Back to Long Tests report for BioC 3.22

This page was generated on 2025-10-11 23:55 -0400 (Sat, 11 Oct 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" 4864
lconwaymacOS 12.7.1 Montereyx86_644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4652
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 8/30HostnameOS / ArchCHECK
biodbNci 1.13.1  (landing page)
Pierrick Roger
Snapshot Date: 2025-10-11 09:55 -0400 (Sat, 11 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 12.7.1 Monterey / x86_64  ERROR  

CHECK results for biodbNci on nebbiolo2

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

raw results


Summary

Package: biodbNci
Version: 1.13.1
Command: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --test-dir=longtests --no-stop-on-test-error --no-codoc --no-examples --no-manual --ignore-vignettes --check-subdirs=no biodbNci_1.13.1.tar.gz
StartedAt: 2025-10-11 16:02:29 -0400 (Sat, 11 Oct 2025)
EndedAt: 2025-10-11 16:03:32 -0400 (Sat, 11 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 [2025-10-11 16:03:28.927][biodb::testContext]
biodb.INFO [2025-10-11 16:03:28.929][biodb::testContext] ********************************************************************************
biodb.INFO [2025-10-11 16:03:28.930][biodb::testContext] Test context - Generic long tests
biodb.INFO [2025-10-11 16:03:28.931][biodb::testContext] ********************************************************************************
biodb.INFO [2025-10-11 16:03:28.932][biodb::testContext]
biodb.INFO [2025-10-11 16:03:28.938][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.17.2.
biodb.DEBUG[2025-10-11 16:03:28.940][self$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.22-bioc/R/site-library/biodb/definitions.yml".
biodb.DEBUG[2025-10-11 16:03:28.946][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-10-11 16:03:28.947][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-10-11 16:03:28.948][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-10-11 16:03:28.949][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:03:28.950][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:03:28.951][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-11 16:03:28.952][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-10-11 16:03:28.970][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-10-11 16:03:28.970][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:03:28.971][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:03:28.972][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-11 16:03:28.973][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-10-11 16:03:28.974][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-10-11 16:03:28.975][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:03:28.976][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:03:28.985][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-11 16:03:28.986][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-10-11 16:03:28.987][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-10-11 16:03:28.988][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-10-11 16:03:28.989][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:03:28.989][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:03:28.990][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-11 16:03:28.991][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-10-11 16:03:28.992][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-10-11 16:03:28.993][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-10-11 16:03:28.994][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:03:28.995][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:03:28.995][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-11 16:03:28.996][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-10-11 16:03:28.997][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-10-11 16:03:28.998][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:03:28.999][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:03:29.000][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-11 16:03:29.001][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-10-11 16:03:29.002][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-10-11 16:03:29.003][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-10-11 16:03:29.003][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:03:29.004][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:03:29.005][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-11 16:03:29.006][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-10-11 16:03:29.007][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-10-11 16:03:29.008][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:03:29.009][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:03:29.009][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-11 16:03:29.010][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-10-11 16:03:29.011][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-10-11 16:03:29.012][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-10-11 16:03:29.013][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:03:29.014][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:03:29.015][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-11 16:03:29.016][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-10-11 16:03:29.017][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-10-11 16:03:29.017][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-10-11 16:03:29.018][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-10-11 16:03:29.019][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-10-11 16:03:29.020][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-10-11 16:03:29.021][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:03:29.022][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:03:29.023][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-11 16:03:29.024][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-10-11 16:03:29.025][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-10-11 16:03:29.025][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:03:29.026][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:03:29.027][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-11 16:03:29.028][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-10-11 16:03:29.029][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-10-11 16:03:29.030][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:03:29.031][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:03:29.031][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-11 16:03:29.032][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-10-11 16:03:29.033][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-10-11 16:03:29.034][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:03:29.035][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:03:29.036][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-11 16:03:29.037][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-10-11 16:03:29.037][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-10-11 16:03:29.038][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-10-11 16:03:29.039][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:03:29.040][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:03:29.041][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-11 16:03:29.042][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-10-11 16:03:29.043][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-10-11 16:03:29.046][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-10-11 16:03:29.047][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:03:29.048][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:03:29.049][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-11 16:03:29.050][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-10-11 16:03:29.050][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-10-11 16:03:29.051][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-10-11 16:03:29.052][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:03:29.053][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:03:29.054][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-11 16:03:29.057][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-10-11 16:03:29.088][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-10-11 16:03:29.102][self$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[2025-10-11 16:03:29.103][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-10-11 16:03:29.104][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-10-11 16:03:29.105][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-10-11 16:03:29.106][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-10-11 16:03:29.107][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-10-11 16:03:29.108][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-10-11 16:03:29.109][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-10-11 16:03:29.110][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-10-11 16:03:29.110][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-10-11 16:03:29.111][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-10-11 16:03:29.112][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-10-11 16:03:29.113][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-10-11 16:03:29.114][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-10-11 16:03:29.115][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-10-11 16:03:29.115][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-10-11 16:03:29.115][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-10-11 16:03:29.115][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-10-11 16:03:29.115][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-10-11 16:03:29.116][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-10-11 16:03:29.117][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-11 16:03:29.118][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-11 16:03:29.119][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-10-11 16:03:29.120][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-11 16:03:29.120][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-11 16:03:29.121][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-10-11 16:03:29.122][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-10-11 16:03:29.123][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-10-11 16:03:29.124][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-10-11 16:03:29.125][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-10-11 16:03:29.126][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-10-11 16:03:29.127][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-10-11 16:03:29.128][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-10-11 16:03:29.129][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-10-11 16:03:29.130][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-10-11 16:03:29.131][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-10-11 16:03:29.132][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-10-11 16:03:29.133][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-10-11 16:03:29.138][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-10-11 16:03:29.139][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-10-11 16:03:29.140][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-10-11 16:03:29.141][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-10-11 16:03:29.142][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-10-11 16:03:29.143][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-10-11 16:03:29.143][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-10-11 16:03:29.144][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-10-11 16:03:29.145][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-10-11 16:03:29.146][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-10-11 16:03:29.146][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-10-11 16:03:29.146][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-10-11 16:03:29.146][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-10-11 16:03:29.146][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-10-11 16:03:29.147][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-10-11 16:03:29.148][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-11 16:03:29.149][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-11 16:03:29.150][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-10-11 16:03:29.151][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-11 16:03:29.152][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-11 16:03:29.152][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-10-11 16:03:29.153][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-10-11 16:03:29.154][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-10-11 16:03:29.155][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-10-11 16:03:29.156][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-10-11 16:03:29.157][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-10-11 16:03:29.158][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-10-11 16:03:29.160][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-10-11 16:03:29.161][self$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[2025-10-11 16:03:29.162][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-10-11 16:03:29.162][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-10-11 16:03:29.163][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-10-11 16:03:29.164][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-10-11 16:03:29.165][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-10-11 16:03:29.166][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-10-11 16:03:29.167][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-10-11 16:03:29.168][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-10-11 16:03:29.169][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-10-11 16:03:29.170][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-10-11 16:03:29.171][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-10-11 16:03:29.172][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-10-11 16:03:29.173][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-10-11 16:03:29.174][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-10-11 16:03:29.174][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-10-11 16:03:29.175][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-11 16:03:29.176][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-11 16:03:29.177][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-10-11 16:03:29.178][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-11 16:03:29.179][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-11 16:03:29.180][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-10-11 16:03:29.181][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-10-11 16:03:29.181][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-10-11 16:03:29.182][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-10-11 16:03:29.183][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-10-11 16:03:29.184][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-10-11 16:03:29.185][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-10-11 16:03:29.187][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-10-11 16:03:29.188][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-10-11 16:03:29.189][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-10-11 16:03:29.190][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-10-11 16:03:29.190][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-10-11 16:03:29.191][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-10-11 16:03:29.192][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-10-11 16:03:29.193][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-10-11 16:03:29.194][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-10-11 16:03:29.195][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-10-11 16:03:29.196][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-10-11 16:03:29.197][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-10-11 16:03:29.198][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-10-11 16:03:29.199][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-10-11 16:03:29.200][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-10-11 16:03:29.201][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-10-11 16:03:29.201][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-10-11 16:03:29.202][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-11 16:03:29.203][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-11 16:03:29.204][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-10-11 16:03:29.205][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-11 16:03:29.206][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-11 16:03:29.207][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-10-11 16:03:29.208][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-10-11 16:03:29.209][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-10-11 16:03:29.209][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-10-11 16:03:29.210][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-10-11 16:03:29.211][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-10-11 16:03:29.215][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-10-11 16:03:29.216][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:03:29.216][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-11 16:03:29.217][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:03:29.218][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:03:29.219][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:03:29.220][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:03:29.221][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-11 16:03:29.221][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:03:29.222][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:03:29.223][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:03:29.224][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:03:29.225][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-11 16:03:29.226][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:03:29.226][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:03:29.227][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:03:29.228][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:03:29.229][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-11 