Back to Long Tests report for BioC 3.22

This page was generated on 2025-11-01 23:55 -0400 (Sat, 01 Nov 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" 4901
lconwaymacOS 12.7.6 Montereyx86_644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4691
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: 2025-11-01 09:55 -0400 (Sat, 01 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 -0400 (Wed, 29 Oct 2025)
nebbiolo2Linux (Ubuntu 24.04.3 LTS) / x86_64  ERROR  
lconwaymacOS 12.7.6 Monterey / x86_64  ERROR  

CHECK results for biodbNci on nebbiolo2

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

raw results


Summary

Package: biodbNci
Version: 1.14.0
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: 2025-11-01 16:02:31 -0400 (Sat, 01 Nov 2025)
EndedAt: 2025-11-01 16:03:34 -0400 (Sat, 01 Nov 2025)
EllapsedTime: 63.0 seconds
RetCode: 1
Status:   ERROR  
CheckDir: biodbNci.Rcheck
Warnings: NA

Tests output

biodbNci.Rcheck/tests/testthat.Rout.fail


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

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> # Script needed to run testthat automatically from ‘R CMD check’. See
> # testthat::test_dir documentation.
> library(testthat)
> library(biodbNci)
Warning message:
In fun(libname, pkgname) :
  Package 'biodbNci' is deprecated and will be removed from Bioconductor
  version 3.23
> Sys.setenv(TESTTHAT_REPORTER="summary")
> Sys.setenv(BIODB_LOG_DST="console")
> test_check("biodbNci")
biodb.INFO [2025-11-01 16:03:31.750][biodb::testContext]
biodb.INFO [2025-11-01 16:03:31.752][biodb::testContext] ********************************************************************************
biodb.INFO [2025-11-01 16:03:31.753][biodb::testContext] Test context - Generic long tests
biodb.INFO [2025-11-01 16:03:31.753][biodb::testContext] ********************************************************************************
biodb.INFO [2025-11-01 16:03:31.754][biodb::testContext]
biodb.INFO [2025-11-01 16:03:31.760][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.18.0.
biodb.DEBUG[2025-11-01 16:03:31.762][self$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.22-bioc/R/site-library/biodb/definitions.yml".
biodb.DEBUG[2025-11-01 16:03:31.769][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-11-01 16:03:31.770][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-11-01 16:03:31.771][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-11-01 16:03:31.772][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:03:31.773][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:03:31.774][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:03:31.775][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-11-01 16:03:31.792][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-11-01 16:03:31.793][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:03:31.801][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:03:31.802][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:03:31.803][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-11-01 16:03:31.804][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-11-01 16:03:31.805][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:03:31.806][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:03:31.807][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:03:31.807][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-11-01 16:03:31.808][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-11-01 16:03:31.809][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-11-01 16:03:31.810][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:03:31.811][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:03:31.812][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[2025-11-01 16:03:31.813][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-11-01 16:03:31.814][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-11-01 16:03:31.815][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-11-01 16:03:31.815][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:03:31.816][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:03:31.817][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:03:31.818][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-11-01 16:03:31.819][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-11-01 16:03:31.820][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:03:31.821][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:03:31.821][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:03:31.822][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-11-01 16:03:31.823][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-11-01 16:03:31.824][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-11-01 16:03:31.825][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:03:31.826][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:03:31.827][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:03:31.828][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-11-01 16:03:31.829][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-11-01 16:03:31.829][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:03:31.830][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:03:31.831][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:03:31.832][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-11-01 16:03:31.833][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-11-01 16:03:31.834][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-11-01 16:03:31.835][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:03:31.835][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:03:31.836][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:03:31.837][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-11-01 16:03:31.838][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-11-01 16:03:31.839][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-11-01 16:03:31.840][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-11-01 16:03:31.841][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-11-01 16:03:31.842][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-11-01 16:03:31.843][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:03:31.844][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:03:31.844][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[2025-11-01 16:03:31.845][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-11-01 16:03:31.846][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-11-01 16:03:31.847][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:03:31.848][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:03:31.849][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:03:31.850][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-11-01 16:03:31.851][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-11-01 16:03:31.851][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:03:31.852][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:03:31.853][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:03:31.854][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-11-01 16:03:31.855][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-11-01 16:03:31.856][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:03:31.857][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:03:31.857][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:03:31.858][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-11-01 16:03:31.859][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-11-01 16:03:31.860][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-11-01 16:03:31.861][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:03:31.862][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:03:31.863][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:03:31.864][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-11-01 16:03:31.864][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-11-01 16:03:31.870][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-11-01 16:03:31.870][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:03:31.871][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:03:31.872][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:03:31.873][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-11-01 16:03:31.874][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-11-01 16:03:31.875][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-11-01 16:03:31.876][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:03:31.876][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:03:31.877][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[2025-11-01 16:03:31.881][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-11-01 16:03:31.911][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-11-01 16:03:31.926][self$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[2025-11-01 16:03:31.927][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-11-01 16:03:31.928][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-11-01 16:03:31.929][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-11-01 16:03:31.930][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-11-01 16:03:31.931][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-11-01 16:03:31.931][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-11-01 16:03:31.932][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-11-01 16:03:31.933][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-11-01 16:03:31.934][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-11-01 16:03:31.935][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-11-01 16:03:31.936][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-11-01 16:03:31.937][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-11-01 16:03:31.938][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-11-01 16:03:31.939][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-11-01 