ef$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:03:31.964][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-10-18 16:03:31.965][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-10-18 16:03:31.966][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:03:31.970][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:03:31.977][ef$get] Asked field names are: accession.
biodb.TRACE[2025-10-18 16:03:31.978][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-18 16:03:31.979][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:03:31.980][ef$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:03:31.984][ef$get] Asked field names are: cas.id.
biodb.TRACE[2025-10-18 16:03:31.985][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-10-18 16:03:31.986][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:03:31.986][ef$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:03:31.990][ef$get] Asked field names are: formula.
biodb.TRACE[2025-10-18 16:03:31.991][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-10-18 16:03:31.992][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:03:31.993][ef$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:03:31.997][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-10-18 16:03:31.998][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-10-18 16:03:31.998][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:03:31.999][ef$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:03:32.003][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-10-18 16:03:32.004][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-10-18 16:03:32.005][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:03:32.006][ef$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:03:32.010][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-10-18 16:03:32.011][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-10-18 16:03:32.011][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:03:32.012][ef$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:03:32.016][ef$get] Asked field names are: name.
biodb.TRACE[2025-10-18 16:03:32.017][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-10-18 16:03:32.018][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:03:32.019][ef$get] fields variable is a list.
biodb.INFO [2025-10-18 16:03:32.025][biodb::testThat]
biodb.INFO [2025-10-18 16:03:32.026][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2025-10-18 16:03:32.027][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-10-18 16:03:32.027][biodb::testThat]
biodb.DEBUG[2025-10-18 16:03:32.029][private$loadEntries] Creating entries from ids [2]: "749674, 750690".
biodb.DEBUG[2025-10-18 16:03:32.032][conn$getEntryContent] Get NCI CACTUS entry content(s) for 2 id(s)...
biodb.DEBUG[2025-10-18 16:03:32.034][self$isDownloaded] Database nci.cactus has already been downloaded.
biodb.DEBUG[2025-10-18 16:03:32.062][self$isDownloaded] Database nci.cactus has already been downloaded.
biodb.INFO [2025-10-18 16:03:32.063][self$download] Extract whole database of nci.cactus.
biodb.INFO [2025-10-18 16:03:32.064][private$doExtractDownload] Extracting content of downloaded biodbNci, a library for connecting to the National Cancer Institute (USA) CACTUS Database....
biodb.INFO [2025-10-18 16:03:32.104][biodb::testThat]
biodb.INFO [2025-10-18 16:03:32.105][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2025-10-18 16:03:32.106][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-10-18 16:03:32.107][biodb::testThat]
biodb.INFO [2025-10-18 16:03:32.112][biodb::testThat]
biodb.INFO [2025-10-18 16:03:32.113][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2025-10-18 16:03:32.113][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-10-18 16:03:32.114][biodb::testThat]
biodb.WARN [2025-10-18 16:03:32.132][self$searchForEntries] This database is not searchable by field "name".
biodb.WARN [2025-10-18 16:03:32.149][self$searchForEntries] This database is not searchable by field "name".
biodb.INFO [2025-10-18 16:03:32.157][biodb::testThat]
biodb.INFO [2025-10-18 16:03:32.158][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2025-10-18 16:03:32.158][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-10-18 16:03:32.159][biodb::testThat]
biodb.DEBUG[2025-10-18 16:03:32.175][private$loadEntries] Creating entries from ids [1]: "749674".
biodb.DEBUG[2025-10-18 16:03:32.223][conn$getEntryContent] Get NCI CACTUS entry content(s) for 1 id(s)...
biodb.DEBUG[2025-10-18 16:03:32.225][self$isDownloaded] Database nci.cactus has already been downloaded.
biodb.DEBUG[2025-10-18 16:03:32.226][self$isDownloaded] Database nci.cactus has already been downloaded.
biodb.INFO [2025-10-18 16:03:32.227][self$download] Extract whole database of nci.cactus.
biodb.INFO [2025-10-18 16:03:32.239][private$doExtractDownload] Extracting content of downloaded biodbNci, a library for connecting to the National Cancer Institute (USA) CACTUS Database....