16:03:29.230][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:03:29.230][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:03:29.231][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:03:29.232][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:03:29.233][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-11 16:03:29.234][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:03:29.235][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:03:29.235][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:03:29.236][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:03:29.237][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-11 16:03:29.238][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:03:29.239][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:03:29.239][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:03:29.240][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:03:29.241][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-11 16:03:29.242][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:03:29.243][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:03:29.244][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:03:29.244][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:03:29.245][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-11 16:03:29.246][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:03:29.247][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:03:29.248][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:03:29.249][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:03:29.249][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-11 16:03:29.250][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:03:29.251][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:03:29.252][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:03:29.253][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:03:29.254][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-11 16:03:29.254][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:03:29.255][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:03:29.256][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:03:29.257][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:03:29.258][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-11 16:03:29.259][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:03:29.259][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:03:29.260][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:03:29.261][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:03:29.262][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-11 16:03:29.263][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:03:29.264][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:03:29.264][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:03:29.265][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:03:29.266][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-11 16:03:29.267][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:03:29.268][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:03:29.269][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:03:29.269][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:03:29.270][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-11 16:03:29.271][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:03:29.272][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:03:29.273][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:03:29.273][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:03:29.274][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-11 16:03:29.275][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:03:29.276][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:03:29.277][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:03:29.278][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:03:29.278][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-11 16:03:29.279][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:03:29.280][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:03:29.281][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:03:29.282][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:03:29.283][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-11 16:03:29.283][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-10-11 16:03:29.288][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-10-11 16:03:29.293][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-10-11 16:03:29.294][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-10-11 16:03:29.295][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-10-11 16:03:29.297][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-10-11 16:03:29.298][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-10-11 16:03:29.299][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-10-11 16:03:29.300][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-10-11 16:03:29.302][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-10-11 16:03:29.303][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-10-11 16:03:29.304][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-10-11 16:03:29.306][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-10-11 16:03:29.307][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-10-11 16:03:29.308][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-10-11 16:03:29.309][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-10-11 16:03:29.311][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-10-11 16:03:29.312][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-10-11 16:03:29.313][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-10-11 16:03:29.315][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-10-11 16:03:29.316][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-10-11 16:03:29.317][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-10-11 16:03:29.319][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-10-11 16:03:29.320][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-10-11 16:03:29.321][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-10-11 16:03:29.322][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-10-11 16:03:29.324][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-10-11 16:03:29.325][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-10-11 16:03:29.326][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-10-11 16:03:29.328][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-10-11 16:03:29.329][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-10-11 16:03:29.330][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-10-11 16:03:29.332][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-10-11 16:03:29.333][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-10-11 16:03:29.334][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-10-11 16:03:29.335][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-10-11 16:03:29.337][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-10-11 16:03:29.338][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-10-11 16:03:29.339][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-10-11 16:03:29.341][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-10-11 16:03:29.342][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-10-11 16:03:29.343][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-10-11 16:03:29.345][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-10-11 16:03:29.346][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-10-11 16:03:29.354][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-10-11 16:03:29.356][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-10-11 16:03:29.358][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-10-11 16:03:29.359][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-10-11 16:03:29.361][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-10-11 16:03:29.362][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-10-11 16:03:29.364][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-10-11 16:03:29.365][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-10-11 16:03:29.367][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-10-11 16:03:29.368][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-10-11 16:03:29.370][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-10-11 16:03:29.371][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-10-11 16:03:29.373][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-10-11 16:03:29.374][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-10-11 16:03:29.375][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-10-11 16:03:29.377][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-10-11 16:03:29.378][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-10-11 16:03:29.380][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-10-11 16:03:29.381][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-10-11 16:03:29.383][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-10-11 16:03:29.384][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-10-11 16:03:29.386][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-10-11 16:03:29.387][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-10-11 16:03:29.388][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-10-11 16:03:29.390][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-10-11 16:03:29.391][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-10-11 16:03:29.393][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-10-11 16:03:29.394][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-10-11 16:03:29.396][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-10-11 16:03:29.397][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-10-11 16:03:29.398][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-10-11 16:03:29.400][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-10-11 16:03:29.401][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-10-11 16:03:29.403][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-10-11 16:03:29.404][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-10-11 16:03:29.406][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-10-11 16:03:29.407][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-10-11 16:03:29.409][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-10-11 16:03:29.410][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-10-11 16:03:29.417][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-10-11 16:03:29.419][initialize] This is biodb version 1.17.2.
biodb.DEBUG[2025-10-11 16:03:29.423][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-10-11 16:03:29.424][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:03:29.424][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:03:29.425][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:03:29.426][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-11 16:03:29.431][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:03:29.432][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-11 16:03:29.433][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-11 16:03:29.434][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:03:29.435][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:03:29.436][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:03:29.437][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-11 16:03:29.438][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:03:29.439][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-11 16:03:29.440][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-11 16:03:29.440][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:03:29.441][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:03:29.442][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:03:29.443][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-11 16:03:29.444][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:03:29.445][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-11 16:03:29.446][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-11 16:03:29.447][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:03:29.448][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:03:29.449][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:03:29.450][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-11 16:03:29.451][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:03:29.451][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-11 16:03:29.452][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-11 16:03:29.453][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:03:29.454][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:03:29.455][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:03:29.456][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-11 16:03:29.470][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:03:29.470][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-11 16:03:29.471][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-11 16:03:29.472][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:03:29.473][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:03:29.474][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:03:29.475][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-11 16:03:29.476][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:03:29.477][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-11 16:03:29.478][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-11 16:03:29.479][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:03:29.480][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:03:29.481][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:03:29.482][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-11 16:03:29.482][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:03:29.483][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-11 16:03:29.484][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-11 16:03:29.485][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:03:29.486][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:03:29.487][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:03:29.488][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-11 16:03:29.489][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:03:29.490][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-11 16:03:29.491][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-11 16:03:29.492][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:03:29.492][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:03:29.493][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:03:29.494][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-11 16:03:29.495][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:03:29.496][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-11 16:03:29.497][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-11 16:03:29.498][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:03:29.499][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:03:29.500][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:03:29.501][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-11 16:03:29.501][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:03:29.502][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-11 16:03:29.503][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-11 16:03:29.504][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:03:29.505][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:03:29.506][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:03:29.507][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-11 16:03:29.508][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:03:29.509][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-11 16:03:29.510][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-11 16:03:29.510][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:03:29.511][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:03:29.512][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:03:29.513][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-11 16:03:29.514][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:03:29.515][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-11 16:03:29.516][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-11 16:03:29.517][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:03:29.518][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:03:29.518][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:03:29.519][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-11 16:03:29.520][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:03:29.521][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-11 16:03:29.522][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-11 16:03:29.523][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:03:29.524][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:03:29.525][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:03:29.526][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[2025-10-11 16:03:29.526][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:03:29.527][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-11 16:03:29.528][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-11 16:03:29.529][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:03:29.530][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:03:29.531][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:03:29.531][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-11 16:03:29.532][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:03:29.533][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-11 16:03:29.534][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-11 16:03:29.535][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:03:29.536][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:03:29.536][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:03:29.537][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-11 16:03:29.538][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:03:29.539][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-11 16:03:29.540][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-11 16:03:29.540][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:03:29.541][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:03:29.542][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:03:29.543][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-11 16:03:29.545][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNci.Rcheck/biodbNci/definitions.yml".
