Back to Long Tests report for BioC 3.22

This page was generated on 2025-11-16 16:54 -0500 (Sun, 16 Nov 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" 4903
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 8/31HostnameOS / ArchCHECK
biodbNci 1.14.0  (landing page)
Pierrick Roger
Snapshot Date: 2025-11-15 09:55 -0500 (Sat, 15 Nov 2025)
git_url: https://git.bioconductor.org/packages/biodbNci
git_branch: RELEASE_3_22
git_last_commit: 4ce22d8
git_last_commit_date: 2025-10-29 11:15:34 -0500 (Wed, 29 Oct 2025)
nebbiolo2Linux (Ubuntu 24.04.3 LTS) / x86_64  ERROR  

CHECK results for biodbNci on nebbiolo2

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

raw results


Summary

Package: biodbNci
Version: 1.14.0
Command: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --test-dir=longtests --no-stop-on-test-error --no-codoc --no-examples --no-manual --ignore-vignettes --check-subdirs=no biodbNci_1.14.0.tar.gz
StartedAt: 2025-11-15 16:02:32 -0500 (Sat, 15 Nov 2025)
EndedAt: 2025-11-15 16:03:36 -0500 (Sat, 15 Nov 2025)
EllapsedTime: 64.0 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 [2025-11-15 16:03:32.476][biodb::testContext]
biodb.INFO [2025-11-15 16:03:32.477][biodb::testContext] ********************************************************************************
biodb.INFO [2025-11-15 16:03:32.478][biodb::testContext] Test context - Generic long tests
biodb.INFO [2025-11-15 16:03:32.479][biodb::testContext] ********************************************************************************
biodb.INFO [2025-11-15 16:03:32.480][biodb::testContext]
biodb.INFO [2025-11-15 16:03:32.486][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.18.0.
biodb.DEBUG[2025-11-15 16:03:32.488][self$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.22-bioc/R/site-library/biodb/definitions.yml".
biodb.DEBUG[2025-11-15 16:03:32.495][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-11-15 16:03:32.496][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-11-15 16:03:32.497][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-11-15 16:03:32.498][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-15 16:03:32.499][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-15 16:03:32.500][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-15 16:03:32.500][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-11-15 16:03:32.517][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-11-15 16:03:32.518][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-15 16:03:32.519][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-15 16:03:32.520][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-15 16:03:32.521][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-11-15 16:03:32.522][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-11-15 16:03:32.522][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-15 16:03:32.531][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-15 16:03:32.532][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-15 16:03:32.533][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-11-15 16:03:32.534][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-11-15 16:03:32.535][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-11-15 16:03:32.536][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-15 16:03:32.537][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-15 16:03:32.538][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-15 16:03:32.538][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-11-15 16:03:32.539][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-11-15 16:03:32.540][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-11-15 16:03:32.541][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-15 16:03:32.542][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-15 16:03:32.543][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-15 16:03:32.544][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-11-15 16:03:32.545][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-11-15 16:03:32.546][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-15 16:03:32.546][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-15 16:03:32.547][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-15 16:03:32.548][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-11-15 16:03:32.549][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-11-15 16:03:32.550][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-11-15 16:03:32.551][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-15 16:03:32.552][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-15 16:03:32.552][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-15 16:03:32.553][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-11-15 16:03:32.554][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-11-15 16:03:32.555][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-15 16:03:32.556][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-15 16:03:32.557][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-15 16:03:32.558][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-11-15 16:03:32.559][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-11-15 16:03:32.560][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-11-15 16:03:32.560][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-15 16:03:32.561][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-15 16:03:32.562][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-15 16:03:32.563][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-11-15 16:03:32.564][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-11-15 16:03:32.565][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-11-15 16:03:32.566][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-11-15 16:03:32.567][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-11-15 16:03:32.568][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-11-15 16:03:32.569][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-15 16:03:32.569][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-15 16:03:32.570][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-15 16:03:32.571][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-11-15 16:03:32.572][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-11-15 16:03:32.573][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-15 16:03:32.574][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-15 16:03:32.574][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-15 16:03:32.575][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-11-15 16:03:32.576][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-11-15 16:03:32.577][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-15 16:03:32.578][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-15 16:03:32.579][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-15 16:03:32.580][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-11-15 16:03:32.581][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-11-15 16:03:32.581][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-15 16:03:32.582][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-15 16:03:32.583][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-15 16:03:32.584][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-11-15 16:03:32.585][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-11-15 16:03:32.586][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-11-15 16:03:32.587][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-15 16:03:32.588][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-15 16:03:32.588][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-15 16:03:32.589][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-11-15 16:03:32.590][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-11-15 16:03:32.595][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-11-15 16:03:32.595][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-15 16:03:32.596][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-15 16:03:32.597][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-15 16:03:32.598][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-11-15 16:03:32.599][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-11-15 16:03:32.600][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-11-15 16:03:32.601][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-15 16:03:32.601][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-15 16:03:32.602][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-15 16:03:32.606][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-11-15 16:03:32.637][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-11-15 16:03:32.651][self$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[2025-11-15 16:03:32.652][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-11-15 16:03:32.653][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-11-15 16:03:32.654][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-11-15 16:03:32.655][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-11-15 16:03:32.656][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-11-15 16:03:32.657][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-11-15 16:03:32.658][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-11-15 16:03:32.659][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-11-15 16:03:32.660][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-11-15 16:03:32.661][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-11-15 16:03:32.662][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-11-15 16:03:32.663][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-11-15 16:03:32.663][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-11-15 16:03:32.664][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-11-15 16:03:32.664][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-11-15 16:03:32.664][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-11-15 16:03:32.664][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-11-15 16:03:32.664][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-11-15 16:03:32.665][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-11-15 16:03:32.666][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-11-15 16:03:32.667][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-11-15 16:03:32.668][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-11-15 16:03:32.669][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-11-15 16:03:32.670][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-11-15 16:03:32.671][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-11-15 16:03:32.672][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-11-15 16:03:32.672][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-11-15 16:03:32.673][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-11-15 16:03:32.674][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-11-15 16:03:32.675][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-11-15 16:03:32.676][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-11-15 16:03:32.678][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-11-15 16:03:32.679][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-11-15 16:03:32.680][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-11-15 16:03:32.681][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-11-15 16:03:32.682][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-11-15 16:03:32.682][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-11-15 16:03:32.683][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-11-15 16:03:32.684][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-11-15 16:03:32.689][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-11-15 16:03:32.690][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-11-15 16:03:32.691][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-11-15 16:03:32.692][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-11-15 16:03:32.693][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-11-15 16:03:32.694][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-11-15 16:03:32.695][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-11-15 16:03:32.696][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-11-15 16:03:32.696][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-11-15 16:03:32.696][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-11-15 16:03:32.696][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-11-15 16:03:32.696][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-11-15 16:03:32.697][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-11-15 16:03:32.698][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-11-15 16:03:32.699][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-11-15 16:03:32.699][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-11-15 16:03:32.700][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-11-15 16:03:32.701][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-11-15 16:03:32.702][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-11-15 16:03:32.703][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-11-15 16:03:32.704][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-11-15 16:03:32.705][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-11-15 16:03:32.706][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-11-15 16:03:32.707][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-11-15 16:03:32.708][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-11-15 16:03:32.709][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-11-15 16:03:32.710][self$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[2025-11-15 16:03:32.711][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-11-15 16:03:32.712][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-11-15 16:03:32.713][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-11-15 16:03:32.714][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-11-15 16:03:32.715][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-11-15 16:03:32.716][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-11-15 16:03:32.717][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-11-15 16:03:32.718][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-11-15 16:03:32.719][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-11-15 16:03:32.720][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-11-15 16:03:32.720][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-11-15 16:03:32.721][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-11-15 16:03:32.722][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-11-15 16:03:32.723][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-11-15 16:03:32.724][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-11-15 16:03:32.725][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-11-15 16:03:32.726][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-11-15 16:03:32.727][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-11-15 16:03:32.728][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-11-15 16:03:32.728][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-11-15 16:03:32.729][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-11-15 16:03:32.730][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-11-15 16:03:32.731][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-11-15 16:03:32.732][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-11-15 16:03:32.733][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-11-15 16:03:32.734][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-11-15 16:03:32.735][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-11-15 16:03:32.736][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-11-15 16:03:32.737][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-11-15 16:03:32.738][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-11-15 16:03:32.739][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-11-15 16:03:32.740][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-11-15 16:03:32.741][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-11-15 16:03:32.742][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-11-15 16:03:32.743][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-11-15 16:03:32.744][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-11-15 16:03:32.745][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-11-15 16:03:32.746][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-11-15 16:03:32.747][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-11-15 16:03:32.748][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-11-15 16:03:32.749][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-11-15 16:03:32.749][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-11-15 16:03:32.750][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-11-15 16:03:32.751][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-11-15 16:03:32.752][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-11-15 16:03:32.753][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-11-15 16:03:32.754][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-11-15 16:03:32.755][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-11-15 16:03:32.756][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-11-15 16:03:32.757][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-11-15 16:03:32.757][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-11-15 16:03:32.758][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-11-15 16:03:32.759][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-11-15 16:03:32.760][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-11-15 16:03:32.761][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-11-15 16:03:32.765][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-11-15 16:03:32.765][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-11-15 16:03:32.766][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-15 16:03:32.767][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-15 16:03:32.768][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-15 16:03:32.769][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-15 16:03:32.770][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-15 16:03:32.770][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-15 16:03:32.771][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-15 16:03:32.772][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-15 16:03:32.773][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-15 16:03:32.774][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-15 16:03:32.775][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-15 16:03:32.775][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-15 16:03:32.776][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-15 16:03:32.777][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-15 16:03:32.778][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-15 