biodb.INFO [2025-10-18 16:03:32.261][biodb::testThat]
biodb.INFO [2025-10-18 16:03:32.262][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2025-10-18 16:03:32.263][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-10-18 16:03:32.263][biodb::testThat]
biodb.INFO [2025-10-18 16:03:32.270][biodb::testThat]
biodb.INFO [2025-10-18 16:03:32.271][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2025-10-18 16:03:32.275][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-10-18 16:03:32.276][biodb::testThat]
biodb.INFO [2025-10-18 16:03:32.282][biodb::testThat]
biodb.INFO [2025-10-18 16:03:32.283][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2025-10-18 16:03:32.284][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-10-18 16:03:32.285][biodb::testThat]
biodb.INFO [2025-10-18 16:03:32.290][biodb::testThat]
biodb.INFO [2025-10-18 16:03:32.291][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2025-10-18 16:03:32.292][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-10-18 16:03:32.293][biodb::testThat]
biodb.INFO [2025-10-18 16:03:32.298][biodb$terminate] Closing BiodbMain instance...
biodb.INFO [2025-10-18 16:03:32.299][self$deleteConn] Connector "nci.cactus" deleted.
biodb.DEBUG[2025-10-18 16:03:32.300][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-10-18 16:03:32.300][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-18 16:03:32.301][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-18 16:03:32.302][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-18 16:03:32.303][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-18 16:03:32.304][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-10-18 16:03:32.304][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2025-10-18 16:03:32.313][biodb::testContext]
biodb.INFO [2025-10-18 16:03:32.314][biodb::testContext] ********************************************************************************
biodb.INFO [2025-10-18 16:03:32.315][biodb::testContext] Test context - Example long tests
biodb.INFO [2025-10-18 16:03:32.316][biodb::testContext] ********************************************************************************
biodb.INFO [2025-10-18 16:03:32.316][biodb::testContext]
biodb.INFO [2025-10-18 16:03:32.318][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.17.2.
biodb.DEBUG[2025-10-18 16:03:32.320][self$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.22-bioc/R/site-library/biodb/definitions.yml".
biodb.DEBUG[2025-10-18 16:03:32.323][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-10-18 16:03:32.324][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-10-18 16:03:32.325][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-10-18 16:03:32.326][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-18 16:03:32.327][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-18 16:03:32.328][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-18 16:03:32.328][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-10-18 16:03:32.329][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-10-18 16:03:32.330][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-18 16:03:32.331][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-18 16:03:32.332][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-18 16:03:32.333][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-10-18 16:03:32.334][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-10-18 16:03:32.335][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-18 16:03:32.335][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-18 16:03:32.336][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-18 16:03:32.337][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-10-18 16:03:32.338][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-10-18 16:03:32.339][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-10-18 16:03:32.340][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-18 16:03:32.341][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-18 16:03:32.341][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-18 16:03:32.342][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-10-18 16:03:32.343][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-10-18 16:03:32.344][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-10-18 16:03:32.345][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-18 16:03:32.346][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-18 16:03:32.347][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[2025-10-18 16:03:32.348][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-10-18 16:03:32.349][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-10-18 16:03:32.349][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-18 16:03:32.350][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-18 16:03:32.351][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-18 16:03:32.352][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-10-18 16:03:32.353][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-10-18 16:03:32.354][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-10-18 16:03:32.355][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-18 16:03:32.355][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-18 16:03:32.356][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-18 16:03:32.357][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-10-18 16:03:32.358][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-10-18 16:03:32.359][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-18 16:03:32.360][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-18 16:03:32.361][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-18 16:03:32.361][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-10-18 16:03:32.362][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-10-18 16:03:32.363][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-10-18 16:03:32.364][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-18 16:03:32.365][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-18 16:03:32.366][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[2025-10-18 16:03:32.367][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-10-18 16:03:32.368][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-10-18 16:03:32.369][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-10-18 16:03:32.369][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-10-18 16:03:32.370][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-10-18 16:03:32.371][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-10-18 16:03:32.372][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-18 16:03:32.373][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-18 16:03:32.374][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-18 16:03:32.375][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-10-18 16:03:32.376][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-10-18 16:03:32.377][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-18 16:03:32.377][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-18 16:03:32.378][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-18 16:03:32.379][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-10-18 16:03:32.384][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-10-18 16:03:32.385][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-18 16:03:32.386][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-18 16:03:32.387][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-18 16:03:32.388][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-10-18 16:03:32.389][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-10-18 16:03:32.389][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-18 16:03:32.390][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-18 16:03:32.391][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[2025-10-18 16:03:32.392][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-10-18 16:03:32.393][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-10-18 16:03:32.394][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-10-18 16:03:32.395][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-18 16:03:32.396][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-18 16:03:32.396][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-18 16:03:32.397][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-10-18 16:03:32.398][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-10-18 16:03:32.402][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-10-18 16:03:32.403][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-18 16:03:32.404][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-18 16:03:32.405][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-18 16:03:32.405][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-10-18 16:03:32.406][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-10-18 16:03:32.407][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-10-18 16:03:32.408][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-18 16:03:32.409][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-18 16:03:32.410][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-18 16:03:32.411][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-10-18 16:03:32.413][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-10-18 16:03:32.414][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2025-10-18 16:03:32.414][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-10-18 16:03:32.415][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-10-18 16:03:32.416][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-10-18 16:03:32.417][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-10-18 16:03:32.418][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-10-18 