biodb.DEBUG[2025-10-11 16:03:29.554][self$getDbsInfo()$define] Define connector nci.cactus.
biodb.DEBUG[2025-10-11 16:03:29.555][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-10-11 16:03:29.556][self$setPropertyValue] Setting property "description" to "National Cancer Institute (USA) CACTUS Database.".
biodb.DEBUG[2025-10-11 16:03:29.557][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-10-11 16:03:29.558][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-10-11 16:03:29.559][self$setPropertyValue] Setting property "downloadable" to "TRUE".
biodb.DEBUG[2025-10-11 16:03:29.560][self$setPropertyValue] Setting property "dwnld.ext" to "gz".
biodb.DEBUG[2025-10-11 16:03:29.561][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-10-11 16:03:29.562][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-10-11 16:03:29.563][self$setPropertyValue] Setting property "entry.content.type" to "sdf".
biodb.DEBUG[2025-10-11 16:03:29.564][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-10-11 16:03:29.565][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-10-11 16:03:29.566][self$setPropertyValue] Setting property "name" to "NCI CACTUS".
biodb.DEBUG[2025-10-11 16:03:29.567][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-10-11 16:03:29.567][self$setPropertyValue] Setting property "parsing.expr" to "NSC".
biodb.DEBUG[2025-10-11 16:03:29.567][self$setPropertyValue] Setting property "parsing.expr" to "DTP names".
biodb.DEBUG[2025-10-11 16:03:29.567][self$setPropertyValue] Setting property "parsing.expr" to "Standard InChI".
biodb.DEBUG[2025-10-11 16:03:29.567][self$setPropertyValue] Setting property "parsing.expr" to "c("Standard InChIKey", "^InChIKey=(.*)$")".
biodb.DEBUG[2025-10-11 16:03:29.567][self$setPropertyValue] Setting property "parsing.expr" to "Formula".
biodb.DEBUG[2025-10-11 16:03:29.567][self$setPropertyValue] Setting property "parsing.expr" to "Molecular Weight".
biodb.DEBUG[2025-10-11 16:03:29.567][self$setPropertyValue] Setting property "parsing.expr" to "CAS".
biodb.DEBUG[2025-10-11 16:03:29.568][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-10-11 16:03:29.569][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-10-11 16:03:29.570][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-10-11 16:03:29.571][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-11 16:03:29.572][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-11 16:03:29.573][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-10-11 16:03:29.574][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-11 16:03:29.575][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-11 16:03:29.575][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-10-11 16:03:29.576][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/".
biodb.DEBUG[2025-10-11 16:03:29.576][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/".
biodb.DEBUG[2025-10-11 16:03:29.576][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/download/nci/".
biodb.DEBUG[2025-10-11 16:03:29.576][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/download/nci/NCI-Open_2012-05-01.sdf.gz".
biodb.DEBUG[2025-10-11 16:03:29.577][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-10-11 16:03:29.578][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-10-11 16:03:29.579][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-10-11 16:03:29.580][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-10-11 16:03:29.586][self$getEntryFields()$define] Define field nci.cactus.id.
biodb.DEBUG[2025-10-11 16:03:29.606][super$initialize] Initialize connector nci.cactus.
biodb.DEBUG[2025-10-11 16:03:29.621][biodb$getFactory()$createConn] Creating new connector nci.cactus for database class nci.cactus .
biodb.INFO [2025-10-11 16:03:29.630][biodb::testThat]
biodb.INFO [2025-10-11 16:03:29.636][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2025-10-11 16:03:29.637][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-10-11 16:03:29.638][biodb::testThat]
biodb.TRACE[2025-10-11 16:03:29.641][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNci.Rcheck/biodbNci/testref/entry-nci.cactus-749674-content.sdf".
biodb.DEBUG[2025-10-11 16:03:29.643][biodb$getFactory()$createEntryFromCo ...] Creating NCI CACTUS entries from 1 content(s).
biodb.DEBUG[2025-10-11 16:03:29.646][biodb$getFactory()$createEntryFromCo ...] Parsing 1 NCI CACTUS entries.
biodb.DEBUG[2025-10-11 16:03:29.653][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-10-11 16:03:29.654][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-11 16:03:29.655][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-11 16:03:29.666][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:03:29.667][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:03:29.667][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:03:29.668][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-10-11 16:03:29.684][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-11 16:03:29.685][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-11 16:03:29.686][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:03:29.687][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:03:29.688][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-11 16:03:29.700][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-11 16:03:29.701][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:03:29.701][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:03:29.704][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-10-11 16:03:29.705][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-10-11 16:03:29.706][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:03:29.706][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:03:29.730][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-10-11 16:03:29.731][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-10-11 16:03:29.732][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:03:29.733][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:03:29.734][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-10-11 16:03:29.735][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-10-11 16:03:29.736][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:03:29.737][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:03:29.738][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-10-11 16:03:29.739][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-10-11 16:03:29.740][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:03:29.741][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:03:29.743][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-10-11 16:03:29.744][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-10-11 16:03:29.745][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:03:29.746][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:03:29.747][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-10-11 16:03:29.747][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-10-11 16:03:29.748][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:03:29.749][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:03:29.751][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-10-11 16:03:29.752][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-10-11 16:03:29.752][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:03:29.753][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:03:29.754][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-10-11 16:03:29.755][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-10-11 16:03:29.756][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:03:29.757][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:03:29.759][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-10-11 16:03:29.760][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-10-11 16:03:29.761][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:03:29.762][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:03:29.762][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-10-11 16:03:29.763][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-10-11 16:03:29.764][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:03:29.765][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:03:29.766][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-11 16:03:29.773][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-11 16:03:29.774][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:03:29.775][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:03:29.776][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-10-11 16:03:29.777][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-10-11 16:03:29.778][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:03:29.778][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:03:29.779][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-11 16:03:29.780][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-11 16:03:29.781][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:03:29.782][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:03:29.783][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-11 16:03:29.784][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-11 16:03:29.785][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:03:29.786][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:03:29.787][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-11 16:03:29.788][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-11 16:03:29.789][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:03:29.789][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:03:29.820][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-11 16:03:29.821][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-11 16:03:29.822][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:03:29.823][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:03:29.824][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-11 16:03:29.825][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-11 16:03:29.826][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:03:29.827][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:03:29.828][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-11 16:03:29.829][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-11 16:03:29.830][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:03:29.831][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-10-11 16:03:29.832][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 749674.