16:03:32.779][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-15 16:03:32.780][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-15 16:03:32.780][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-15 16:03:32.781][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-15 16:03:32.782][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-15 16:03:32.783][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-15 16:03:32.784][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-15 16:03:32.785][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-15 16:03:32.785][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-15 16:03:32.786][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-15 16:03:32.787][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-15 16:03:32.788][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-15 16:03:32.789][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-15 16:03:32.790][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-15 16:03:32.790][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-15 16:03:32.791][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-15 16:03:32.792][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-15 16:03:32.793][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-15 16:03:32.794][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-15 16:03:32.795][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-15 16:03:32.795][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-15 16:03:32.796][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-15 16:03:32.797][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-15 16:03:32.798][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-15 16:03:32.799][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-15 16:03:32.799][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-15 16:03:32.800][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-15 16:03:32.801][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-15 16:03:32.802][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-15 16:03:32.803][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-15 16:03:32.804][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-15 16:03:32.804][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-15 16:03:32.805][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-15 16:03:32.806][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-15 16:03:32.807][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-15 16:03:32.808][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-15 16:03:32.809][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-15 16:03:32.809][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-15 16:03:32.810][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-15 16:03:32.811][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-15 16:03:32.812][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-15 16:03:32.813][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-15 16:03:32.814][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-15 16:03:32.814][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-15 16:03:32.815][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-15 16:03:32.816][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-15 16:03:32.817][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-15 16:03:32.818][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-15 16:03:32.819][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-15 16:03:32.819][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-15 16:03:32.820][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-15 16:03:32.821][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-15 16:03:32.822][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-15 16:03:32.823][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-15 16:03:32.824][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-15 16:03:32.824][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-15 16:03:32.825][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-15 16:03:32.826][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-15 16:03:32.827][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-15 16:03:32.828][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-15 16:03:32.829][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-15 16:03:32.829][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-15 16:03:32.830][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-15 16:03:32.831][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-15 16:03:32.832][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-15 16:03:32.833][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-15 16:03:32.834][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-11-15 16:03:32.838][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-11-15 16:03:32.839][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-11-15 16:03:32.841][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-11-15 16:03:32.842][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-11-15 16:03:32.847][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-11-15 16:03:32.848][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-11-15 16:03:32.850][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-11-15 16:03:32.851][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-11-15 16:03:32.852][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-11-15 16:03:32.854][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-11-15 16:03:32.855][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-11-15 16:03:32.856][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-11-15 16:03:32.857][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-11-15 16:03:32.859][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-11-15 16:03:32.860][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-11-15 16:03:32.861][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-11-15 16:03:32.863][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-11-15 16:03:32.864][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-11-15 16:03:32.865][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-11-15 16:03:32.866][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-11-15 16:03:32.868][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-11-15 16:03:32.869][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-11-15 16:03:32.870][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-11-15 16:03:32.872][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-11-15 16:03:32.873][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-11-15 16:03:32.874][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-11-15 16:03:32.875][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-11-15 16:03:32.877][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-11-15 16:03:32.878][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-11-15 16:03:32.879][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-11-15 16:03:32.881][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-11-15 16:03:32.882][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-11-15 16:03:32.883][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-11-15 16:03:32.885][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-11-15 16:03:32.886][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-11-15 16:03:32.887][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-11-15 16:03:32.894][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-11-15 16:03:32.896][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-11-15 16:03:32.898][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-11-15 16:03:32.899][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-11-15 16:03:32.901][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-11-15 16:03:32.902][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-11-15 16:03:32.904][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-11-15 16:03:32.905][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-11-15 16:03:32.907][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-11-15 16:03:32.908][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-11-15 16:03:32.910][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-11-15 16:03:32.911][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-11-15 16:03:32.913][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-11-15 16:03:32.914][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-11-15 16:03:32.916][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-11-15 16:03:32.917][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-11-15 16:03:32.919][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-11-15 16:03:32.920][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-11-15 16:03:32.922][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-11-15 16:03:32.923][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-11-15 16:03:32.924][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-11-15 16:03:32.926][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-11-15 16:03:32.927][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-11-15 16:03:32.929][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-11-15 16:03:32.930][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-11-15 16:03:32.932][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-11-15 16:03:32.933][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-11-15 16:03:32.935][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-11-15 16:03:32.936][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-11-15 16:03:32.938][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-11-15 16:03:32.939][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-11-15 16:03:32.940][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-11-15 16:03:32.942][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-11-15 16:03:32.943][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-11-15 16:03:32.945][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-11-15 16:03:32.946][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-11-15 16:03:32.948][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-11-15 16:03:32.949][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-11-15 16:03:32.951][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-11-15 16:03:32.952][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-11-15 16:03:32.954][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-11-15 16:03:32.955][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-11-15 16:03:32.956][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-11-15 16:03:32.958][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-11-15 16:03:32.959][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-11-15 16:03:32.961][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-11-15 16:03:32.968][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-11-15 16:03:32.970][initialize] This is biodb version 1.18.0.
biodb.DEBUG[2025-11-15 16:03:32.973][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-11-15 16:03:32.974][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-11-15 16:03:32.975][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-15 16:03:32.976][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-11-15 16:03:32.977][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-15 16:03:32.982][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-15 16:03:32.983][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-15 16:03:32.984][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-15 16:03:32.985][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-15 16:03:32.986][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-15 16:03:32.987][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-15 16:03:32.988][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-15 16:03:32.989][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-15 16:03:32.990][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-15 16:03:32.991][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-15 16:03:32.992][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-15 16:03:32.993][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-15 16:03:32.993][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-15 16:03:32.994][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[2025-11-15 16:03:32.995][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-15 16:03:32.996][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-15 16:03:32.997][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-15 16:03:32.998][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-15 16:03:32.999][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-15 16:03:33.000][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-15 16:03:33.001][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-15 16:03:33.002][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-15 16:03:33.003][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-15 16:03:33.004][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-15 16:03:33.005][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-15 16:03:33.006][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-15 16:03:33.006][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-15 16:03:33.007][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[2025-11-15 16:03:33.008][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-15 16:03:33.009][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-15 16:03:33.010][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-15 16:03:33.011][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-15 16:03:33.012][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-15 16:03:33.013][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-15 16:03:33.014][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-15 16:03:33.015][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-15 16:03:33.028][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-15 16:03:33.029][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-15 16:03:33.030][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-15 16:03:33.031][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-15 16:03:33.032][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-15 16:03:33.033][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-15 16:03:33.034][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-15 16:03:33.034][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-15 16:03:33.035][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-15 16:03:33.036][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-15 16:03:33.037][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-15 16:03:33.038][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-15 16:03:33.039][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-15 16:03:33.040][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-15 16:03:33.041][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-15 16:03:33.042][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-15 16:03:33.043][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-15 16:03:33.044][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-15 16:03:33.045][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-15 16:03:33.046][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-15 16:03:33.047][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-15 16:03:33.047][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-15 16:03:33.048][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-15 16:03:33.049][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-15 16:03:33.050][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-15 16:03:33.051][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-15 16:03:33.052][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-15 16:03:33.053][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-15 16:03:33.054][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-15 16:03:33.055][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-15 16:03:33.056][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-15 16:03:33.057][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-15 16:03:33.057][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-15 16:03:33.058][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-15 16:03:33.059][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-15 16:03:33.060][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-15 16:03:33.061][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-15 16:03:33.062][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-15 16:03:33.063][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-15 16:03:33.064][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-15 16:03:33.065][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-15 16:03:33.066][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-15 16:03:33.066][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-15 16:03:33.067][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-15 16:03:33.068][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-15 16:03:33.069][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-15 16:03:33.070][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-15 16:03:33.071][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-15 16:03:33.072][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-15 16:03:33.073][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-15 16:03:33.073][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-15 16:03:33.074][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-15 16:03:33.075][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-15 16:03:33.076][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-15 16:03:33.077][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-15 16:03:33.078][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-15 16:03:33.078][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-15 16:03:33.079][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-15 16:03:33.080][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-15 16:03:33.081][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-15 16:03:33.082][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-15 16:03:33.083][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-15 16:03:33.083][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-15 16:03:33.084][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-15 16:03:33.085][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-15 16:03:33.086][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-15 16:03:33.087][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-15 16:03:33.087][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-15 16:03:33.088][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-15 16:03:33.089][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-15 16:03:33.090][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-15 16:03:33.091][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-15 16:03:33.092][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-15 16:03:33.092][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-15 16:03:33.093][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-15 16:03:33.094][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-15 16:03:33.096][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNci.Rcheck/biodbNci/definitions.yml".