16:03:31.939][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-11-01 16:03:31.939][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-11-01 16:03:31.939][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-11-01 16:03:31.939][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-11-01 16:03:31.940][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-11-01 16:03:31.941][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-11-01 16:03:31.942][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-11-01 16:03:31.942][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-11-01 16:03:31.943][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-11-01 16:03:31.944][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-11-01 16:03:31.945][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-11-01 16:03:31.946][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-11-01 16:03:31.947][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-11-01 16:03:31.948][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-11-01 16:03:31.949][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-11-01 16:03:31.950][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-11-01 16:03:31.951][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-11-01 16:03:31.957][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-11-01 16:03:31.957][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-11-01 16:03:31.958][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-11-01 16:03:31.959][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-11-01 16:03:31.960][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-11-01 16:03:31.961][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-11-01 16:03:31.962][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-11-01 16:03:31.963][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-11-01 16:03:31.964][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-11-01 16:03:31.965][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-11-01 16:03:31.966][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-11-01 16:03:31.967][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-11-01 16:03:31.968][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-11-01 16:03:31.969][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-11-01 16:03:31.969][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-11-01 16:03:31.970][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-11-01 16:03:31.970][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-11-01 16:03:31.970][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-11-01 16:03:31.970][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-11-01 16:03:31.970][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-11-01 16:03:31.971][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-11-01 16:03:31.972][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-11-01 16:03:31.973][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-11-01 16:03:31.974][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-11-01 16:03:31.975][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-11-01 16:03:31.976][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-11-01 16:03:31.977][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-11-01 16:03:31.978][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-11-01 16:03:31.979][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-11-01 16:03:31.979][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-11-01 16:03:31.980][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-11-01 16:03:31.981][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-11-01 16:03:31.982][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-11-01 16:03:31.984][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-11-01 16:03:31.985][self$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[2025-11-01 16:03:31.986][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-11-01 16:03:31.987][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-11-01 16:03:31.988][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-11-01 16:03:31.989][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-11-01 16:03:31.990][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-11-01 16:03:31.991][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-11-01 16:03:31.991][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-11-01 16:03:31.992][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-11-01 16:03:31.993][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-11-01 16:03:31.994][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-11-01 16:03:31.995][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-11-01 16:03:31.996][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-11-01 16:03:31.997][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-11-01 16:03:31.998][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-11-01 16:03:31.999][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-11-01 16:03:32.000][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-11-01 16:03:32.001][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-11-01 16:03:32.002][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-11-01 16:03:32.002][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-11-01 16:03:32.003][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-11-01 16:03:32.004][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-11-01 16:03:32.005][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-11-01 16:03:32.006][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-11-01 16:03:32.007][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-11-01 16:03:32.008][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-11-01 16:03:32.009][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-11-01 16:03:32.010][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-11-01 16:03:32.011][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-11-01 16:03:32.012][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-11-01 16:03:32.013][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-11-01 16:03:32.014][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-11-01 16:03:32.015][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-11-01 16:03:32.016][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-11-01 16:03:32.017][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-11-01 16:03:32.018][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-11-01 16:03:32.019][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-11-01 16:03:32.020][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-11-01 16:03:32.021][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-11-01 16:03:32.022][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-11-01 16:03:32.023][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-11-01 16:03:32.024][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-11-01 16:03:32.025][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-11-01 16:03:32.025][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-11-01 16:03:32.026][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-11-01 16:03:32.027][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-11-01 16:03:32.028][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-11-01 16:03:32.029][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-11-01 16:03:32.030][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-11-01 16:03:32.031][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-11-01 16:03:32.032][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-11-01 16:03:32.033][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-11-01 16:03:32.033][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-11-01 16:03:32.034][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-11-01 16:03:32.035][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-11-01 16:03:32.036][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-11-01 16:03:32.040][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-11-01 16:03:32.040][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:03:32.041][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:03:32.042][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:03:32.043][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-01 16:03:32.044][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-01 16:03:32.045][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:03:32.045][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:03:32.046][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:03:32.047][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-01 16:03:32.048][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-01 16:03:32.049][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:03:32.050][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:03:32.050][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:03:32.051][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-01 16:03:32.052][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-01 16:03:32.053][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:03:32.054][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:03:32.055][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:03:32.055][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-01 16:03:32.056][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-01 16:03:32.057][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:03:32.058][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[2025-11-01 16:03:32.059][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:03:32.060][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-01 16:03:32.060][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-01 16:03:32.061][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:03:32.062][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:03:32.063][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:03:32.064][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-01 