biodb.TRACE[2025-10-11 16:03:29.834][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-10-11 16:03:29.835][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-10-11 16:03:29.836][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:03:29.836][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:03:29.837][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-10-11 16:03:29.838][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-10-11 16:03:29.839][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:03:29.840][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:03:29.841][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-10-11 16:03:29.842][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-10-11 16:03:29.843][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:03:29.844][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:03:29.845][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-10-11 16:03:29.846][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-10-11 16:03:29.847][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:03:29.847][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:03:29.849][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-11 16:03:29.850][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-11 16:03:29.851][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:03:29.852][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:03:29.864][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-10-11 16:03:29.865][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-10-11 16:03:29.866][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:03:29.867][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:03:29.871][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-11 16:03:29.872][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-11 16:03:29.873][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:03:29.874][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:03:29.875][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-11 16:03:29.876][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-11 16:03:29.917][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:03:29.918][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:03:29.919][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-11 16:03:29.920][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-11 16:03:29.921][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:03:29.922][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:03:29.924][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-11 16:03:29.925][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-11 16:03:29.926][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:03:29.927][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:03:29.928][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-11 16:03:29.929][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-11 16:03:29.930][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:03:29.931][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:03:29.932][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-11 16:03:29.933][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-11 16:03:29.934][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:03:29.934][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:03:29.936][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-10-11 16:03:29.937][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-10-11 16:03:29.937][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:03:29.938][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:03:29.939][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-10-11 16:03:29.940][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-10-11 16:03:29.941][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:03:29.942][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:03:29.943][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-10-11 16:03:29.944][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-10-11 16:03:29.945][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:03:29.946][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:03:29.952][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-11 16:03:29.953][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-11 16:03:29.954][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:03:29.955][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:03:29.956][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-11 16:03:29.957][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-11 16:03:29.958][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:03:29.959][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:03:29.960][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-11 16:03:29.961][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-11 16:03:29.962][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:03:29.963][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:03:29.964][ef$get] Asked field names are: accession.
biodb.TRACE[2025-10-11 16:03:29.965][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-11 16:03:29.965][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:03:29.966][ef$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:03:29.967][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-11 16:03:29.968][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-11 16:03:29.969][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:03:29.970][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:03:29.978][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-10-11 16:03:29.979][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-10-11 16:03:29.979][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:03:29.980][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:03:29.981][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-10-11 16:03:29.982][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-10-11 16:03:29.983][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:03:29.984][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:03:29.985][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-10-11 16:03:29.986][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-10-11 16:03:29.987][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:03:29.988][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:03:29.989][ef$get] Asked field names are: formula.
biodb.TRACE[2025-10-11 16:03:29.990][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-10-11 16:03:29.990][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:03:29.991][ef$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:03:29.992][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-10-11 16:03:29.993][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-10-11 16:03:29.994][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:03:29.995][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:03:30.002][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-10-11 16:03:30.003][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-10-11 16:03:30.004][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:03:30.005][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:03:30.006][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-10-11 16:03:30.007][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-10-11 16:03:30.008][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:03:30.009][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:03:30.009][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-10-11 16:03:30.010][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-10-11 16:03:30.011][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:03:30.012][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:03:30.013][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-10-11 16:03:30.014][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-10-11 16:03:30.015][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:03:30.016][ef$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:03:30.017][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-10-11 16:03:30.018][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-10-11 16:03:30.019][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:03:30.020][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:03:30.027][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-10-11 16:03:30.028][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-10-11 16:03:30.029][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:03:30.029][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:03:30.030][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-10-11 16:03:30.031][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-10-11 16:03:30.036][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:03:30.037][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:03:30.038][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-10-11 16:03:30.039][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-10-11 16:03:30.040][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:03:30.041][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:03:30.042][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-10-11 16:03:30.043][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-10-11 16:03:30.043][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:03:30.044][ef$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:03:30.045][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-10-11 16:03:30.046][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-10-11 16:03:30.047][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:03:30.048][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:03:30.055][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-10-11 16:03:30.056][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-10-11 16:03:30.057][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:03:30.058][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:03:30.059][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-10-11 16:03:30.060][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-10-11 16:03:30.061][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:03:30.062][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:03:30.063][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-10-11 16:03:30.064][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-10-11 16:03:30.065][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:03:30.065][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:03:30.066][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-10-11 16:03:30.067][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-10-11 16:03:30.068][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:03:30.069][ef$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:03:30.070][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-10-11 16:03:30.071][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-10-11 16:03:30.072][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:03:30.073][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:03:30.080][ef$get] Asked field names are: accession.
biodb.TRACE[2025-10-11 16:03:30.081][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-11 16:03:30.082][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:03:30.083][ef$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:03:30.086][ef$get] Asked field names are: formula.
biodb.TRACE[2025-10-11 16:03:30.087][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-10-11 16:03:30.088][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:03:30.089][ef$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:03:30.093][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-10-11 16:03:30.094][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-10-11 16:03:30.095][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:03:30.096][ef$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:03:30.099][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-10-11 16:03:30.100][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-10-11 16:03:30.101][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:03:30.102][ef$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:03:30.106][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-10-11 16:03:30.107][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-10-11 16:03:30.108][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:03:30.108][ef$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:03:30.124][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNci.Rcheck/biodbNci/testref/entry-nci.cactus-750690-content.sdf".
biodb.DEBUG[2025-10-11 16:03:30.161][biodb$getFactory()$createEntryFromCo ...] Creating NCI CACTUS entries from 1 content(s).
biodb.DEBUG[2025-10-11 16:03:30.162][biodb$getFactory()$createEntryFromCo ...] Parsing 1 NCI CACTUS entries.
biodb.DEBUG[2025-10-11 16:03:30.163][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-10-11 16:03:30.164][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-11 16:03:30.165][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-11 16:03:30.169][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:03:30.170][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:03:30.171][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:03:30.171][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-10-11 16:03:30.180][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-11 16:03:30.181][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-11 16:03:30.182][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:03:30.183][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:03:30.184][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-11 16:03:30.185][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-11 16:03:30.186][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:03:30.187][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:03:30.204][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-10-11 16:03:30.205][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-10-11 16:03:30.206][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:03:30.207][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:03:30.208][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-10-11 16:03:30.209][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-10-11 16:03:30.210][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:03:30.210][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:03:30.212][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-10-11 16:03:30.213][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-10-11 16:03:30.214][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:03:30.215][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:03:30.216][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-10-11 16:03:30.217][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-10-11 16:03:30.218][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:03:30.218][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:03:30.220][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-10-11 16:03:30.221][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-10-11 16:03:30.222][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:03:30.223][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:03:30.224][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-10-11 16:03:30.225][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-10-11 16:03:30.225][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:03:30.226][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:03:30.228][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-10-11 16:03:30.229][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-10-11 16:03:30.230][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:03:30.230][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:03:30.231][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-10-11 16:03:30.232][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-10-11 16:03:30.233][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:03:30.234][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:03:30.235][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-10-11 16:03:30.236][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-10-11 16:03:30.237][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:03:30.238][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:03:30.239][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-10-11 16:03:30.240][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-10-11 16:03:30.241][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:03:30.242][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:03:30.243][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-10-11 16:03:30.244][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-10-11 16:03:30.245][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:03:30.245][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:03:30.246][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-10-11 16:03:30.247][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-10-11 16:03:30.248][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:03:30.249][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:03:30.250][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-10-11 16:03:30.251][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-10-11 16:03:30.252][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:03:30.253][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:03:30.258][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-10-11 16:03:30.259][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-10-11 16:03:30.260][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:03:30.261][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:03:30.262][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-10-11 16:03:30.263][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-10-11 16:03:30.264][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:03:30.265][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:03:30.266][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-10-11 16:03:30.267][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-10-11 16:03:30.268][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:03:30.269][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:03:30.270][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-10-11 16:03:30.271][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-10-11 16:03:30.272][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:03:30.273][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:03:30.274][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-10-11 16:03:30.275][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-10-11 16:03:30.276][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:03:30.277][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:03:30.278][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-10-11 16:03:30.279][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-10-11 16:03:30.280][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:03:30.281][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:03:30.282][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-11 16:03:30.283][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-11 16:03:30.283][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:03:30.284][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:03:30.285][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-10-11 16:03:30.286][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-10-11 16:03:30.287][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:03:30.288][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:03:30.289][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-11 16:03:30.290][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-11 16:03:30.291][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:03:30.292][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:03:30.293][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-11 16:03:30.294][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-11 16:03:30.295][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:03:30.295][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:03:30.296][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-11 16:03:30.297][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-11 16:03:30.298][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:03:30.299][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:03:30.300][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-11 16:03:30.301][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-11 16:03:30.302][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:03:30.303][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:03:30.304][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-11 16:03:30.305][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-11 16:03:30.306][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:03:30.307][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:03:30.308][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-11 16:03:30.309][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-11 16:03:30.310][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:03:30.310][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-10-11 16:03:30.311][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 750690.