biodb.DEBUG[2025-11-15 16:03:33.105][self$getDbsInfo()$define] Define connector nci.cactus.
biodb.DEBUG[2025-11-15 16:03:33.106][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-11-15 16:03:33.107][self$setPropertyValue] Setting property "description" to "National Cancer Institute (USA) CACTUS Database.".
biodb.DEBUG[2025-11-15 16:03:33.108][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-11-15 16:03:33.109][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-11-15 16:03:33.110][self$setPropertyValue] Setting property "downloadable" to "TRUE".
biodb.DEBUG[2025-11-15 16:03:33.111][self$setPropertyValue] Setting property "dwnld.ext" to "gz".
biodb.DEBUG[2025-11-15 16:03:33.112][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-11-15 16:03:33.113][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-11-15 16:03:33.114][self$setPropertyValue] Setting property "entry.content.type" to "sdf".
biodb.DEBUG[2025-11-15 16:03:33.115][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-11-15 16:03:33.116][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-11-15 16:03:33.117][self$setPropertyValue] Setting property "name" to "NCI CACTUS".
biodb.DEBUG[2025-11-15 16:03:33.118][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-11-15 16:03:33.119][self$setPropertyValue] Setting property "parsing.expr" to "NSC".
biodb.DEBUG[2025-11-15 16:03:33.119][self$setPropertyValue] Setting property "parsing.expr" to "DTP names".
biodb.DEBUG[2025-11-15 16:03:33.119][self$setPropertyValue] Setting property "parsing.expr" to "Standard InChI".
biodb.DEBUG[2025-11-15 16:03:33.119][self$setPropertyValue] Setting property "parsing.expr" to "c("Standard InChIKey", "^InChIKey=(.*)$")".
biodb.DEBUG[2025-11-15 16:03:33.119][self$setPropertyValue] Setting property "parsing.expr" to "Formula".
biodb.DEBUG[2025-11-15 16:03:33.119][self$setPropertyValue] Setting property "parsing.expr" to "Molecular Weight".
biodb.DEBUG[2025-11-15 16:03:33.119][self$setPropertyValue] Setting property "parsing.expr" to "CAS".
biodb.DEBUG[2025-11-15 16:03:33.120][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-11-15 16:03:33.121][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-11-15 16:03:33.121][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-11-15 16:03:33.122][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-11-15 16:03:33.123][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-11-15 16:03:33.124][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-11-15 16:03:33.125][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-11-15 16:03:33.126][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-11-15 16:03:33.127][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-11-15 16:03:33.128][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/".
biodb.DEBUG[2025-11-15 16:03:33.128][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/".
biodb.DEBUG[2025-11-15 16:03:33.128][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/download/nci/".
biodb.DEBUG[2025-11-15 16:03:33.128][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/download/nci/NCI-Open_2012-05-01.sdf.gz".
biodb.DEBUG[2025-11-15 16:03:33.129][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-11-15 16:03:33.129][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-11-15 16:03:33.130][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-11-15 16:03:33.131][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-11-15 16:03:33.137][self$getEntryFields()$define] Define field nci.cactus.id.
biodb.DEBUG[2025-11-15 16:03:33.157][super$initialize] Initialize connector nci.cactus.
biodb.DEBUG[2025-11-15 16:03:33.172][biodb$getFactory()$createConn] Creating new connector nci.cactus for database class nci.cactus .
biodb.INFO [2025-11-15 16:03:33.180][biodb::testThat]
biodb.INFO [2025-11-15 16:03:33.181][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2025-11-15 16:03:33.182][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-11-15 16:03:33.183][biodb::testThat]
biodb.TRACE[2025-11-15 16:03:33.186][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNci.Rcheck/biodbNci/testref/entry-nci.cactus-749674-content.sdf".
biodb.DEBUG[2025-11-15 16:03:33.188][biodb$getFactory()$createEntryFromCo ...] Creating NCI CACTUS entries from 1 content(s).
biodb.DEBUG[2025-11-15 16:03:33.191][biodb$getFactory()$createEntryFromCo ...] Parsing 1 NCI CACTUS entries.
biodb.DEBUG[2025-11-15 16:03:33.205][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-11-15 16:03:33.206][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-15 16:03:33.207][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-15 16:03:33.218][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-11-15 16:03:33.219][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-15 16:03:33.219][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-11-15 16:03:33.220][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-11-15 16:03:33.237][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-15 16:03:33.238][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-15 16:03:33.239][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:03:33.239][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:03:33.240][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-15 16:03:33.252][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-15 16:03:33.253][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:03:33.254][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:03:33.256][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-11-15 16:03:33.257][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-11-15 16:03:33.258][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:03:33.259][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:03:33.283][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-11-15 16:03:33.284][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-11-15 16:03:33.285][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:03:33.286][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:03:33.287][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-11-15 16:03:33.288][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-11-15 16:03:33.289][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:03:33.290][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:03:33.291][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-11-15 16:03:33.292][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-11-15 16:03:33.293][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:03:33.294][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:03:33.296][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-11-15 16:03:33.297][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-11-15 16:03:33.297][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:03:33.298][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:03:33.299][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-11-15 16:03:33.300][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-11-15 16:03:33.301][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:03:33.302][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:03:33.303][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-11-15 16:03:33.304][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-11-15 16:03:33.305][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:03:33.306][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:03:33.307][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-11-15 16:03:33.308][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-11-15 16:03:33.309][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:03:33.310][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:03:33.311][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-11-15 16:03:33.312][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-11-15 16:03:33.313][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:03:33.314][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:03:33.315][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-11-15 16:03:33.316][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-11-15 16:03:33.317][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:03:33.318][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:03:33.319][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-15 16:03:33.320][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-15 16:03:33.321][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:03:33.322][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:03:33.323][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-11-15 16:03:33.324][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-11-15 16:03:33.324][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:03:33.325][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:03:33.326][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-15 16:03:33.327][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-15 16:03:33.334][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:03:33.335][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:03:33.335][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-15 16:03:33.336][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-15 16:03:33.337][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:03:33.338][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:03:33.339][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-15 16:03:33.340][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-15 16:03:33.341][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:03:33.342][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:03:33.373][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-15 16:03:33.374][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-15 16:03:33.375][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:03:33.376][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:03:33.377][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-15 16:03:33.378][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-15 16:03:33.379][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:03:33.380][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:03:33.381][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-15 16:03:33.382][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-15 16:03:33.383][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:03:33.383][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-11-15 16:03:33.384][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 749674.
biodb.TRACE[2025-11-15 16:03:33.387][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-11-15 16:03:33.388][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-11-15 16:03:33.389][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:03:33.389][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:03:33.390][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-11-15 16:03:33.391][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-11-15 16:03:33.392][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:03:33.393][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:03:33.394][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-11-15 16:03:33.395][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-11-15 16:03:33.396][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:03:33.397][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:03:33.398][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-11-15 16:03:33.399][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-11-15 16:03:33.400][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:03:33.401][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:03:33.403][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-15 16:03:33.404][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-15 16:03:33.405][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:03:33.406][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:03:33.418][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-11-15 16:03:33.419][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-11-15 16:03:33.420][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:03:33.421][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:03:33.425][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-15 16:03:33.426][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-15 16:03:33.427][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:03:33.428][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:03:33.429][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-15 16:03:33.430][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-15 16:03:33.431][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:03:33.431][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:03:33.432][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-15 16:03:33.433][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-15 16:03:33.434][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:03:33.435][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:03:33.438][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-15 16:03:33.439][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-15 16:03:33.440][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:03:33.440][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:03:33.441][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-15 16:03:33.483][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-15 16:03:33.484][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:03:33.485][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:03:33.486][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-15 16:03:33.487][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-15 16:03:33.488][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:03:33.489][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:03:33.490][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-11-15 16:03:33.491][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-11-15 16:03:33.492][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:03:33.493][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:03:33.494][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-11-15 16:03:33.495][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-11-15 16:03:33.496][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:03:33.497][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:03:33.498][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-11-15 16:03:33.499][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-11-15 16:03:33.500][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:03:33.500][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:03:33.507][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-15 16:03:33.508][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-15 16:03:33.509][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:03:33.510][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:03:33.511][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-15 16:03:33.512][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-15 16:03:33.513][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:03:33.514][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:03:33.515][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-15 16:03:33.516][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-15 16:03:33.517][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:03:33.517][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:03:33.519][ef$get] Asked field names are: accession.
biodb.TRACE[2025-11-15 16:03:33.519][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-15 16:03:33.520][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:03:33.521][ef$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:03:33.522][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-15 16:03:33.523][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-15 16:03:33.524][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:03:33.525][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:03:33.533][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-11-15 16:03:33.534][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-11-15 16:03:33.535][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:03:33.536][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:03:33.537][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-11-15 16:03:33.538][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-11-15 16:03:33.538][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:03:33.539][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:03:33.540][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-11-15 16:03:33.541][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-11-15 16:03:33.542][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:03:33.543][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:03:33.544][ef$get] Asked field names are: formula.