16:03:32.065][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-01 16:03:32.065][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:03:32.066][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:03:32.067][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:03:32.068][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-01 16:03:32.069][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-01 16:03:32.070][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:03:32.070][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:03:32.071][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:03:32.072][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-01 16:03:32.073][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-01 16:03:32.074][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:03:32.075][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:03:32.075][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:03:32.076][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-01 16:03:32.077][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-01 16:03:32.078][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:03:32.079][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:03:32.080][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:03:32.080][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-01 16:03:32.081][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-01 16:03:32.082][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:03:32.083][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[2025-11-01 16:03:32.084][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:03:32.085][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-01 16:03:32.085][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-01 16:03:32.086][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:03:32.087][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:03:32.088][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:03:32.089][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-01 16:03:32.089][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-01 16:03:32.090][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:03:32.091][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:03:32.092][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:03:32.093][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-01 16:03:32.094][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-01 16:03:32.094][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:03:32.095][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:03:32.096][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:03:32.097][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-01 16:03:32.098][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-01 16:03:32.099][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:03:32.099][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:03:32.100][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:03:32.101][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-01 16:03:32.102][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-01 16:03:32.103][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:03:32.104][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:03:32.104][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:03:32.105][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-01 16:03:32.110][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-01 16:03:32.110][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:03:32.111][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:03:32.112][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-11-01 16:03:32.116][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-11-01 16:03:32.118][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-11-01 16:03:32.119][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-11-01 16:03:32.120][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-11-01 16:03:32.122][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-11-01 16:03:32.123][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-11-01 16:03:32.124][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-11-01 16:03:32.126][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-11-01 16:03:32.127][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-11-01 16:03:32.128][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-11-01 16:03:32.130][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-11-01 16:03:32.131][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-11-01 16:03:32.132][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-11-01 16:03:32.133][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-11-01 16:03:32.135][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-11-01 16:03:32.136][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-11-01 16:03:32.137][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-11-01 16:03:32.139][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-11-01 16:03:32.140][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-11-01 16:03:32.141][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-11-01 16:03:32.143][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-11-01 16:03:32.144][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-11-01 16:03:32.145][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-11-01 16:03:32.146][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-11-01 16:03:32.148][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-11-01 16:03:32.149][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-11-01 16:03:32.150][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-11-01 16:03:32.152][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-11-01 16:03:32.153][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-11-01 16:03:32.154][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-11-01 16:03:32.156][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-11-01 16:03:32.157][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-11-01 16:03:32.158][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-11-01 16:03:32.159][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-11-01 16:03:32.161][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-11-01 16:03:32.162][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-11-01 16:03:32.163][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-11-01 16:03:32.165][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-11-01 16:03:32.166][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-11-01 16:03:32.173][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-11-01 16:03:32.175][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-11-01 16:03:32.177][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-11-01 16:03:32.178][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-11-01 16:03:32.180][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-11-01 16:03:32.182][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-11-01 16:03:32.183][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-11-01 16:03:32.185][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-11-01 16:03:32.186][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-11-01 16:03:32.188][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-11-01 16:03:32.189][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-11-01 16:03:32.190][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-11-01 16:03:32.192][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-11-01 16:03:32.193][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-11-01 16:03:32.195][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-11-01 16:03:32.196][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-11-01 16:03:32.198][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-11-01 16:03:32.199][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-11-01 16:03:32.201][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-11-01 16:03:32.202][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-11-01 16:03:32.204][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-11-01 16:03:32.205][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-11-01 16:03:32.206][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-11-01 16:03:32.208][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-11-01 16:03:32.209][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-11-01 16:03:32.211][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-11-01 16:03:32.212][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-11-01 16:03:32.214][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-11-01 16:03:32.215][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-11-01 16:03:32.217][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-11-01 16:03:32.218][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-11-01 16:03:32.219][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-11-01 16:03:32.221][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-11-01 16:03:32.222][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-11-01 16:03:32.224][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-11-01 16:03:32.225][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-11-01 16:03:32.227][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-11-01 16:03:32.228][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-11-01 16:03:32.230][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-11-01 16:03:32.231][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-11-01 16:03:32.232][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-11-01 16:03:32.234][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-11-01 16:03:32.235][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-11-01 16:03:32.242][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-11-01 16:03:32.244][initialize] This is biodb version 1.18.0.