biodb.TRACE[2025-10-11 16:03:30.331][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-10-11 16:03:30.332][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-10-11 16:03:30.333][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:03:30.334][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:03:30.335][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-10-11 16:03:30.336][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-10-11 16:03:30.336][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:03:30.337][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:03:30.338][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-10-11 16:03:30.339][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-10-11 16:03:30.340][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:03:30.341][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:03:30.342][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-10-11 16:03:30.343][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-10-11 16:03:30.344][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:03:30.345][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:03:30.347][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-11 16:03:30.348][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-11 16:03:30.348][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:03:30.349][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:03:30.354][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-10-11 16:03:30.355][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-10-11 16:03:30.356][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:03:30.357][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:03:30.361][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-11 16:03:30.362][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-11 16:03:30.363][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:03:30.363][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:03:30.364][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-11 16:03:30.365][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-11 16:03:30.366][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:03:30.367][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:03:30.368][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-11 16:03:30.373][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-11 16:03:30.374][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:03:30.375][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:03:30.377][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-11 16:03:30.378][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-11 16:03:30.379][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:03:30.380][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:03:30.381][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-11 16:03:30.382][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-11 16:03:30.383][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:03:30.384][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:03:30.385][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-11 16:03:30.386][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-11 16:03:30.387][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:03:30.388][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:03:30.389][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-10-11 16:03:30.390][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-10-11 16:03:30.391][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:03:30.392][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:03:30.392][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-10-11 16:03:30.393][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-10-11 16:03:30.394][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:03:30.395][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:03:30.396][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-10-11 16:03:30.397][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-10-11 16:03:30.398][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:03:30.399][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:03:30.415][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-11 16:03:30.416][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-11 16:03:30.417][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:03:30.417][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:03:30.418][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-11 16:03:30.419][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-11 16:03:30.420][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:03:30.421][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:03:30.422][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-11 16:03:30.423][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-11 16:03:30.424][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:03:30.425][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:03:30.426][ef$get] Asked field names are: accession.
biodb.TRACE[2025-10-11 16:03:30.427][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-11 16:03:30.428][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:03:30.429][ef$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:03:30.430][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-11 16:03:30.431][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-11 16:03:30.431][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:03:30.432][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:03:30.440][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-10-11 16:03:30.441][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-10-11 16:03:30.442][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:03:30.442][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:03:30.443][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-10-11 16:03:30.444][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-10-11 16:03:30.445][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:03:30.446][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:03:30.447][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-10-11 16:03:30.448][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-10-11 16:03:30.449][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:03:30.450][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:03:30.451][ef$get] Asked field names are: cas.id.
biodb.TRACE[2025-10-11 16:03:30.452][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-10-11 16:03:30.453][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:03:30.454][ef$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:03:30.454][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-10-11 16:03:30.455][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-10-11 16:03:30.456][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:03:30.457][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:03:30.465][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-10-11 16:03:30.466][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-10-11 16:03:30.466][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:03:30.467][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:03:30.468][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-10-11 16:03:30.469][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-10-11 16:03:30.470][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:03:30.471][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:03:30.472][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-10-11 16:03:30.473][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-10-11 16:03:30.474][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:03:30.475][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:03:30.476][ef$get] Asked field names are: name.
biodb.TRACE[2025-10-11 16:03:30.477][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-10-11 16:03:30.478][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:03:30.478][ef$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:03:30.479][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-10-11 16:03:30.480][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-10-11 16:03:30.481][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:03:30.482][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:03:30.493][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-10-11 16:03:30.494][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-10-11 16:03:30.495][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:03:30.496][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:03:30.497][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-10-11 16:03:30.498][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-10-11 16:03:30.499][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:03:30.500][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:03:30.501][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-10-11 16:03:30.502][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-10-11 16:03:30.503][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:03:30.504][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:03:30.505][ef$get] Asked field names are: formula.
biodb.TRACE[2025-10-11 16:03:30.506][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-10-11 16:03:30.506][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:03:30.507][ef$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:03:30.508][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-10-11 16:03:30.509][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-10-11 16:03:30.510][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:03:30.511][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:03:30.518][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-10-11 16:03:30.519][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-10-11 16:03:30.520][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:03:30.521][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:03:30.522][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-10-11 16:03:30.523][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-10-11 16:03:30.524][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:03:30.525][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:03:30.526][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-10-11 16:03:30.527][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-10-11 16:03:30.528][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:03:30.529][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:03:30.530][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-10-11 16:03:30.531][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-10-11 16:03:30.531][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:03:30.532][ef$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:03:30.533][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-10-11 16:03:30.534][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-10-11 16:03:30.535][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:03:30.536][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:03:30.544][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-10-11 16:03:30.545][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-10-11 16:03:30.546][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:03:30.547][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:03:30.548][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-10-11 16:03:30.549][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-10-11 16:03:30.549][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:03:30.550][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:03:30.551][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-10-11 16:03:30.552][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-10-11 16:03:30.553][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:03:30.554][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:03:30.555][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-10-11 16:03:30.556][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-10-11 16:03:30.557][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:03:30.558][ef$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:03:30.559][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-10-11 16:03:30.560][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-10-11 16:03:30.561][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:03:30.562][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:03:30.569][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-10-11 16:03:30.570][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-10-11 16:03:30.571][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:03:30.572][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:03:30.573][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-10-11 16:03:30.574][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-10-11 16:03:30.575][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:03:30.575][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:03:30.576][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-10-11 16:03:30.577][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-10-11 16:03:30.578][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:03:30.579][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:03:30.580][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-10-11 16:03:30.581][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-10-11 16:03:30.582][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:03:30.583][ef$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:03:30.584][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-10-11 16:03:30.585][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-10-11 16:03:30.586][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:03:30.587][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:03:30.594][ef$get] Asked field names are: accession.
biodb.TRACE[2025-10-11 16:03:30.595][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-11 16:03:30.596][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:03:30.597][ef$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:03:30.600][ef$get] Asked field names are: cas.id.
biodb.TRACE[2025-10-11 16:03:30.602][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-10-11 16:03:30.602][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:03:30.607][ef$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:03:30.611][ef$get] Asked field names are: formula.
biodb.TRACE[2025-10-11 16:03:30.612][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-10-11 16:03:30.613][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:03:30.613][ef$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:03:30.617][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-10-11 16:03:30.618][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-10-11 16:03:30.619][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:03:30.620][ef$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:03:30.624][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-10-11 16:03:30.625][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-10-11 16:03:30.626][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:03:30.626][ef$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:03:30.630][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-10-11 16:03:30.631][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-10-11 16:03:30.632][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:03:30.633][ef$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:03:30.637][ef$get] Asked field names are: name.
biodb.TRACE[2025-10-11 16:03:30.638][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-10-11 16:03:30.639][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:03:30.639][ef$get] fields variable is a list.