biodb.TRACE[2025-11-15 16:03:33.545][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-11-15 16:03:33.546][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:03:33.547][ef$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:03:33.548][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-11-15 16:03:33.549][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-11-15 16:03:33.550][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:03:33.550][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:03:33.558][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-11-15 16:03:33.559][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-11-15 16:03:33.560][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:03:33.561][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:03:33.562][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-11-15 16:03:33.563][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-11-15 16:03:33.563][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:03:33.564][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:03:33.565][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-11-15 16:03:33.566][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-11-15 16:03:33.567][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:03:33.568][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:03:33.569][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-11-15 16:03:33.570][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-11-15 16:03:33.571][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:03:33.572][ef$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:03:33.573][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-11-15 16:03:33.574][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-11-15 16:03:33.575][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:03:33.576][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:03:33.583][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-11-15 16:03:33.584][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-11-15 16:03:33.585][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:03:33.586][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:03:33.587][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-11-15 16:03:33.588][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-11-15 16:03:33.589][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:03:33.589][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:03:33.590][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-11-15 16:03:33.591][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-11-15 16:03:33.592][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:03:33.593][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:03:33.594][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-11-15 16:03:33.595][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-11-15 16:03:33.596][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:03:33.597][ef$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:03:33.598][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-11-15 16:03:33.599][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-11-15 16:03:33.600][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:03:33.601][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:03:33.612][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-11-15 16:03:33.613][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-11-15 16:03:33.614][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:03:33.615][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:03:33.616][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-11-15 16:03:33.617][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-11-15 16:03:33.618][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:03:33.619][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:03:33.620][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-11-15 16:03:33.621][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-11-15 16:03:33.622][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:03:33.623][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:03:33.624][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-11-15 16:03:33.625][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-11-15 16:03:33.626][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:03:33.626][ef$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:03:33.627][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-11-15 16:03:33.628][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-11-15 16:03:33.629][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:03:33.630][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:03:33.638][ef$get] Asked field names are: accession.
biodb.TRACE[2025-11-15 16:03:33.639][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-15 16:03:33.639][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:03:33.640][ef$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:03:33.644][ef$get] Asked field names are: formula.
biodb.TRACE[2025-11-15 16:03:33.645][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-11-15 16:03:33.646][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:03:33.647][ef$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:03:33.651][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-11-15 16:03:33.652][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-11-15 16:03:33.653][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:03:33.654][ef$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:03:33.657][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-11-15 16:03:33.658][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-11-15 16:03:33.659][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:03:33.660][ef$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:03:33.664][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-11-15 16:03:33.665][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-11-15 16:03:33.666][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:03:33.667][ef$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:03:33.682][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNci.Rcheck/biodbNci/testref/entry-nci.cactus-750690-content.sdf".
biodb.DEBUG[2025-11-15 16:03:33.719][biodb$getFactory()$createEntryFromCo ...] Creating NCI CACTUS entries from 1 content(s).
biodb.DEBUG[2025-11-15 16:03:33.720][biodb$getFactory()$createEntryFromCo ...] Parsing 1 NCI CACTUS entries.
biodb.DEBUG[2025-11-15 16:03:33.722][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-11-15 16:03:33.723][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-15 16:03:33.724][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-15 16:03:33.728][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-11-15 16:03:33.728][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-15 16:03:33.729][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-11-15 16:03:33.730][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-11-15 16:03:33.740][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-15 16:03:33.741][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-15 16:03:33.741][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:03:33.742][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:03:33.743][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-15 16:03:33.744][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-15 16:03:33.745][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:03:33.746][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:03:33.763][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-11-15 16:03:33.764][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-11-15 16:03:33.765][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:03:33.766][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:03:33.767][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-11-15 16:03:33.768][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-11-15 16:03:33.769][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:03:33.770][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:03:33.771][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-11-15 16:03:33.772][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-11-15 16:03:33.773][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:03:33.774][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:03:33.775][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-11-15 16:03:33.776][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-11-15 16:03:33.777][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:03:33.778][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:03:33.779][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-11-15 16:03:33.780][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-11-15 16:03:33.781][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:03:33.782][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:03:33.783][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-11-15 16:03:33.784][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-11-15 16:03:33.785][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:03:33.786][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:03:33.787][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-11-15 16:03:33.788][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-11-15 16:03:33.789][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:03:33.790][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:03:33.791][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-11-15 16:03:33.792][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-11-15 16:03:33.793][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:03:33.794][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:03:33.795][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-11-15 16:03:33.796][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-11-15 16:03:33.797][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:03:33.798][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:03:33.799][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-11-15 16:03:33.800][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-11-15 16:03:33.800][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:03:33.801][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:03:33.802][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-11-15 16:03:33.803][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-11-15 16:03:33.804][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:03:33.805][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:03:33.806][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-11-15 16:03:33.807][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-11-15 16:03:33.808][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:03:33.809][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:03:33.810][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-11-15 16:03:33.811][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-11-15 16:03:33.812][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:03:33.813][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:03:33.814][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-11-15 16:03:33.815][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-11-15 16:03:33.816][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:03:33.817][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:03:33.818][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-11-15 16:03:33.819][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-11-15 16:03:33.820][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:03:33.821][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:03:33.822][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-11-15 16:03:33.823][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-11-15 16:03:33.824][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:03:33.825][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:03:33.826][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-11-15 16:03:33.827][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-11-15 16:03:33.828][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:03:33.829][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:03:33.830][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-11-15 16:03:33.835][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-11-15 16:03:33.836][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:03:33.837][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:03:33.838][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-11-15 16:03:33.839][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-11-15 16:03:33.840][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:03:33.841][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:03:33.842][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-15 16:03:33.843][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-15 16:03:33.843][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:03:33.844][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:03:33.845][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-11-15 16:03:33.846][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-11-15 16:03:33.847][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:03:33.848][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:03:33.849][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-15 16:03:33.850][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-15 16:03:33.851][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:03:33.852][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:03:33.853][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-15 16:03:33.854][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-15 16:03:33.855][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:03:33.856][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:03:33.857][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-15 16:03:33.858][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-15 16:03:33.858][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:03:33.859][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:03:33.860][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-15 16:03:33.861][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-15 16:03:33.862][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:03:33.863][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:03:33.864][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-15 16:03:33.865][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-15 16:03:33.866][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:03:33.867][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:03:33.868][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-15 16:03:33.869][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-15 16:03:33.870][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:03:33.870][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-11-15 16:03:33.871][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 750690.
biodb.TRACE[2025-11-15 16:03:33.891][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-11-15 16:03:33.892][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-11-15 16:03:33.893][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:03:33.894][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:03:33.894][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-11-15 16:03:33.895][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-11-15 16:03:33.896][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:03:33.897][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:03:33.898][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-11-15 16:03:33.899][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-11-15 16:03:33.900][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:03:33.901][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:03:33.902][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-11-15 16:03:33.903][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-11-15 16:03:33.904][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:03:33.905][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:03:33.906][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-15 16:03:33.907][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-15 16:03:33.908][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:03:33.909][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:03:33.914][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-11-15 16:03:33.915][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-11-15 16:03:33.916][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:03:33.916][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:03:33.921][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-15 16:03:33.922][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-15 16:03:33.923][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:03:33.923][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:03:33.924][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-15 16:03:33.925][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-15 16:03:33.926][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:03:33.927][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:03:33.928][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-15 16:03:33.929][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-15 16:03:33.930][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:03:33.931][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:03:33.933][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-15 16:03:33.934][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-15 16:03:33.935][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:03:33.936][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:03:33.937][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-15 16:03:33.938][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-15 16:03:33.939][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:03:33.940][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:03:33.941][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-15 16:03:33.942][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-15 16:03:33.943][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:03:33.944][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:03:33.945][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-11-15 16:03:33.946][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-11-15 16:03:33.947][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:03:33.947][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:03:33.948][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-11-15 16:03:33.953][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-11-15 16:03:33.954][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:03:33.955][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:03:33.956][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-11-15 16:03:33.957][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-11-15 16:03:33.958][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:03:33.959][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:03:33.975][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-15 16:03:33.976][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-15 16:03:33.977][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:03:33.977][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:03:33.978][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-15 16:03:33.979][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-15 16:03:33.980][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:03:33.981][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:03:33.982][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-15 16:03:33.983][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-15 16:03:33.984][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:03:33.985][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:03:33.986][ef$get] Asked field names are: accession.