biodb.DEBUG[2025-11-01 16:03:32.248][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-11-01 16:03:32.249][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-11-01 16:03:32.250][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-01 16:03:32.251][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:03:32.252][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:03:32.257][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:03:32.258][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-01 16:03:32.259][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-01 16:03:32.259][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-01 16:03:32.260][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-01 16:03:32.261][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:03:32.262][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:03:32.263][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:03:32.264][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-01 16:03:32.265][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-01 16:03:32.266][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-01 16:03:32.267][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-01 16:03:32.268][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:03:32.269][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:03:32.270][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:03:32.270][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-01 16:03:32.271][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-01 16:03:32.272][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-01 16:03:32.273][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-01 16:03:32.287][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:03:32.288][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:03:32.289][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:03:32.290][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-01 16:03:32.291][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-01 16:03:32.292][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-01 16:03:32.293][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-01 16:03:32.294][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:03:32.295][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:03:32.296][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:03:32.297][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-01 16:03:32.297][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-01 16:03:32.298][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-01 16:03:32.299][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-01 16:03:32.300][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:03:32.301][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:03:32.302][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:03:32.303][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-01 16:03:32.304][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-01 16:03:32.305][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-01 16:03:32.306][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-01 16:03:32.307][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:03:32.308][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:03:32.308][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:03:32.309][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-01 16:03:32.310][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-01 16:03:32.311][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-01 16:03:32.312][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-01 16:03:32.313][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:03:32.314][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:03:32.315][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:03:32.316][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-01 16:03:32.317][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-01 16:03:32.317][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-01 16:03:32.318][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-01 16:03:32.319][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:03:32.320][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:03:32.321][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:03:32.322][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-01 16:03:32.323][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-01 16:03:32.324][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-01 16:03:32.325][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-01 16:03:32.325][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:03:32.326][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:03:32.327][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:03:32.328][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-01 16:03:32.329][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-01 16:03:32.330][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-01 16:03:32.331][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-01 16:03:32.332][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:03:32.333][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:03:32.334][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:03:32.334][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-01 16:03:32.335][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-01 16:03:32.336][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-01 16:03:32.337][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-01 16:03:32.338][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:03:32.339][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:03:32.340][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:03:32.341][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-01 16:03:32.342][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-01 16:03:32.342][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-01 16:03:32.343][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-01 16:03:32.344][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:03:32.345][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:03:32.346][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:03:32.347][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-01 16:03:32.348][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-01 16:03:32.349][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-01 16:03:32.349][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-01 16:03:32.350][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:03:32.351][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:03:32.352][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:03:32.353][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-01 16:03:32.354][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-01 16:03:32.354][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-01 16:03:32.355][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-01 16:03:32.356][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:03:32.357][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:03:32.358][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:03:32.359][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-01 16:03:32.359][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-01 16:03:32.360][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-01 16:03:32.361][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-01 16:03:32.362][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:03:32.363][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:03:32.363][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:03:32.364][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-01 16:03:32.365][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-01 16:03:32.366][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-01 16:03:32.367][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-01 16:03:32.368][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:03:32.368][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:03:32.370][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNci.Rcheck/biodbNci/definitions.yml".
biodb.DEBUG[2025-11-01 16:03:32.379][self$getDbsInfo()$define] Define connector nci.cactus.
biodb.DEBUG[2025-11-01 16:03:32.381][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-11-01 16:03:32.382][self$setPropertyValue] Setting property "description" to "National Cancer Institute (USA) CACTUS Database.".
biodb.DEBUG[2025-11-01 16:03:32.383][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-11-01 16:03:32.384][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-11-01 16:03:32.385][self$setPropertyValue] Setting property "downloadable" to "TRUE".
biodb.DEBUG[2025-11-01 16:03:32.385][self$setPropertyValue] Setting property "dwnld.ext" to "gz".
biodb.DEBUG[2025-11-01 16:03:32.386][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-11-01 16:03:32.387][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-11-01 16:03:32.388][self$setPropertyValue] Setting property "entry.content.type" to "sdf".
biodb.DEBUG[2025-11-01 16:03:32.389][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-11-01 16:03:32.390][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-11-01 16:03:32.391][self$setPropertyValue] Setting property "name" to "NCI CACTUS".
biodb.DEBUG[2025-11-01 16:03:32.392][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-11-01 16:03:32.393][self$setPropertyValue] Setting property "parsing.expr" to "NSC".
biodb.DEBUG[2025-11-01 16:03:32.393][self$setPropertyValue] Setting property "parsing.expr" to "DTP names".
biodb.DEBUG[2025-11-01 16:03:32.393][self$setPropertyValue] Setting property "parsing.expr" to "Standard InChI".