biodb.INFO [2025-10-11 16:03:30.645][biodb::testThat]
biodb.INFO [2025-10-11 16:03:30.646][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2025-10-11 16:03:30.647][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-10-11 16:03:30.648][biodb::testThat]
biodb.DEBUG[2025-10-11 16:03:30.650][private$loadEntries] Creating entries from ids [2]: "749674, 750690".
biodb.DEBUG[2025-10-11 16:03:30.652][conn$getEntryContent] Get NCI CACTUS entry content(s) for 2 id(s)...
biodb.DEBUG[2025-10-11 16:03:30.655][self$isDownloaded] Database nci.cactus has already been downloaded.
biodb.DEBUG[2025-10-11 16:03:30.682][self$isDownloaded] Database nci.cactus has already been downloaded.
biodb.INFO [2025-10-11 16:03:30.684][self$download] Extract whole database of nci.cactus.
biodb.INFO [2025-10-11 16:03:30.684][private$doExtractDownload] Extracting content of downloaded biodbNci, a library for connecting to the National Cancer Institute (USA) CACTUS Database....
biodb.INFO [2025-10-11 16:03:30.726][biodb::testThat]
biodb.INFO [2025-10-11 16:03:30.727][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2025-10-11 16:03:30.727][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-10-11 16:03:30.728][biodb::testThat]
biodb.INFO [2025-10-11 16:03:30.733][biodb::testThat]
biodb.INFO [2025-10-11 16:03:30.734][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2025-10-11 16:03:30.735][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-10-11 16:03:30.736][biodb::testThat]
biodb.WARN [2025-10-11 16:03:30.754][self$searchForEntries] This database is not searchable by field "name".
biodb.WARN [2025-10-11 16:03:30.771][self$searchForEntries] This database is not searchable by field "name".
biodb.INFO [2025-10-11 16:03:30.778][biodb::testThat]
biodb.INFO [2025-10-11 16:03:30.779][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2025-10-11 16:03:30.780][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-10-11 16:03:30.781][biodb::testThat]
biodb.DEBUG[2025-10-11 16:03:30.796][private$loadEntries] Creating entries from ids [1]: "749674".
biodb.DEBUG[2025-10-11 16:03:30.844][conn$getEntryContent] Get NCI CACTUS entry content(s) for 1 id(s)...
biodb.DEBUG[2025-10-11 16:03:30.845][self$isDownloaded] Database nci.cactus has already been downloaded.
biodb.DEBUG[2025-10-11 16:03:30.846][self$isDownloaded] Database nci.cactus has already been downloaded.
biodb.INFO [2025-10-11 16:03:30.847][self$download] Extract whole database of nci.cactus.
biodb.INFO [2025-10-11 16:03:30.859][private$doExtractDownload] Extracting content of downloaded biodbNci, a library for connecting to the National Cancer Institute (USA) CACTUS Database....
biodb.INFO [2025-10-11 16:03:30.881][biodb::testThat]
biodb.INFO [2025-10-11 16:03:30.882][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2025-10-11 16:03:30.883][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-10-11 16:03:30.884][biodb::testThat]
biodb.INFO [2025-10-11 16:03:30.890][biodb::testThat]
biodb.INFO [2025-10-11 16:03:30.891][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2025-10-11 16:03:30.892][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-10-11 16:03:30.893][biodb::testThat]
biodb.INFO [2025-10-11 16:03:30.899][biodb::testThat]
biodb.INFO [2025-10-11 16:03:30.899][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2025-10-11 16:03:30.900][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-10-11 16:03:30.901][biodb::testThat]
biodb.INFO [2025-10-11 16:03:30.906][biodb::testThat]
biodb.INFO [2025-10-11 16:03:30.907][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2025-10-11 16:03:30.908][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-10-11 16:03:30.909][biodb::testThat]
biodb.INFO [2025-10-11 16:03:30.917][biodb$terminate] Closing BiodbMain instance...
biodb.INFO [2025-10-11 16:03:30.918][self$deleteConn] Connector "nci.cactus" deleted.
biodb.DEBUG[2025-10-11 16:03:30.919][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-10-11 16:03:30.920][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-11 16:03:30.921][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-11 16:03:30.922][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:03:30.922][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:03:30.923][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:03:30.924][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2025-10-11 16:03:30.933][biodb::testContext]
biodb.INFO [2025-10-11 16:03:30.933][biodb::testContext] ********************************************************************************
biodb.INFO [2025-10-11 16:03:30.934][biodb::testContext] Test context - Example long tests
biodb.INFO [2025-10-11 16:03:30.935][biodb::testContext] ********************************************************************************
biodb.INFO [2025-10-11 16:03:30.936][biodb::testContext]
biodb.INFO [2025-10-11 16:03:30.938][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.17.2.
biodb.DEBUG[2025-10-11 16:03:30.940][self$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.22-bioc/R/site-library/biodb/definitions.yml".
biodb.DEBUG[2025-10-11 16:03:30.943][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-10-11 16:03:30.944][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-10-11 16:03:30.945][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-10-11 16:03:30.946][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:03:30.946][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:03:30.947][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-11 16:03:30.948][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-10-11 16:03:30.949][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-10-11 16:03:30.950][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:03:30.951][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:03:30.952][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-11 16:03:30.953][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-10-11 16:03:30.954][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-10-11 16:03:30.954][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:03:30.955][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:03:30.956][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-11 16:03:30.957][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-10-11 16:03:30.958][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-10-11 16:03:30.959][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-10-11 16:03:30.960][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:03:30.961][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:03:30.961][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-11 16:03:30.962][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-10-11 16:03:30.963][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-10-11 16:03:30.964][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-10-11 16:03:30.965][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:03:30.966][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:03:30.967][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-11 16:03:30.968][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-10-11 16:03:30.969][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-10-11 16:03:30.969][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:03:30.970][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:03:30.971][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-11 16:03:30.972][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-10-11 16:03:30.973][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-10-11 16:03:30.974][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-10-11 16:03:30.975][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:03:30.975][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:03:30.976][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-11 16:03:30.977][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-10-11 16:03:30.978][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-10-11 16:03:30.979][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:03:30.980][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:03:30.981][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-11 16:03:30.981][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-10-11 16:03:30.982][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-10-11 16:03:30.983][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-10-11 16:03:30.984][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:03:30.985][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:03:30.986][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-11 16:03:30.987][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-10-11 16:03:30.988][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-10-11 16:03:30.989][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-10-11 16:03:30.990][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-10-11 16:03:30.990][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-10-11 16:03:30.991][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-10-11 16:03:30.992][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:03:30.993][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:03:30.994][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-11 16:03:30.995][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-10-11 16:03:30.996][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-10-11 16:03:30.997][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:03:30.997][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:03:30.998][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-11 16:03:30.999][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-10-11 16:03:31.000][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-10-11 16:03:31.001][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:03:31.002][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:03:31.002][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-11 16:03:31.003][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-10-11 16:03:31.004][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-10-11 16:03:31.005][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:03:31.006][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:03:31.007][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-11 16:03:31.008][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-10-11 16:03:31.009][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-10-11 16:03:31.010][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-10-11 16:03:31.010][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:03:31.011][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:03:31.012][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-11 16:03:31.013][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-10-11 16:03:31.014][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-10-11 16:03:31.019][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-10-11 16:03:31.019][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:03:31.020][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:03:31.021][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-11 16:03:31.022][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-10-11 16:03:31.023][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-10-11 16:03:31.028][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-10-11 16:03:31.029][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:03:31.030][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:03:31.030][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-11 16:03:31.031][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-10-11 16:03:31.033][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-10-11 16:03:31.034][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2025-10-11 16:03:31.035][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-10-11 16:03:31.036][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-10-11 16:03:31.037][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-10-11 16:03:31.038][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-10-11 16:03:31.039][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-10-11 16:03:31.040][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-10-11 16:03:31.041][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-10-11 16:03:31.041][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-10-11 16:03:31.042][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-10-11 16:03:31.043][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-10-11 16:03:31.044][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-10-11 16:03:31.045][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-10-11 16:03:31.046][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-10-11 16:03:31.047][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-10-11 16:03:31.047][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-10-11 16:03:31.047][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-10-11 16:03:31.047][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-10-11 16:03:31.047][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-10-11 16:03:31.048][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-10-11 16:03:31.049][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-11 16:03:31.050][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-11 16:03:31.051][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-10-11 16:03:31.052][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-11 16:03:31.052][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-11 16:03:31.053][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-10-11 16:03:31.054][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-10-11 16:03:31.055][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-10-11 16:03:31.056][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-10-11 16:03:31.057][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-10-11 16:03:31.058][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-10-11 16:03:31.059][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-10-11 16:03:31.060][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-10-11 16:03:31.061][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-10-11 16:03:31.062][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-10-11 16:03:31.063][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-10-11 16:03:31.064][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-10-11 16:03:31.065][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-10-11 16:03:31.066][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-10-11 16:03:31.067][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-10-11 16:03:31.068][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-10-11 16:03:31.069][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-10-11 16:03:31.070][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-10-11 16:03:31.071][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-10-11 16:03:31.071][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-10-11 16:03:31.072][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-10-11 16:03:31.073][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-10-11 16:03:31.074][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-10-11 16:03:31.074][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-10-11 16:03:31.074][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-10-11 16:03:31.074][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-10-11 16:03:31.074][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-10-11 16:03:31.075][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-10-11 16:03:31.076][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-11 16:03:31.077][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-11 16:03:31.078][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-10-11 16:03:31.079][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-11 16:03:31.079][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-11 16:03:31.080][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-10-11 16:03:31.081][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-10-11 16:03:31.082][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-10-11 