biodb.TRACE[2025-11-15 16:03:33.987][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-15 16:03:33.988][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:03:33.989][ef$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:03:33.990][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-15 16:03:33.991][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-15 16:03:33.992][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:03:33.992][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:03:34.000][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-11-15 16:03:34.001][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-11-15 16:03:34.002][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:03:34.003][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:03:34.004][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-11-15 16:03:34.005][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-11-15 16:03:34.006][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:03:34.007][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:03:34.008][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-11-15 16:03:34.009][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-11-15 16:03:34.010][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:03:34.011][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:03:34.012][ef$get] Asked field names are: cas.id.
biodb.TRACE[2025-11-15 16:03:34.013][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-11-15 16:03:34.013][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:03:34.014][ef$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:03:34.015][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-11-15 16:03:34.016][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-11-15 16:03:34.017][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:03:34.018][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:03:34.026][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-11-15 16:03:34.027][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-11-15 16:03:34.028][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:03:34.029][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:03:34.030][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-11-15 16:03:34.031][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-11-15 16:03:34.031][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:03:34.032][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:03:34.033][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-11-15 16:03:34.034][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-11-15 16:03:34.035][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:03:34.036][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:03:34.037][ef$get] Asked field names are: name.
biodb.TRACE[2025-11-15 16:03:34.038][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-11-15 16:03:34.039][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:03:34.040][ef$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:03:34.041][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-11-15 16:03:34.042][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-11-15 16:03:34.043][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:03:34.043][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:03:34.051][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-11-15 16:03:34.052][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-11-15 16:03:34.053][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:03:34.054][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:03:34.054][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-11-15 16:03:34.055][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-11-15 16:03:34.056][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:03:34.057][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:03:34.058][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-11-15 16:03:34.059][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-11-15 16:03:34.060][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:03:34.061][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:03:34.062][ef$get] Asked field names are: formula.
biodb.TRACE[2025-11-15 16:03:34.063][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-11-15 16:03:34.064][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:03:34.065][ef$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:03:34.066][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-11-15 16:03:34.067][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-11-15 16:03:34.067][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:03:34.068][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:03:34.079][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-11-15 16:03:34.080][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-11-15 16:03:34.081][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:03:34.082][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:03:34.083][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-11-15 16:03:34.084][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-11-15 16:03:34.085][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:03:34.086][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:03:34.087][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-11-15 16:03:34.088][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-11-15 16:03:34.089][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:03:34.090][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:03:34.091][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-11-15 16:03:34.092][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-11-15 16:03:34.093][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:03:34.093][ef$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:03:34.094][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-11-15 16:03:34.095][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-11-15 16:03:34.096][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:03:34.097][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:03:34.104][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-11-15 16:03:34.105][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-11-15 16:03:34.106][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:03:34.107][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:03:34.108][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-11-15 16:03:34.109][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-11-15 16:03:34.110][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:03:34.111][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:03:34.112][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-11-15 16:03:34.113][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-11-15 16:03:34.114][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:03:34.115][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:03:34.116][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-11-15 16:03:34.116][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-11-15 16:03:34.117][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:03:34.118][ef$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:03:34.119][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-11-15 16:03:34.120][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-11-15 16:03:34.121][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:03:34.122][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:03:34.129][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-11-15 16:03:34.130][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-11-15 16:03:34.131][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:03:34.132][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:03:34.133][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-11-15 16:03:34.134][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-11-15 16:03:34.135][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:03:34.136][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:03:34.137][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-11-15 16:03:34.138][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-11-15 16:03:34.139][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:03:34.140][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:03:34.140][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-11-15 16:03:34.141][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-11-15 16:03:34.142][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:03:34.143][ef$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:03:34.144][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-11-15 16:03:34.145][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-11-15 16:03:34.146][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:03:34.147][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:03:34.154][ef$get] Asked field names are: accession.
biodb.TRACE[2025-11-15 16:03:34.155][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-15 16:03:34.156][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:03:34.157][ef$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:03:34.161][ef$get] Asked field names are: cas.id.
biodb.TRACE[2025-11-15 16:03:34.162][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-11-15 16:03:34.163][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:03:34.163][ef$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:03:34.167][ef$get] Asked field names are: formula.
biodb.TRACE[2025-11-15 16:03:34.168][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-11-15 16:03:34.169][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:03:34.170][ef$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:03:34.174][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-11-15 16:03:34.175][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-11-15 16:03:34.176][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:03:34.177][ef$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:03:34.180][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-11-15 16:03:34.181][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-11-15 16:03:34.182][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:03:34.183][ef$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:03:34.190][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-11-15 16:03:34.191][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-11-15 16:03:34.192][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:03:34.193][ef$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:03:34.197][ef$get] Asked field names are: name.
biodb.TRACE[2025-11-15 16:03:34.198][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-11-15 16:03:34.199][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:03:34.200][ef$get] fields variable is a list.
biodb.INFO [2025-11-15 16:03:34.206][biodb::testThat]
biodb.INFO [2025-11-15 16:03:34.207][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2025-11-15 16:03:34.208][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-11-15 16:03:34.209][biodb::testThat]
biodb.DEBUG[2025-11-15 16:03:34.211][private$loadEntries] Creating entries from ids [2]: "749674, 750690".
biodb.DEBUG[2025-11-15 16:03:34.213][conn$getEntryContent] Get NCI CACTUS entry content(s) for 2 id(s)...
biodb.DEBUG[2025-11-15 16:03:34.216][self$isDownloaded] Database nci.cactus has already been downloaded.
biodb.DEBUG[2025-11-15 16:03:34.243][self$isDownloaded] Database nci.cactus has already been downloaded.
biodb.INFO [2025-11-15 16:03:34.245][self$download] Extract whole database of nci.cactus.
biodb.INFO [2025-11-15 16:03:34.245][private$doExtractDownload] Extracting content of downloaded biodbNci, a library for connecting to the National Cancer Institute (USA) CACTUS Database....
Saving _problems/test_long_100_generic-38.R
biodb.INFO [2025-11-15 16:03:34.374][biodb::testThat]
biodb.INFO [2025-11-15 16:03:34.375][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2025-11-15 16:03:34.376][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-11-15 16:03:34.377][biodb::testThat]
biodb.INFO [2025-11-15 16:03:34.382][biodb::testThat]
biodb.INFO [2025-11-15 16:03:34.383][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2025-11-15 16:03:34.384][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-11-15 16:03:34.385][biodb::testThat]
biodb.WARN [2025-11-15 16:03:34.407][self$searchForEntries] This database is not searchable by field "name".
biodb.WARN [2025-11-15 16:03:34.425][self$searchForEntries] This database is not searchable by field "name".
biodb.INFO [2025-11-15 16:03:34.432][biodb::testThat]
biodb.INFO [2025-11-15 16:03:34.433][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2025-11-15 16:03:34.434][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-11-15 16:03:34.435][biodb::testThat]
biodb.DEBUG[2025-11-15 16:03:34.451][private$loadEntries] Creating entries from ids [1]: "749674".
biodb.DEBUG[2025-11-15 16:03:34.499][conn$getEntryContent] Get NCI CACTUS entry content(s) for 1 id(s)...
biodb.DEBUG[2025-11-15 16:03:34.500][self$isDownloaded] Database nci.cactus has already been downloaded.
biodb.DEBUG[2025-11-15 16:03:34.501][self$isDownloaded] Database nci.cactus has already been downloaded.
biodb.INFO [2025-11-15 16:03:34.503][self$download] Extract whole database of nci.cactus.
biodb.INFO [2025-11-15 16:03:34.515][private$doExtractDownload] Extracting content of downloaded biodbNci, a library for connecting to the National Cancer Institute (USA) CACTUS Database....
Saving _problems/test_long_100_generic-38.R
biodb.INFO [2025-11-15 16:03:34.566][biodb::testThat]
biodb.INFO [2025-11-15 16:03:34.567][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2025-11-15 16:03:34.568][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-11-15 16:03:34.568][biodb::testThat]
biodb.INFO [2025-11-15 16:03:34.575][biodb::testThat]
biodb.INFO [2025-11-15 16:03:34.576][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2025-11-15 16:03:34.577][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-11-15 16:03:34.578][biodb::testThat]
biodb.INFO [2025-11-15 16:03:34.589][biodb::testThat]
biodb.INFO [2025-11-15 16:03:34.590][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2025-11-15 16:03:34.591][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-11-15 16:03:34.591][biodb::testThat]
biodb.INFO [2025-11-15 16:03:34.597][biodb::testThat]
biodb.INFO [2025-11-15 16:03:34.598][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2025-11-15 16:03:34.599][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-11-15 16:03:34.600][biodb::testThat]
biodb.INFO [2025-11-15 16:03:34.605][biodb$terminate] Closing BiodbMain instance...
biodb.INFO [2025-11-15 16:03:34.606][self$deleteConn] Connector "nci.cactus" deleted.
biodb.DEBUG[2025-11-15 16:03:34.607][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-11-15 16:03:34.607][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-15 16:03:34.608][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-15 16:03:34.609][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-15 16:03:34.610][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-15 16:03:34.611][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-11-15 16:03:34.612][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2025-11-15 16:03:34.620][biodb::testContext]
biodb.INFO [2025-11-15 16:03:34.621][biodb::testContext] ********************************************************************************
biodb.INFO [2025-11-15 16:03:34.622][biodb::testContext] Test context - Example long tests
biodb.INFO [2025-11-15 16:03:34.623][biodb::testContext] ********************************************************************************
biodb.INFO [2025-11-15 16:03:34.624][biodb::testContext]
biodb.INFO [2025-11-15 16:03:34.626][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.18.0.
biodb.DEBUG[2025-11-15 16:03:34.627][self$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.22-bioc/R/site-library/biodb/definitions.yml".
biodb.DEBUG[2025-11-15 16:03:34.631][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-11-15 16:03:34.632][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-11-15 16:03:34.633][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-11-15 16:03:34.634][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-15 16:03:34.634][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-15 16:03:34.635][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-15 16:03:34.636][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-11-15 16:03:34.637][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-11-15 16:03:34.638][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-15 16:03:34.639][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-15 16:03:34.640][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-15 16:03:34.640][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-11-15 16:03:34.641][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-11-15 16:03:34.642][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-15 16:03:34.643][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-15 16:03:34.644][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-15 16:03:34.645][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-11-15 16:03:34.646][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-11-15 16:03:34.647][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-11-15 16:03:34.648][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-15 16:03:34.648][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-15 16:03:34.649][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-15 16:03:34.650][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-11-15 16:03:34.651][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-11-15 16:03:34.652][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-11-15 16:03:34.653][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-15 16:03:34.654][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-15 16:03:34.655][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-15 16:03:34.655][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-11-15 16:03:34.656][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-11-15 16:03:34.657][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-15 16:03:34.658][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-15 16:03:34.659][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-15 16:03:34.660][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-11-15 16:03:34.661][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-11-15 16:03:34.662][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-11-15 16:03:34.663][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-15 16:03:34.663][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-15 16:03:34.664][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-15 16:03:34.665][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-11-15 16:03:34.666][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-11-15 16:03:34.667][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-15 16:03:34.668][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-15 