16:03:32.419][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-10-18 16:03:32.420][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-10-18 16:03:32.421][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-10-18 16:03:32.422][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-10-18 16:03:32.423][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-10-18 16:03:32.424][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-10-18 16:03:32.425][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-10-18 16:03:32.426][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-10-18 16:03:32.427][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-10-18 16:03:32.427][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-10-18 16:03:32.427][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-10-18 16:03:32.427][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-10-18 16:03:32.427][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-10-18 16:03:32.428][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-10-18 16:03:32.428][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-18 16:03:32.429][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-18 16:03:32.430][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-10-18 16:03:32.431][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-18 16:03:32.432][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-18 16:03:32.433][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-10-18 16:03:32.434][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-10-18 16:03:32.435][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-10-18 16:03:32.435][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-10-18 16:03:32.436][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-10-18 16:03:32.437][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-10-18 16:03:32.438][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-10-18 16:03:32.440][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-10-18 16:03:32.441][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-10-18 16:03:32.442][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-10-18 16:03:32.443][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-10-18 16:03:32.444][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-10-18 16:03:32.445][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-10-18 16:03:32.446][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-10-18 16:03:32.447][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-10-18 16:03:32.448][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-10-18 16:03:32.448][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-10-18 16:03:32.449][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-10-18 16:03:32.450][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-10-18 16:03:32.451][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-10-18 16:03:32.452][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-10-18 16:03:32.453][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-10-18 16:03:32.454][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-10-18 16:03:32.454][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-10-18 16:03:32.454][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-10-18 16:03:32.454][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-10-18 16:03:32.454][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-10-18 16:03:32.455][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-10-18 16:03:32.456][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-18 16:03:32.457][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-18 16:03:32.458][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-10-18 16:03:32.458][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-18 16:03:32.459][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-18 16:03:32.460][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-10-18 16:03:32.461][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-10-18 16:03:32.462][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-10-18 16:03:32.463][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-10-18 16:03:32.464][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-10-18 16:03:32.465][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-10-18 16:03:32.466][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-10-18 16:03:32.467][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-10-18 16:03:32.468][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2025-10-18 16:03:32.469][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-10-18 16:03:32.470][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-10-18 16:03:32.471][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-10-18 16:03:32.472][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-10-18 16:03:32.473][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-10-18 16:03:32.474][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-10-18 16:03:32.475][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-10-18 16:03:32.476][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-10-18 16:03:32.477][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-10-18 16:03:32.478][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-10-18 16:03:32.479][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-10-18 16:03:32.480][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-10-18 16:03:32.480][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-10-18 16:03:32.481][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-10-18 16:03:32.482][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-10-18 16:03:32.483][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-18 16:03:32.484][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-18 16:03:32.485][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-10-18 16:03:32.486][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-18 16:03:32.487][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-18 16:03:32.487][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-10-18 16:03:32.488][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-10-18 16:03:32.489][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-10-18 16:03:32.490][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-10-18 16:03:32.491][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-10-18 16:03:32.496][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-10-18 16:03:32.497][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-10-18 16:03:32.498][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-10-18 16:03:32.499][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-10-18 16:03:32.500][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-10-18 16:03:32.501][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-10-18 16:03:32.502][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-10-18 16:03:32.503][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-10-18 16:03:32.504][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-10-18 16:03:32.505][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-10-18 16:03:32.506][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-10-18 16:03:32.507][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-10-18 16:03:32.508][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-10-18 16:03:32.509][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-10-18 16:03:32.510][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-10-18 16:03:32.510][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-10-18 16:03:32.511][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-10-18 16:03:32.512][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-10-18 16:03:32.513][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-10-18 16:03:32.514][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-18 16:03:32.515][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-18 16:03:32.516][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-10-18 16:03:32.517][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-18 16:03:32.518][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-18 16:03:32.518][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-10-18 16:03:32.519][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-10-18 16:03:32.520][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-10-18 16:03:32.521][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-10-18 16:03:32.522][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-10-18 16:03:32.523][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-10-18 16:03:32.524][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-10-18 16:03:32.525][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-10-18 16:03:32.526][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-18 16:03:32.527][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-18 16:03:32.527][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-18 16:03:32.528][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-18 16:03:32.529][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-18 16:03:32.530][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-18 16:03:32.531][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-18 16:03:32.532][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-18 16:03:32.532][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-18 16:03:32.533][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-18 16:03:32.534][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-18 16:03:32.535][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-18 16:03:32.536][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-18 16:03:32.537][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-18 