16:03:31.083][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-10-11 16:03:31.084][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-10-11 16:03:31.085][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-10-11 16:03:31.086][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-10-11 16:03:31.087][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-10-11 16:03:31.088][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2025-10-11 16:03:31.089][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-10-11 16:03:31.090][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-10-11 16:03:31.091][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-10-11 16:03:31.092][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-10-11 16:03:31.093][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-10-11 16:03:31.094][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-10-11 16:03:31.095][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-10-11 16:03:31.096][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-10-11 16:03:31.097][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-10-11 16:03:31.098][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-10-11 16:03:31.099][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-10-11 16:03:31.099][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-10-11 16:03:31.100][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-10-11 16:03:31.101][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-10-11 16:03:31.102][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-10-11 16:03:31.103][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-11 16:03:31.104][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-11 16:03:31.105][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-10-11 16:03:31.106][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-11 16:03:31.107][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-11 16:03:31.107][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-10-11 16:03:31.108][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-10-11 16:03:31.109][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-10-11 16:03:31.110][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-10-11 16:03:31.111][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-10-11 16:03:31.112][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-10-11 16:03:31.113][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-10-11 16:03:31.115][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-10-11 16:03:31.116][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-10-11 16:03:31.116][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-10-11 16:03:31.117][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-10-11 16:03:31.118][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-10-11 16:03:31.119][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-10-11 16:03:31.120][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-10-11 16:03:31.121][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-10-11 16:03:31.122][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-10-11 16:03:31.123][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-10-11 16:03:31.124][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-10-11 16:03:31.125][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-10-11 16:03:31.126][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-10-11 16:03:31.127][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-10-11 16:03:31.128][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-10-11 16:03:31.129][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-10-11 16:03:31.130][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-10-11 16:03:31.130][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-11 16:03:31.131][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-11 16:03:31.132][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-10-11 16:03:31.137][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-11 16:03:31.138][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-11 16:03:31.139][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-10-11 16:03:31.139][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-10-11 16:03:31.140][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-10-11 16:03:31.141][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-10-11 16:03:31.142][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-10-11 16:03:31.143][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-10-11 16:03:31.144][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-10-11 16:03:31.145][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:03:31.146][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-11 16:03:31.147][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:03:31.148][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:03:31.148][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:03:31.149][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:03:31.150][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-11 16:03:31.151][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:03:31.152][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:03:31.153][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:03:31.153][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:03:31.154][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-11 16:03:31.155][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:03:31.156][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:03:31.157][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:03:31.158][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:03:31.158][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-11 16:03:31.159][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:03:31.160][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:03:31.161][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:03:31.162][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:03:31.163][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-11 16:03:31.163][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:03:31.164][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:03:31.165][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:03:31.166][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:03:31.167][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-11 16:03:31.168][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:03:31.168][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:03:31.169][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:03:31.170][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:03:31.171][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-11 16:03:31.172][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:03:31.172][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:03:31.173][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:03:31.174][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:03:31.175][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-11 16:03:31.176][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:03:31.177][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:03:31.177][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:03:31.178][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:03:31.179][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-11 16:03:31.180][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:03:31.181][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:03:31.182][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:03:31.182][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:03:31.183][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-11 16:03:31.184][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:03:31.185][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:03:31.186][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:03:31.187][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:03:31.187][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-11 16:03:31.188][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:03:31.189][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:03:31.190][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:03:31.191][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:03:31.192][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-11 16:03:31.192][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:03:31.193][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:03:31.194][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:03:31.195][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:03:31.196][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-11 16:03:31.196][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:03:31.197][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:03:31.198][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:03:31.199][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:03:31.200][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-11 16:03:31.201][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:03:31.201][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:03:31.202][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:03:31.203][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:03:31.204][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-11 16:03:31.205][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:03:31.206][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:03:31.206][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:03:31.207][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:03:31.208][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-11 16:03:31.209][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:03:31.210][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:03:31.210][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:03:31.211][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:03:31.212][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-11 16:03:31.213][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-10-11 16:03:31.214][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-10-11 16:03:31.216][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-10-11 16:03:31.217][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-10-11 16:03:31.218][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-10-11 16:03:31.220][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-10-11 16:03:31.221][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-10-11 16:03:31.222][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-10-11 16:03:31.224][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-10-11 16:03:31.225][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-10-11 16:03:31.226][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-10-11 16:03:31.227][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-10-11 16:03:31.229][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-10-11 16:03:31.230][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-10-11 16:03:31.231][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-10-11 16:03:31.233][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-10-11 16:03:31.234][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-10-11 16:03:31.235][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-10-11 16:03:31.237][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-10-11 16:03:31.238][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-10-11 16:03:31.239][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-10-11 16:03:31.244][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-10-11 16:03:31.246][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-10-11 16:03:31.247][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-10-11 16:03:31.248][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-10-11 16:03:31.249][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-10-11 16:03:31.251][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-10-11 16:03:31.252][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-10-11 16:03:31.253][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-10-11 16:03:31.254][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-10-11 16:03:31.256][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-10-11 16:03:31.257][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-10-11 16:03:31.258][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-10-11 16:03:31.260][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-10-11 16:03:31.261][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-10-11 16:03:31.262][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-10-11 16:03:31.264][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-10-11 16:03:31.265][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-10-11 16:03:31.266][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-10-11 16:03:31.268][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-10-11 16:03:31.269][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-10-11 16:03:31.270][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-10-11 16:03:31.271][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-10-11 16:03:31.273][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-10-11 16:03:31.274][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-10-11 16:03:31.275][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-10-11 16:03:31.277][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-10-11 16:03:31.278][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-10-11 16:03:31.279][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-10-11 16:03:31.281][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-10-11 16:03:31.282][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-10-11 16:03:31.283][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-10-11 16:03:31.284][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-10-11 16:03:31.286][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-10-11 16:03:31.287][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-10-11 16:03:31.288][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-10-11 16:03:31.289][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-10-11 16:03:31.291][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-10-11 16:03:31.292][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-10-11 16:03:31.293][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-10-11 16:03:31.295][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-10-11 16:03:31.296][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-10-11 16:03:31.297][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-10-11 16:03:31.298][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-10-11 16:03:31.300][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-10-11 16:03:31.301][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-10-11 16:03:31.302][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-10-11 16:03:31.304][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-10-11 16:03:31.305][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-10-11 16:03:31.306][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-10-11 16:03:31.307][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-10-11 16:03:31.309][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-10-11 16:03:31.310][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-10-11 16:03:31.311][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-10-11 16:03:31.313][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-10-11 16:03:31.314][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-10-11 16:03:31.315][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-10-11 16:03:31.316][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-10-11 16:03:31.318][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-10-11 16:03:31.319][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-10-11 16:03:31.320][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-10-11 16:03:31.322][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-10-11 16:03:31.323][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-10-11 16:03:31.324][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-10-11 16:03:31.326][initialize] This is biodb version 1.17.2.