16:03:34.669][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-15 16:03:34.670][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-11-15 16:03:34.670][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-11-15 16:03:34.671][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-11-15 16:03:34.672][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-15 16:03:34.673][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-15 16:03:34.674][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-15 16:03:34.675][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-11-15 16:03:34.676][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-11-15 16:03:34.677][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-11-15 16:03:34.678][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-11-15 16:03:34.679][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-11-15 16:03:34.680][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-11-15 16:03:34.680][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-15 16:03:34.681][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-15 16:03:34.682][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-15 16:03:34.683][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-11-15 16:03:34.684][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-11-15 16:03:34.685][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-15 16:03:34.686][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-15 16:03:34.686][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-15 16:03:34.687][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-11-15 16:03:34.688][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-11-15 16:03:34.689][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-15 16:03:34.690][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-15 16:03:34.691][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-15 16:03:34.696][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-11-15 16:03:34.697][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-11-15 16:03:34.698][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-15 16:03:34.698][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-15 16:03:34.699][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-15 16:03:34.700][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-11-15 16:03:34.701][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-11-15 16:03:34.702][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-11-15 16:03:34.703][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-15 16:03:34.704][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-15 16:03:34.705][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-15 16:03:34.705][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-11-15 16:03:34.706][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-11-15 16:03:34.711][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-11-15 16:03:34.712][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-15 16:03:34.713][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-15 16:03:34.714][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-15 16:03:34.715][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-11-15 16:03:34.716][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-11-15 16:03:34.717][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-11-15 16:03:34.718][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-15 16:03:34.718][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-15 16:03:34.719][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-15 16:03:34.720][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-11-15 16:03:34.722][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-11-15 16:03:34.723][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2025-11-15 16:03:34.724][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-11-15 16:03:34.725][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-11-15 16:03:34.726][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-11-15 16:03:34.727][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-11-15 16:03:34.728][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-11-15 16:03:34.729][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-11-15 16:03:34.730][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-11-15 16:03:34.730][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-11-15 16:03:34.731][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-11-15 16:03:34.732][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-11-15 16:03:34.733][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-11-15 16:03:34.734][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-11-15 16:03:34.735][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-11-15 16:03:34.736][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-11-15 16:03:34.736][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-11-15 16:03:34.736][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-11-15 16:03:34.736][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-11-15 16:03:34.736][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-11-15 16:03:34.737][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-11-15 16:03:34.738][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-11-15 16:03:34.739][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-11-15 16:03:34.740][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-11-15 16:03:34.741][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-11-15 16:03:34.741][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-11-15 16:03:34.742][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-11-15 16:03:34.743][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-11-15 16:03:34.744][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-11-15 16:03:34.745][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-11-15 16:03:34.746][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-11-15 16:03:34.747][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-11-15 16:03:34.748][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-11-15 16:03:34.750][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-11-15 16:03:34.751][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-11-15 16:03:34.751][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-11-15 16:03:34.752][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-11-15 16:03:34.753][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-11-15 16:03:34.754][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-11-15 16:03:34.755][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-11-15 16:03:34.756][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-11-15 16:03:34.757][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-11-15 16:03:34.758][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-11-15 16:03:34.759][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-11-15 16:03:34.760][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-11-15 16:03:34.761][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-11-15 16:03:34.762][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-11-15 16:03:34.763][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-11-15 16:03:34.763][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-11-15 16:03:34.763][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-11-15 16:03:34.763][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-11-15 16:03:34.763][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-11-15 16:03:34.763][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-11-15 16:03:34.764][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-11-15 16:03:34.765][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-11-15 16:03:34.766][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-11-15 16:03:34.767][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-11-15 16:03:34.768][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-11-15 16:03:34.769][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-11-15 16:03:34.770][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-11-15 16:03:34.771][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-11-15 16:03:34.772][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-11-15 16:03:34.772][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-11-15 16:03:34.773][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-11-15 16:03:34.774][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-11-15 16:03:34.775][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-11-15 16:03:34.777][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-11-15 16:03:34.778][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2025-11-15 16:03:34.779][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-11-15 16:03:34.780][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-11-15 16:03:34.781][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-11-15 16:03:34.782][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-11-15 16:03:34.783][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-11-15 16:03:34.783][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-11-15 16:03:34.784][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-11-15 16:03:34.785][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-11-15 16:03:34.786][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-11-15 16:03:34.787][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-11-15 16:03:34.788][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-11-15 16:03:34.789][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-11-15 16:03:34.790][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-11-15 16:03:34.791][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-11-15 16:03:34.792][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-11-15 16:03:34.793][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-11-15 16:03:34.794][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-11-15 16:03:34.795][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-11-15 16:03:34.796][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-11-15 16:03:34.796][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-11-15 16:03:34.797][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-11-15 16:03:34.798][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-11-15 16:03:34.799][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-11-15 16:03:34.800][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-11-15 16:03:34.801][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-11-15 16:03:34.805][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-11-15 16:03:34.807][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-11-15 16:03:34.808][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-11-15 16:03:34.809][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-11-15 16:03:34.810][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-11-15 16:03:34.811][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-11-15 16:03:34.812][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-11-15 16:03:34.813][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-11-15 16:03:34.814][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-11-15 16:03:34.815][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-11-15 16:03:34.816][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-11-15 16:03:34.817][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-11-15 16:03:34.818][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-11-15 16:03:34.818][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-11-15 16:03:34.819][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-11-15 16:03:34.820][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-11-15 16:03:34.821][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-11-15 16:03:34.822][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-11-15 16:03:34.823][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-11-15 16:03:34.824][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-11-15 16:03:34.825][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-11-15 16:03:34.826][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-11-15 16:03:34.827][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-11-15 16:03:34.827][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-11-15 16:03:34.828][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-11-15 16:03:34.829][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-11-15 16:03:34.830][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-11-15 16:03:34.831][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-11-15 16:03:34.832][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-11-15 16:03:34.833][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-11-15 16:03:34.834][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-11-15 16:03:34.835][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-11-15 16:03:34.836][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-15 16:03:34.837][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-15 16:03:34.837][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-15 16:03:34.838][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-15 16:03:34.839][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-15 16:03:34.840][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-15 16:03:34.841][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-15 16:03:34.842][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-15 16:03:34.842][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-15 16:03:34.843][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-15 16:03:34.844][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-15 16:03:34.845][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-15 16:03:34.846][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-15 16:03:34.846][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-15 16:03:34.847][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-15 16:03:34.848][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-15 16:03:34.849][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-15 16:03:34.850][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-15 16:03:34.851][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-15 16:03:34.851][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-15 16:03:34.852][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-15 16:03:34.853][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-15 16:03:34.854][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-15 16:03:34.855][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-15 16:03:34.856][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-15 16:03:34.856][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-15 16:03:34.857][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-15 16:03:34.858][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-15 16:03:34.859][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-15 16:03:34.860][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-15 16:03:34.861][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-15 16:03:34.861][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-15 16:03:34.862][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-15 16:03:34.863][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-15 16:03:34.864][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-15 16:03:34.865][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-15 16:03:34.866][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-15 16:03:34.866][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-15 16:03:34.867][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-15 16:03:34.868][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-15 16:03:34.869][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-15 16:03:34.870][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-15 16:03:34.871][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-15 16:03:34.871][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-15 16:03:34.872][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-15 16:03:34.873][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-15 16:03:34.874][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-15 16:03:34.875][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-15 16:03:34.876][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-15 16:03:34.876][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-15 16:03:34.877][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-15 16:03:34.878][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-15 16:03:34.879][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-15 16:03:34.880][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-15 16:03:34.881][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-15 16:03:34.881][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-15 16:03:34.882][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-15 16:03:34.883][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-15 16:03:34.884][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-15 16:03:34.885][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-15 16:03:34.886][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-15 16:03:34.886][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-15 16:03:34.887][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-15 16:03:34.888][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-15 16:03:34.889][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-15 16:03:34.890][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-15 16:03:34.891][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-15 16:03:34.891][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-15 16:03:34.892][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-15 16:03:34.893][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-15 16:03:34.894][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-15 16:03:34.895][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-15 16:03:34.896][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-15 16:03:34.896][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-15 16:03:34.897][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-15 16:03:34.898][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-15 16:03:34.899][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-15 16:03:34.900][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-15 16:03:34.901][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-15 16:03:34.901][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-15 16:03:34.902][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-15 16:03:34.903][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-11-15 16:03:34.905][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-11-15 16:03:34.906][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-11-15 16:03:34.911][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-11-15 