biodb.DEBUG[2025-11-01 16:03:32.393][self$setPropertyValue] Setting property "parsing.expr" to "c("Standard InChIKey", "^InChIKey=(.*)$")".
biodb.DEBUG[2025-11-01 16:03:32.393][self$setPropertyValue] Setting property "parsing.expr" to "Formula".
biodb.DEBUG[2025-11-01 16:03:32.393][self$setPropertyValue] Setting property "parsing.expr" to "Molecular Weight".
biodb.DEBUG[2025-11-01 16:03:32.393][self$setPropertyValue] Setting property "parsing.expr" to "CAS".
biodb.DEBUG[2025-11-01 16:03:32.394][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-11-01 16:03:32.395][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-11-01 16:03:32.396][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-11-01 16:03:32.397][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-11-01 16:03:32.398][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-11-01 16:03:32.398][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-11-01 16:03:32.399][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-11-01 16:03:32.400][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-11-01 16:03:32.401][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-11-01 16:03:32.402][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/".
biodb.DEBUG[2025-11-01 16:03:32.402][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/".
biodb.DEBUG[2025-11-01 16:03:32.402][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/download/nci/".
biodb.DEBUG[2025-11-01 16:03:32.402][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/download/nci/NCI-Open_2012-05-01.sdf.gz".
biodb.DEBUG[2025-11-01 16:03:32.403][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-11-01 16:03:32.404][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-11-01 16:03:32.405][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-11-01 16:03:32.406][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-11-01 16:03:32.411][self$getEntryFields()$define] Define field nci.cactus.id.
biodb.DEBUG[2025-11-01 16:03:32.432][super$initialize] Initialize connector nci.cactus.
biodb.DEBUG[2025-11-01 16:03:32.452][biodb$getFactory()$createConn] Creating new connector nci.cactus for database class nci.cactus .
biodb.INFO [2025-11-01 16:03:32.460][biodb::testThat]
biodb.INFO [2025-11-01 16:03:32.461][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2025-11-01 16:03:32.462][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-11-01 16:03:32.463][biodb::testThat]
biodb.TRACE[2025-11-01 16:03:32.466][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNci.Rcheck/biodbNci/testref/entry-nci.cactus-749674-content.sdf".
biodb.DEBUG[2025-11-01 16:03:32.467][biodb$getFactory()$createEntryFromCo ...] Creating NCI CACTUS entries from 1 content(s).
biodb.DEBUG[2025-11-01 16:03:32.470][biodb$getFactory()$createEntryFromCo ...] Parsing 1 NCI CACTUS entries.
biodb.DEBUG[2025-11-01 16:03:32.477][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-11-01 16:03:32.478][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-01 16:03:32.479][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-01 16:03:32.490][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-11-01 16:03:32.491][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-01 16:03:32.492][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:03:32.493][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-11-01 16:03:32.509][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-01 16:03:32.510][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-01 16:03:32.511][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:03:32.511][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:03:32.512][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-01 16:03:32.524][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-01 16:03:32.525][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:03:32.526][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:03:32.528][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-11-01 16:03:32.529][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-11-01 16:03:32.530][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:03:32.531][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:03:32.554][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-11-01 16:03:32.555][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-11-01 16:03:32.556][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:03:32.557][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:03:32.558][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-11-01 16:03:32.559][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-11-01 16:03:32.560][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:03:32.561][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:03:32.562][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-11-01 16:03:32.563][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-11-01 16:03:32.564][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:03:32.565][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:03:32.567][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-11-01 16:03:32.568][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-11-01 16:03:32.569][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:03:32.570][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:03:32.571][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-11-01 16:03:32.572][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-11-01 16:03:32.573][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:03:32.573][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:03:32.575][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-11-01 16:03:32.576][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-11-01 16:03:32.577][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:03:32.578][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:03:32.579][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-11-01 16:03:32.580][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-11-01 16:03:32.580][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:03:32.581][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:03:32.583][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-11-01 16:03:32.590][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-11-01 16:03:32.591][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:03:32.592][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:03:32.593][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-11-01 16:03:32.594][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-11-01 16:03:32.595][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:03:32.596][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:03:32.597][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-01 16:03:32.598][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-01 16:03:32.599][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:03:32.599][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:03:32.600][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-11-01 16:03:32.601][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-11-01 16:03:32.602][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:03:32.603][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:03:32.604][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-01 16:03:32.605][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-01 16:03:32.606][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:03:32.607][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:03:32.608][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-01 16:03:32.609][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-01 16:03:32.610][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:03:32.611][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:03:32.612][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-01 16:03:32.612][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-01 16:03:32.613][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:03:32.614][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:03:32.646][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-01 16:03:32.647][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-01 16:03:32.648][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:03:32.648][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:03:32.649][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-01 16:03:32.650][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-01 16:03:32.651][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:03:32.652][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:03:32.653][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-01 16:03:32.654][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-01 16:03:32.655][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:03:32.656][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-11-01 16:03:32.657][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 749674.