biodb.DEBUG[2025-10-11 16:03:31.327][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-10-11 16:03:31.328][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:03:31.328][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:03:31.329][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:03:31.330][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-11 16:03:31.331][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:03:31.332][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-11 16:03:31.333][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-11 16:03:31.333][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:03:31.334][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:03:31.335][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:03:31.336][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[2025-10-11 16:03:31.337][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:03:31.338][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-11 16:03:31.338][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-11 16:03:31.339][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:03:31.340][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:03:31.341][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:03:31.342][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-11 16:03:31.343][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:03:31.343][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-11 16:03:31.344][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-11 16:03:31.345][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:03:31.346][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:03:31.351][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:03:31.352][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-11 16:03:31.353][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:03:31.353][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-11 16:03:31.354][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-11 16:03:31.355][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:03:31.356][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:03:31.357][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:03:31.357][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-11 16:03:31.358][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:03:31.359][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-11 16:03:31.360][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-11 16:03:31.361][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:03:31.362][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:03:31.362][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:03:31.363][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-11 16:03:31.364][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:03:31.365][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-11 16:03:31.366][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-11 16:03:31.367][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:03:31.367][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:03:31.368][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:03:31.369][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-11 16:03:31.370][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:03:31.371][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-11 16:03:31.372][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-11 16:03:31.372][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:03:31.373][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:03:31.374][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:03:31.375][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-11 16:03:31.376][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:03:31.377][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-11 16:03:31.377][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-11 16:03:31.378][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:03:31.379][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:03:31.380][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:03:31.381][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-11 16:03:31.381][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:03:31.382][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-11 16:03:31.383][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-11 16:03:31.384][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:03:31.385][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:03:31.386][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:03:31.386][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-11 16:03:31.387][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:03:31.388][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-11 16:03:31.389][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-11 16:03:31.390][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:03:31.391][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:03:31.391][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:03:31.392][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-11 16:03:31.393][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:03:31.394][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-11 16:03:31.395][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-11 16:03:31.395][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:03:31.396][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:03:31.397][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:03:31.398][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[2025-10-11 16:03:31.399][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:03:31.400][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-11 16:03:31.400][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-11 16:03:31.401][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:03:31.402][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:03:31.403][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:03:31.404][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-11 16:03:31.405][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:03:31.405][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-11 16:03:31.406][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-11 16:03:31.407][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:03:31.408][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:03:31.409][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:03:31.409][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-11 16:03:31.410][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:03:31.411][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-11 16:03:31.412][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-11 16:03:31.413][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:03:31.414][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:03:31.414][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:03:31.415][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-11 16:03:31.416][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:03:31.417][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-11 16:03:31.418][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-11 16:03:31.419][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:03:31.419][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:03:31.420][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:03:31.421][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-11 16:03:31.422][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:03:31.423][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-11 16:03:31.423][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-11 16:03:31.424][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:03:31.425][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:03:31.426][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:03:31.427][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-11 16:03:31.428][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNci.Rcheck/biodbNci/definitions.yml".
biodb.DEBUG[2025-10-11 16:03:31.430][self$getDbsInfo()$define] Define connector nci.cactus.
biodb.DEBUG[2025-10-11 16:03:31.431][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-10-11 16:03:31.432][self$setPropertyValue] Setting property "description" to "National Cancer Institute (USA) CACTUS Database.".
biodb.DEBUG[2025-10-11 16:03:31.433][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-10-11 16:03:31.434][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-10-11 16:03:31.435][self$setPropertyValue] Setting property "downloadable" to "TRUE".
biodb.DEBUG[2025-10-11 16:03:31.436][self$setPropertyValue] Setting property "dwnld.ext" to "gz".
biodb.DEBUG[2025-10-11 16:03:31.437][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-10-11 16:03:31.438][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-10-11 16:03:31.439][self$setPropertyValue] Setting property "entry.content.type" to "sdf".
biodb.DEBUG[2025-10-11 16:03:31.440][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-10-11 16:03:31.441][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-10-11 16:03:31.442][self$setPropertyValue] Setting property "name" to "NCI CACTUS".
biodb.DEBUG[2025-10-11 16:03:31.443][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-10-11 16:03:31.444][self$setPropertyValue] Setting property "parsing.expr" to "NSC".
biodb.DEBUG[2025-10-11 16:03:31.444][self$setPropertyValue] Setting property "parsing.expr" to "DTP names".
biodb.DEBUG[2025-10-11 16:03:31.444][self$setPropertyValue] Setting property "parsing.expr" to "Standard InChI".
biodb.DEBUG[2025-10-11 16:03:31.444][self$setPropertyValue] Setting property "parsing.expr" to "c("Standard InChIKey", "^InChIKey=(.*)$")".
biodb.DEBUG[2025-10-11 16:03:31.444][self$setPropertyValue] Setting property "parsing.expr" to "Formula".
biodb.DEBUG[2025-10-11 16:03:31.444][self$setPropertyValue] Setting property "parsing.expr" to "Molecular Weight".
biodb.DEBUG[2025-10-11 16:03:31.444][self$setPropertyValue] Setting property "parsing.expr" to "CAS".
biodb.DEBUG[2025-10-11 16:03:31.445][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-10-11 16:03:31.445][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-10-11 16:03:31.446][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-10-11 16:03:31.447][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-11 16:03:31.448][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-11 16:03:31.449][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-10-11 16:03:31.450][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-11 16:03:31.451][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-11 16:03:31.452][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-10-11 16:03:31.453][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/".
biodb.DEBUG[2025-10-11 16:03:31.453][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/".
biodb.DEBUG[2025-10-11 16:03:31.453][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/download/nci/".
biodb.DEBUG[2025-10-11 16:03:31.453][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/download/nci/NCI-Open_2012-05-01.sdf.gz".
biodb.DEBUG[2025-10-11 16:03:31.454][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-10-11 16:03:31.458][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-10-11 16:03:31.459][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-10-11 16:03:31.460][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-10-11 16:03:31.461][self$getEntryFields()$define] Define field nci.cactus.id.
biodb.DEBUG[2025-10-11 16:03:31.464][super$initialize] Initialize connector nci.cactus.
biodb.DEBUG[2025-10-11 16:03:31.467][biodb$getFactory()$createConn] Creating new connector nci.cactus for database class nci.cactus .
biodb.INFO [2025-10-11 16:03:31.468][biodb$terminate] Closing BiodbMain instance...
biodb.INFO [2025-10-11 16:03:31.469][self$deleteConn] Connector "nci.cactus" deleted.
biodb.DEBUG[2025-10-11 16:03:31.470][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-10-11 16:03:31.471][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-11 16:03:31.472][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-11 16:03:31.472][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:03:31.473][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:03:31.474][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:03:31.475][FUN] Functions in observer 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)