16:03:34.912][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-11-15 16:03:34.914][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-11-15 16:03:34.915][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-11-15 16:03:34.916][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-11-15 16:03:34.917][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-11-15 16:03:34.919][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-11-15 16:03:34.920][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-11-15 16:03:34.921][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-11-15 16:03:34.923][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-11-15 16:03:34.924][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-11-15 16:03:34.925][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-11-15 16:03:34.926][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-11-15 16:03:34.928][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-11-15 16:03:34.929][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-11-15 16:03:34.930][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-11-15 16:03:34.932][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-11-15 16:03:34.933][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-11-15 16:03:34.934][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-11-15 16:03:34.936][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-11-15 16:03:34.937][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-11-15 16:03:34.938][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-11-15 16:03:34.939][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-11-15 16:03:34.941][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-11-15 16:03:34.942][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-11-15 16:03:34.943][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-11-15 16:03:34.945][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-11-15 16:03:34.946][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-11-15 16:03:34.947][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-11-15 16:03:34.948][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-11-15 16:03:34.950][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-11-15 16:03:34.951][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-11-15 16:03:34.952][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-11-15 16:03:34.954][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-11-15 16:03:34.955][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-11-15 16:03:34.956][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-11-15 16:03:34.957][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-11-15 16:03:34.959][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-11-15 16:03:34.960][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-11-15 16:03:34.961][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-11-15 16:03:34.963][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-11-15 16:03:34.964][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-11-15 16:03:34.965][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-11-15 16:03:34.967][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-11-15 16:03:34.968][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-11-15 16:03:34.969][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-11-15 16:03:34.970][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-11-15 16:03:34.972][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-11-15 16:03:34.973][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-11-15 16:03:34.974][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-11-15 16:03:34.976][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-11-15 16:03:34.977][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-11-15 16:03:34.978][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-11-15 16:03:34.980][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-11-15 16:03:34.981][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-11-15 16:03:34.982][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-11-15 16:03:34.983][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-11-15 16:03:34.985][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-11-15 16:03:34.986][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-11-15 16:03:34.987][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-11-15 16:03:34.989][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-11-15 16:03:34.990][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-11-15 16:03:34.991][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-11-15 16:03:34.992][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-11-15 16:03:34.994][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-11-15 16:03:34.995][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-11-15 16:03:34.996][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-11-15 16:03:34.998][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-11-15 16:03:34.999][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-11-15 16:03:35.000][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-11-15 16:03:35.002][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-11-15 16:03:35.003][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-11-15 16:03:35.004][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-11-15 16:03:35.005][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-11-15 16:03:35.007][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-11-15 16:03:35.008][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-11-15 16:03:35.009][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-11-15 16:03:35.015][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-11-15 16:03:35.016][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-11-15 16:03:35.017][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-11-15 16:03:35.019][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-11-15 16:03:35.020][initialize] This is biodb version 1.18.0.
biodb.DEBUG[2025-11-15 16:03:35.021][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-11-15 16:03:35.022][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-11-15 16:03:35.023][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-15 16:03:35.024][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-11-15 16:03:35.024][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-15 16:03:35.025][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-15 16:03:35.026][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-15 16:03:35.027][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-15 16:03:35.028][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-15 16:03:35.029][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-15 16:03:35.029][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-15 16:03:35.030][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[2025-11-15 16:03:35.031][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-15 16:03:35.032][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-15 16:03:35.033][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-15 16:03:35.034][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-15 16:03:35.034][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-15 16:03:35.035][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-15 16:03:35.036][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[2025-11-15 16:03:35.037][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-15 16:03:35.038][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-15 16:03:35.039][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-15 16:03:35.039][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-15 16:03:35.040][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-15 16:03:35.041][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-15 16:03:35.042][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-15 16:03:35.043][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-15 16:03:35.044][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-15 16:03:35.044][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-15 16:03:35.045][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-15 16:03:35.046][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-15 16:03:35.047][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-15 16:03:35.048][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-15 16:03:35.049][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-15 16:03:35.049][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-15 16:03:35.050][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-15 16:03:35.051][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-15 16:03:35.052][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-15 16:03:35.053][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-15 16:03:35.053][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-15 16:03:35.054][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-15 16:03:35.055][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-15 16:03:35.056][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-15 16:03:35.057][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-15 16:03:35.058][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-15 16:03:35.058][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-15 16:03:35.059][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-15 16:03:35.060][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-15 16:03:35.061][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-15 16:03:35.062][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-15 16:03:35.063][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-15 16:03:35.063][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-15 16:03:35.064][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-15 16:03:35.065][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-15 16:03:35.066][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-15 16:03:35.067][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-15 16:03:35.068][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-15 16:03:35.068][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-15 16:03:35.069][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-15 16:03:35.070][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-15 16:03:35.071][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-15 16:03:35.072][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-15 16:03:35.073][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-15 16:03:35.073][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-15 16:03:35.074][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-15 16:03:35.075][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-15 16:03:35.076][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-15 16:03:35.077][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-15 16:03:35.078][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-15 16:03:35.078][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-15 16:03:35.079][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-15 16:03:35.080][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-15 16:03:35.081][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-15 16:03:35.082][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-15 16:03:35.083][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-15 16:03:35.083][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-15 16:03:35.084][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-15 16:03:35.085][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-15 16:03:35.086][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-15 16:03:35.087][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-15 16:03:35.088][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-15 16:03:35.088][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-15 16:03:35.089][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-15 16:03:35.090][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-15 16:03:35.091][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-15 16:03:35.092][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-15 16:03:35.093][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-15 16:03:35.093][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-15 16:03:35.094][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-15 16:03:35.095][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-15 16:03:35.096][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-15 16:03:35.097][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-15 16:03:35.098][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-15 16:03:35.098][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-15 16:03:35.099][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-15 16:03:35.100][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-15 16:03:35.101][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-15 16:03:35.102][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-15 16:03:35.103][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-15 16:03:35.103][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-15 16:03:35.104][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-15 16:03:35.105][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-15 16:03:35.106][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-15 16:03:35.107][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-15 16:03:35.108][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-15 16:03:35.108][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-15 16:03:35.109][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-15 16:03:35.110][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-15 16:03:35.111][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-15 16:03:35.112][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-15 16:03:35.113][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-15 16:03:35.117][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-15 16:03:35.118][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-15 16:03:35.119][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-15 16:03:35.120][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-15 16:03:35.121][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-15 16:03:35.122][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-15 16:03:35.123][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNci.Rcheck/biodbNci/definitions.yml".
biodb.DEBUG[2025-11-15 16:03:35.124][self$getDbsInfo()$define] Define connector nci.cactus.
biodb.DEBUG[2025-11-15 16:03:35.126][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-11-15 16:03:35.127][self$setPropertyValue] Setting property "description" to "National Cancer Institute (USA) CACTUS Database.".
biodb.DEBUG[2025-11-15 16:03:35.128][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-11-15 16:03:35.129][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-11-15 16:03:35.130][self$setPropertyValue] Setting property "downloadable" to "TRUE".
biodb.DEBUG[2025-11-15 16:03:35.131][self$setPropertyValue] Setting property "dwnld.ext" to "gz".
biodb.DEBUG[2025-11-15 16:03:35.132][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-11-15 16:03:35.133][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-11-15 16:03:35.134][self$setPropertyValue] Setting property "entry.content.type" to "sdf".
biodb.DEBUG[2025-11-15 16:03:35.135][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-11-15 16:03:35.135][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-11-15 16:03:35.136][self$setPropertyValue] Setting property "name" to "NCI CACTUS".
biodb.DEBUG[2025-11-15 16:03:35.137][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-11-15 16:03:35.138][self$setPropertyValue] Setting property "parsing.expr" to "NSC".
biodb.DEBUG[2025-11-15 16:03:35.138][self$setPropertyValue] Setting property "parsing.expr" to "DTP names".
biodb.DEBUG[2025-11-15 16:03:35.138][self$setPropertyValue] Setting property "parsing.expr" to "Standard InChI".
biodb.DEBUG[2025-11-15 16:03:35.138][self$setPropertyValue] Setting property "parsing.expr" to "c("Standard InChIKey", "^InChIKey=(.*)$")".
biodb.DEBUG[2025-11-15 16:03:35.138][self$setPropertyValue] Setting property "parsing.expr" to "Formula".
biodb.DEBUG[2025-11-15 16:03:35.138][self$setPropertyValue] Setting property "parsing.expr" to "Molecular Weight".
biodb.DEBUG[2025-11-15 16:03:35.138][self$setPropertyValue] Setting property "parsing.expr" to "CAS".
biodb.DEBUG[2025-11-15 16:03:35.139][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-11-15 16:03:35.140][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-11-15 16:03:35.141][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-11-15 16:03:35.142][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-11-15 16:03:35.143][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-11-15 16:03:35.144][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-11-15 16:03:35.145][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-11-15 16:03:35.146][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-11-15 16:03:35.146][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-11-15 16:03:35.147][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/".
biodb.DEBUG[2025-11-15 16:03:35.147][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/".
biodb.DEBUG[2025-11-15 16:03:35.147][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/download/nci/".
biodb.DEBUG[2025-11-15 16:03:35.147][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/download/nci/NCI-Open_2012-05-01.sdf.gz".
biodb.DEBUG[2025-11-15 16:03:35.148][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-11-15 16:03:35.149][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-11-15 16:03:35.150][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-11-15 16:03:35.151][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-11-15 16:03:35.152][self$getEntryFields()$define] Define field nci.cactus.id.
biodb.DEBUG[2025-11-15 16:03:35.155][super$initialize] Initialize connector nci.cactus.
biodb.DEBUG[2025-11-15 16:03:35.158][biodb$getFactory()$createConn] Creating new connector nci.cactus for database class nci.cactus .
biodb.INFO [2025-11-15 16:03:35.159][biodb$terminate] Closing BiodbMain instance...
biodb.INFO [2025-11-15 16:03:35.160][self$deleteConn] Connector "nci.cactus" deleted.
biodb.DEBUG[2025-11-15 16:03:35.161][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-11-15 16:03:35.162][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-15 16:03:35.163][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-15 16:03:35.164][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-15 16:03:35.164][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-15 16:03:35.165][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-11-15 16:03:35.166][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
[ FAIL 2 | WARN 0 | SKIP 2 | PASS 85 ]