16:03:32.537][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-18 16:03:32.538][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-18 16:03:32.539][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-18 16:03:32.540][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-18 16:03:32.541][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-18 16:03:32.542][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-18 16:03:32.542][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-18 16:03:32.543][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-18 16:03:32.544][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-18 16:03:32.545][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-18 16:03:32.546][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-18 16:03:32.547][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-18 16:03:32.547][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-18 16:03:32.548][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-18 16:03:32.549][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-18 16:03:32.550][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-18 16:03:32.551][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-18 16:03:32.552][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-18 16:03:32.552][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-18 16:03:32.553][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-18 16:03:32.554][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-18 16:03:32.555][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-18 16:03:32.556][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-18 16:03:32.557][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-18 16:03:32.557][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-18 16:03:32.558][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-18 16:03:32.559][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-18 16:03:32.560][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-18 16:03:32.561][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-18 16:03:32.562][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-18 16:03:32.562][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-18 16:03:32.563][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-18 16:03:32.564][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-18 16:03:32.565][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-18 16:03:32.566][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-18 16:03:32.567][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-18 16:03:32.567][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-18 16:03:32.568][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-18 16:03:32.569][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-18 16:03:32.570][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-18 16:03:32.571][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-18 16:03:32.572][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-18 16:03:32.572][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-18 16:03:32.573][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-18 16:03:32.574][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-18 16:03:32.575][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-18 16:03:32.576][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-18 16:03:32.577][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-18 16:03:32.577][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-18 16:03:32.578][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-18 16:03:32.579][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-18 16:03:32.580][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-18 16:03:32.581][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-18 16:03:32.581][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-18 16:03:32.582][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-18 16:03:32.583][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-18 16:03:32.584][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-18 16:03:32.585][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-18 16:03:32.586][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-18 16:03:32.586][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-18 16:03:32.587][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-18 16:03:32.588][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-18 16:03:32.589][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-18 16:03:32.590][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-18 16:03:32.591][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-18 16:03:32.591][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-18 16:03:32.592][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-18 16:03:32.593][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-10-18 16:03:32.595][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-10-18 16:03:32.596][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-10-18 16:03:32.597][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-10-18 16:03:32.602][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-10-18 16:03:32.604][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-10-18 16:03:32.605][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-10-18 16:03:32.606][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-10-18 16:03:32.607][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-10-18 16:03:32.609][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-10-18 16:03:32.610][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-10-18 16:03:32.611][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-10-18 16:03:32.613][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-10-18 16:03:32.614][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-10-18 16:03:32.615][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-10-18 16:03:32.617][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-10-18 16:03:32.618][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-10-18 16:03:32.619][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-10-18 16:03:32.621][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-10-18 16:03:32.622][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-10-18 16:03:32.623][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-10-18 16:03:32.624][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-10-18 16:03:32.626][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-10-18 16:03:32.627][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-10-18 16:03:32.628][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-10-18 16:03:32.630][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-10-18 16:03:32.631][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-10-18 16:03:32.632][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-10-18 16:03:32.634][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-10-18 16:03:32.635][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-10-18 16:03:32.636][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-10-18 16:03:32.638][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-10-18 16:03:32.639][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-10-18 16:03:32.640][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-10-18 16:03:32.641][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-10-18 16:03:32.643][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-10-18 16:03:32.644][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-10-18 16:03:32.645][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-10-18 16:03:32.647][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-10-18 16:03:32.648][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-10-18 16:03:32.649][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-10-18 16:03:32.651][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-10-18 16:03:32.652][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-10-18 16:03:32.653][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-10-18 16:03:32.654][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-10-18 16:03:32.656][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-10-18 16:03:32.657][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-10-18 16:03:32.658][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-10-18 16:03:32.660][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-10-18 16:03:32.661][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-10-18 16:03:32.662][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-10-18 16:03:32.664][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-10-18 16:03:32.665][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-10-18 16:03:32.666][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-10-18 16:03:32.667][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-10-18 16:03:32.669][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-10-18 16:03:32.670][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-10-18 16:03:32.671][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-10-18 16:03:32.673][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-10-18 16:03:32.674][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-10-18 16:03:32.675][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-10-18 16:03:32.676][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-10-18 16:03:32.678][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-10-18 16:03:32.679][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-10-18 16:03:32.680][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-10-18 16:03:32.682][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-10-18 16:03:32.683][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-10-18 16:03:32.684][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-10-18 16:03:32.686][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-10-18 16:03:32.687][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-10-18 16:03:32.688][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-10-18 16:03:32.689][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-10-18 16:03:32.691][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-10-18 16:03:32.692][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-10-18 16:03:32.693][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-10-18 16:03:32.695][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-10-18 16:03:32.696][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-10-18 16:03:32.697][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-10-18 16:03:32.699][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-10-18 16:03:32.700][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-10-18 16:03:32.701][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-10-18 16:03:32.703][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-10-18 16:03:32.708][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-10-18 16:03:32.710][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-10-18 16:03:32.711][initialize] This is biodb version 1.17.2.