biodb.TRACE[2025-11-01 16:03:32.659][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-11-01 16:03:32.660][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-11-01 16:03:32.661][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:03:32.662][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:03:32.663][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-11-01 16:03:32.664][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-11-01 16:03:32.665][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:03:32.666][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:03:32.666][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-11-01 16:03:32.667][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-11-01 16:03:32.668][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:03:32.669][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:03:32.670][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-11-01 16:03:32.671][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-11-01 16:03:32.672][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:03:32.673][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:03:32.675][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-01 16:03:32.676][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-01 16:03:32.677][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:03:32.678][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:03:32.690][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-11-01 16:03:32.691][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-11-01 16:03:32.692][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:03:32.693][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:03:32.738][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-01 16:03:32.739][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-01 16:03:32.740][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:03:32.741][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:03:32.742][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-01 16:03:32.743][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-01 16:03:32.744][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:03:32.744][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:03:32.745][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-01 16:03:32.746][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-01 16:03:32.747][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:03:32.748][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:03:32.751][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-01 16:03:32.752][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-01 16:03:32.752][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:03:32.753][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:03:32.754][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-01 16:03:32.755][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-01 16:03:32.756][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:03:32.757][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:03:32.758][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-01 16:03:32.759][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-01 16:03:32.760][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:03:32.761][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:03:32.762][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-11-01 16:03:32.763][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-11-01 16:03:32.764][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:03:32.765][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:03:32.765][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-11-01 16:03:32.766][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-11-01 16:03:32.767][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:03:32.768][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:03:32.769][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-11-01 16:03:32.770][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-11-01 16:03:32.771][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:03:32.772][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:03:32.779][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-01 16:03:32.780][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-01 16:03:32.781][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:03:32.782][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:03:32.783][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-01 16:03:32.785][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-01 16:03:32.786][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:03:32.786][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:03:32.788][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-01 16:03:32.789][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-01 16:03:32.790][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:03:32.791][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:03:32.792][ef$get] Asked field names are: accession.
biodb.TRACE[2025-11-01 16:03:32.793][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-01 16:03:32.794][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:03:32.795][ef$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:03:32.796][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-01 16:03:32.797][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-01 16:03:32.798][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:03:32.799][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:03:32.808][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-11-01 16:03:32.809][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-11-01 16:03:32.810][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:03:32.811][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:03:32.812][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-11-01 16:03:32.813][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-11-01 16:03:32.814][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:03:32.815][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:03:32.816][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-11-01 16:03:32.817][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-11-01 16:03:32.818][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:03:32.819][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:03:32.820][ef$get] Asked field names are: formula.
biodb.TRACE[2025-11-01 16:03:32.821][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-11-01 16:03:32.822][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:03:32.823][ef$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:03:32.824][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-11-01 16:03:32.825][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-11-01 16:03:32.826][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:03:32.827][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:03:32.835][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-11-01 16:03:32.836][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-11-01 16:03:32.837][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:03:32.838][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:03:32.839][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-11-01 16:03:32.840][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-11-01 16:03:32.841][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:03:32.842][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:03:32.843][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-11-01 16:03:32.844][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-11-01 16:03:32.845][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:03:32.846][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:03:32.847][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-11-01 16:03:32.848][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-11-01 16:03:32.849][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:03:32.850][ef$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:03:32.851][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-11-01 16:03:32.852][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-11-01 16:03:32.853][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:03:32.854][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:03:32.868][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-11-01 16:03:32.869][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-11-01 16:03:32.870][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:03:32.871][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:03:32.872][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-11-01 16:03:32.873][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-11-01 16:03:32.874][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:03:32.875][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:03:32.876][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-11-01 16:03:32.877][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-11-01 16:03:32.878][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:03:32.879][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:03:32.880][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-11-01 16:03:32.881][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-11-01 16:03:32.882][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:03:32.883][ef$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:03:32.884][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-11-01 16:03:32.885][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-11-01 16:03:32.886][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:03:32.887][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:03:32.895][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-11-01 16:03:32.896][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-11-01 16:03:32.897][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:03:32.898][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:03:32.899][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-11-01 16:03:32.900][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-11-01 16:03:32.901][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:03:32.902][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:03:32.903][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-11-01 16:03:32.904][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-11-01 16:03:32.905][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:03:32.906][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:03:32.907][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-11-01 16:03:32.908][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-11-01 16:03:32.909][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:03:32.910][ef$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:03:32.911][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-11-01 16:03:32.912][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-11-01 16:03:32.913][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:03:32.914][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:03:32.922][ef$get] Asked field names are: accession.