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

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

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

'R CMD check' output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --test-dir=longtests --no-stop-on-test-error --no-codoc --no-examples --no-manual --ignore-vignettes --check-subdirs=no biodbNci_1.14.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNci.Rcheck’
* using R version 4.5.1 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 ‘1.14.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘biodbNci’ can be installed ... OK
* used C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
* checking installed package size ... INFO
  installed size is  6.1Mb
  sub-directories of 1Mb or more:
    libs   5.8Mb
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking whether startup messages can be suppressed ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  NciCactusConn.Rd: BiodbConn
  NciCactusEntry.Rd: BiodbSdfEntry
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... SKIPPED
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... OK
* checking files in ‘vignettes’ ... SKIPPED
* checking examples ... SKIPPED
* checking for unstated dependencies in ‘longtests’ ... OK
* checking tests in ‘longtests’ ...
  Running ‘testthat.R’
 ERROR
Running the tests in ‘longtests/testthat.R’ failed.
Last 13 lines of output:
      ▆
   1. ├─base::do.call(fct, params)
   2. └─biodb (local) `<fn>`(conn = `<NcCctsCn>`, opt = `<named list>`)
   3.   └─opt$refEntries$getRealEntry(id)
   4.     └─self$getRealEntries(ids = id)
   5.       └─private$bdb$getFactory()$getEntry(...)
   6.         └─private$loadEntries(conn$getId(), missing.ids, drop = FALSE)
   7.           └─conn$getEntryContent(ids)
   8.             └─self$download()
   9.               └─private$doExtractDownload()
  
  [ FAIL 2 | WARN 0 | SKIP 2 | PASS 85 ]
  Error:
  ! Test failures.
  Execution halted
* DONE

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

Installation output

biodbNci.Rcheck/00install.out

* installing *source* package ‘biodbNci’ ...
** this is package ‘biodbNci’ version ‘1.14.0’
** using staged installation
** libs
using C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/testthat/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/testthat/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c extractEntries.cpp -o extractEntries.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/testthat/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c test-100-example.cpp -o test-100-example.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/testthat/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c test-runner.cpp -o test-runner.o
g++ -std=gnu++17 -shared -L/home/biocbuild/bbs-3.22-bioc/R/lib -L/usr/local/lib -o biodbNci.so RcppExports.o extractEntries.o test-100-example.o test-runner.o -L/home/biocbuild/bbs-3.22-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNci.Rcheck/00LOCK-biodbNci/00new/biodbNci/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning in fun(libname, pkgname) :
  Package 'biodbNci' is deprecated and will be removed from Bioconductor
  version 3.23
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
Warning in fun(libname, pkgname) :
  Package 'biodbNci' is deprecated and will be removed from Bioconductor
  version 3.23
** testing if installed package keeps a record of temporary installation path
* DONE (biodbNci)