biodb.DEBUG[2025-10-18 16:03:32.712][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-10-18 16:03:32.713][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-10-18 16:03:32.714][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-18 16:03:32.714][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-10-18 16:03:32.715][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-18 16:03:32.716][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-18 16:03:32.717][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-18 16:03:32.718][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-18 16:03:32.719][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-18 16:03:32.720][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-18 16:03:32.720][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-18 16:03:32.721][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-18 16:03:32.722][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-18 16:03:32.723][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-18 16:03:32.724][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-18 16:03:32.725][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-18 16:03:32.725][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-18 16:03:32.726][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-18 16:03:32.727][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-18 16:03:32.728][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-18 16:03:32.729][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-18 16:03:32.730][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-18 16:03:32.730][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-18 16:03:32.731][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-18 16:03:32.732][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-18 16:03:32.733][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-18 16:03:32.734][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-18 16:03:32.735][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-18 16:03:32.735][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-18 16:03:32.736][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-18 16:03:32.737][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-18 16:03:32.738][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-18 16:03:32.739][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-18 16:03:32.739][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-18 16:03:32.740][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-18 16:03:32.741][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-18 16:03:32.742][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-18 16:03:32.743][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-18 16:03:32.744][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-18 16:03:32.744][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-18 16:03:32.745][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-18 16:03:32.746][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-18 16:03:32.747][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-18 16:03:32.748][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-18 16:03:32.749][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-18 16:03:32.749][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-18 16:03:32.750][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-18 16:03:32.751][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-18 16:03:32.752][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-18 16:03:32.753][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-18 16:03:32.753][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-18 16:03:32.754][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-18 16:03:32.755][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-18 16:03:32.756][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-18 16:03:32.757][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-18 16:03:32.758][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-18 16:03:32.758][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-18 16:03:32.759][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-18 16:03:32.760][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-18 16:03:32.761][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-18 16:03:32.762][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-18 16:03:32.763][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-18 16:03:32.763][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-18 16:03:32.764][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-18 16:03:32.765][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-18 16:03:32.766][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-18 16:03:32.767][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-18 16:03:32.768][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-18 16:03:32.768][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-18 16:03:32.769][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-18 16:03:32.770][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-18 16:03:32.771][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-18 16:03:32.772][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-18 16:03:32.772][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-18 16:03:32.773][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-18 16:03:32.774][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-18 16:03:32.775][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-18 16:03:32.776][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-18 16:03:32.777][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-18 16:03:32.777][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-18 16:03:32.778][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-18 16:03:32.779][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.DEBUG[2025-10-18 16:03:32.780][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-18 16:03:32.781][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-18 16:03:32.782][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-18 16:03:32.782][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-18 16:03:32.783][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-18 16:03:32.784][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-18 16:03:32.785][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-18 16:03:32.786][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-18 16:03:32.786][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-18 16:03:32.787][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-18 16:03:32.788][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-18 16:03:32.789][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-18 16:03:32.790][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-18 16:03:32.791][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-18 16:03:32.791][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-18 16:03:32.792][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-18 16:03:32.793][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-18 16:03:32.794][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-18 16:03:32.795][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-18 16:03:32.796][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-18 16:03:32.796][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-18 16:03:32.797][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-18 16:03:32.798][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-18 16:03:32.799][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-18 16:03:32.800][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-18 16:03:32.801][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-18 16:03:32.801][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-18 16:03:32.802][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-18 16:03:32.803][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-18 16:03:32.804][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-18 16:03:32.805][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-18 16:03:32.805][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-18 16:03:32.806][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-18 16:03:32.807][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-18 16:03:32.808][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-18 16:03:32.813][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNci.Rcheck/biodbNci/definitions.yml".