biodb.TRACE[2025-11-01 16:03:32.923][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-01 16:03:32.924][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:03:32.925][ef$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:03:32.930][ef$get] Asked field names are: formula.
biodb.TRACE[2025-11-01 16:03:32.931][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-11-01 16:03:32.932][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:03:32.933][ef$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:03:32.937][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-11-01 16:03:32.938][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-11-01 16:03:32.939][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:03:32.940][ef$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:03:32.944][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-11-01 16:03:32.945][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-11-01 16:03:32.946][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:03:32.947][ef$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:03:32.951][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-11-01 16:03:32.952][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-11-01 16:03:32.953][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:03:32.954][ef$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:03:32.972][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNci.Rcheck/biodbNci/testref/entry-nci.cactus-750690-content.sdf".
biodb.DEBUG[2025-11-01 16:03:33.014][biodb$getFactory()$createEntryFromCo ...] Creating NCI CACTUS entries from 1 content(s).
biodb.DEBUG[2025-11-01 16:03:33.015][biodb$getFactory()$createEntryFromCo ...] Parsing 1 NCI CACTUS entries.
biodb.DEBUG[2025-11-01 16:03:33.017][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-11-01 16:03:33.018][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-01 16:03:33.019][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-01 16:03:33.023][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-11-01 16:03:33.024][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-01 16:03:33.025][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:03:33.026][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-11-01 16:03:33.036][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-01 16:03:33.037][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-01 16:03:33.038][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:03:33.039][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:03:33.040][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-01 16:03:33.041][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-01 16:03:33.042][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:03:33.043][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:03:33.062][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-11-01 16:03:33.063][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-11-01 16:03:33.064][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:03:33.065][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:03:33.066][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-11-01 16:03:33.067][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-11-01 16:03:33.068][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:03:33.069][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:03:33.071][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-11-01 16:03:33.072][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-11-01 16:03:33.073][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:03:33.074][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:03:33.075][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-11-01 16:03:33.076][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-11-01 16:03:33.077][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:03:33.078][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:03:33.079][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-11-01 16:03:33.080][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-11-01 16:03:33.081][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:03:33.082][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:03:33.083][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-11-01 16:03:33.085][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-11-01 16:03:33.085][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:03:33.086][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:03:33.088][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-11-01 16:03:33.089][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-11-01 16:03:33.090][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:03:33.091][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:03:33.092][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-11-01 16:03:33.093][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-11-01 16:03:33.094][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:03:33.095][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:03:33.096][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-11-01 16:03:33.097][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-11-01 16:03:33.098][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:03:33.099][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:03:33.100][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-11-01 16:03:33.101][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-11-01 16:03:33.107][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:03:33.108][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:03:33.109][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-11-01 16:03:33.110][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-11-01 16:03:33.111][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:03:33.112][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:03:33.113][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-11-01 16:03:33.114][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-11-01 16:03:33.115][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:03:33.116][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:03:33.117][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-11-01 16:03:33.118][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-11-01 16:03:33.119][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:03:33.120][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:03:33.122][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-11-01 16:03:33.124][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-11-01 16:03:33.124][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:03:33.125][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:03:33.126][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-11-01 16:03:33.128][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-11-01 16:03:33.128][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:03:33.129][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:03:33.131][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-11-01 16:03:33.132][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-11-01 16:03:33.133][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:03:33.134][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:03:33.135][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-11-01 16:03:33.136][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-11-01 16:03:33.137][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:03:33.138][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:03:33.140][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-11-01 16:03:33.141][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-11-01 16:03:33.142][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:03:33.143][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:03:33.144][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-11-01 16:03:33.145][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-11-01 16:03:33.146][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:03:33.147][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:03:33.148][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-01 16:03:33.149][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-01 16:03:33.150][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:03:33.151][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:03:33.152][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-11-01 16:03:33.153][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-11-01 16:03:33.154][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:03:33.155][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:03:33.156][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-01 16:03:33.157][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-01 16:03:33.158][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:03:33.159][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:03:33.160][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-01 16:03:33.161][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-01 16:03:33.162][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:03:33.163][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:03:33.164][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-01 16:03:33.165][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-01 16:03:33.166][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:03:33.167][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:03:33.168][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-01 16:03:33.169][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-01 16:03:33.170][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:03:33.171][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:03:33.172][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-01 16:03:33.173][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-01 16:03:33.174][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:03:33.175][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:03:33.176][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-01 16:03:33.177][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-01 16:03:33.178][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:03:33.179][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-11-01 16:03:33.180][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 750690.