biodb.DEBUG[2025-10-18 16:03:32.814][self$getDbsInfo()$define] Define connector nci.cactus.
biodb.DEBUG[2025-10-18 16:03:32.816][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-10-18 16:03:32.817][self$setPropertyValue] Setting property "description" to "National Cancer Institute (USA) CACTUS Database.".
biodb.DEBUG[2025-10-18 16:03:32.818][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-10-18 16:03:32.819][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-10-18 16:03:32.820][self$setPropertyValue] Setting property "downloadable" to "TRUE".
biodb.DEBUG[2025-10-18 16:03:32.821][self$setPropertyValue] Setting property "dwnld.ext" to "gz".
biodb.DEBUG[2025-10-18 16:03:32.822][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-10-18 16:03:32.823][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-10-18 16:03:32.824][self$setPropertyValue] Setting property "entry.content.type" to "sdf".
biodb.DEBUG[2025-10-18 16:03:32.825][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-10-18 16:03:32.826][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-10-18 16:03:32.827][self$setPropertyValue] Setting property "name" to "NCI CACTUS".
biodb.DEBUG[2025-10-18 16:03:32.827][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-10-18 16:03:32.828][self$setPropertyValue] Setting property "parsing.expr" to "NSC".
biodb.DEBUG[2025-10-18 16:03:32.828][self$setPropertyValue] Setting property "parsing.expr" to "DTP names".
biodb.DEBUG[2025-10-18 16:03:32.828][self$setPropertyValue] Setting property "parsing.expr" to "Standard InChI".
biodb.DEBUG[2025-10-18 16:03:32.828][self$setPropertyValue] Setting property "parsing.expr" to "c("Standard InChIKey", "^InChIKey=(.*)$")".
biodb.DEBUG[2025-10-18 16:03:32.828][self$setPropertyValue] Setting property "parsing.expr" to "Formula".
biodb.DEBUG[2025-10-18 16:03:32.828][self$setPropertyValue] Setting property "parsing.expr" to "Molecular Weight".
biodb.DEBUG[2025-10-18 16:03:32.828][self$setPropertyValue] Setting property "parsing.expr" to "CAS".
biodb.DEBUG[2025-10-18 16:03:32.829][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-10-18 16:03:32.830][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-10-18 16:03:32.831][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-10-18 16:03:32.832][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-18 16:03:32.833][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-18 16:03:32.834][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-10-18 16:03:32.835][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-18 16:03:32.836][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-18 16:03:32.836][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-10-18 16:03:32.837][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/".
biodb.DEBUG[2025-10-18 16:03:32.837][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/".
biodb.DEBUG[2025-10-18 16:03:32.837][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/download/nci/".
biodb.DEBUG[2025-10-18 16:03:32.837][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/download/nci/NCI-Open_2012-05-01.sdf.gz".
biodb.DEBUG[2025-10-18 16:03:32.838][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-10-18 16:03:32.839][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-10-18 16:03:32.840][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-10-18 16:03:32.841][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-10-18 16:03:32.842][self$getEntryFields()$define] Define field nci.cactus.id.
biodb.DEBUG[2025-10-18 16:03:32.845][super$initialize] Initialize connector nci.cactus.
biodb.DEBUG[2025-10-18 16:03:32.848][biodb$getFactory()$createConn] Creating new connector nci.cactus for database class nci.cactus .
biodb.INFO [2025-10-18 16:03:32.849][biodb$terminate] Closing BiodbMain instance...
biodb.INFO [2025-10-18 16:03:32.850][self$deleteConn] Connector "nci.cactus" deleted.
biodb.DEBUG[2025-10-18 16:03:32.851][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-10-18 16:03:32.852][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-18 16:03:32.853][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-18 16:03:32.854][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-18 16:03:32.854][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-18 16:03:32.855][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-10-18 16:03:32.856][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
[ 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)