biodb.TRACE[2025-11-01 16:03:33.202][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-11-01 16:03:33.203][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-11-01 16:03:33.204][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:03:33.205][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:03:33.206][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-11-01 16:03:33.207][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-11-01 16:03:33.208][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:03:33.209][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:03:33.210][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-11-01 16:03:33.211][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-11-01 16:03:33.212][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:03:33.213][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:03:33.214][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-11-01 16:03:33.215][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-11-01 16:03:33.216][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:03:33.217][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:03:33.219][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-01 16:03:33.220][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-01 16:03:33.221][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:03:33.222][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:03:33.227][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-11-01 16:03:33.233][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-11-01 16:03:33.234][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:03:33.235][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:03:33.240][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-01 16:03:33.241][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-01 16:03:33.242][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:03:33.243][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:03:33.244][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-01 16:03:33.245][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-01 16:03:33.246][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:03:33.247][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:03:33.248][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-01 16:03:33.249][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-01 16:03:33.250][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:03:33.251][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:03:33.254][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-01 16:03:33.255][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-01 16:03:33.256][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:03:33.257][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:03:33.258][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-01 16:03:33.259][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-01 16:03:33.260][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:03:33.261][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:03:33.262][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-01 16:03:33.263][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-01 16:03:33.264][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:03:33.265][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:03:33.266][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-11-01 16:03:33.267][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-11-01 16:03:33.268][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:03:33.269][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:03:33.270][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-11-01 16:03:33.271][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-11-01 16:03:33.272][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:03:33.273][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:03:33.274][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-11-01 16:03:33.275][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-11-01 16:03:33.276][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:03:33.277][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:03:33.295][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-01 16:03:33.296][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-01 16:03:33.297][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:03:33.298][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:03:33.299][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-01 16:03:33.300][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-01 16:03:33.301][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:03:33.302][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:03:33.303][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-01 16:03:33.304][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-01 16:03:33.305][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:03:33.306][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:03:33.307][ef$get] Asked field names are: accession.
biodb.TRACE[2025-11-01 16:03:33.309][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-01 16:03:33.310][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:03:33.310][ef$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:03:33.311][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-01 16:03:33.313][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-01 16:03:33.314][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:03:33.314][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:03:33.323][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-11-01 16:03:33.324][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-11-01 16:03:33.325][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:03:33.326][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:03:33.327][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-11-01 16:03:33.328][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-11-01 16:03:33.329][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:03:33.330][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:03:33.331][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-11-01 16:03:33.332][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-11-01 16:03:33.333][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:03:33.334][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:03:33.335][ef$get] Asked field names are: cas.id.
biodb.TRACE[2025-11-01 16:03:33.336][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-11-01 16:03:33.337][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:03:33.338][ef$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:03:33.339][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-11-01 16:03:33.340][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-11-01 16:03:33.341][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:03:33.342][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:03:33.350][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-11-01 16:03:33.351][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-11-01 16:03:33.352][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:03:33.353][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:03:33.354][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-11-01 16:03:33.360][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-11-01 16:03:33.361][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:03:33.362][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:03:33.363][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-11-01 16:03:33.364][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-11-01 16:03:33.365][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:03:33.366][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:03:33.367][ef$get] Asked field names are: name.
biodb.TRACE[2025-11-01 16:03:33.368][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-11-01 16:03:33.369][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:03:33.370][ef$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:03:33.371][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-11-01 16:03:33.372][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-11-01 16:03:33.373][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:03:33.374][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:03:33.383][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-11-01 16:03:33.384][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-11-01 16:03:33.385][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:03:33.386][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:03:33.387][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-11-01 16:03:33.388][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-11-01 16:03:33.389][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:03:33.390][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:03:33.391][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-11-01 16:03:33.392][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-11-01 16:03:33.393][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:03:33.394][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:03:33.395][ef$get] Asked field names are: formula.
biodb.TRACE[2025-11-01 16:03:33.396][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-11-01 16:03:33.397][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:03:33.398][ef$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:03:33.399][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-11-01 16:03:33.400][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-11-01 16:03:33.401][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:03:33.402][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:03:33.410][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-11-01 16:03:33.411][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-11-01 16:03:33.412][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:03:33.413][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:03:33.414][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-11-01 16:03:33.415][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-11-01 16:03:33.416][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:03:33.417][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:03:33.418][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-11-01 16:03:33.419][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-11-01 16:03:33.420][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:03:33.421][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:03:33.422][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-11-01 16:03:33.423][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-11-01 16:03:33.424][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:03:33.425][ef$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:03:33.426][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-11-01 16:03:33.427][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-11-01 16:03:33.428][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:03:33.429][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:03:33.437][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-11-01 16:03:33.438][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-11-01 16:03:33.439][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:03:33.440][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:03:33.441][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-11-01 16:03:33.442][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-11-01 16:03:33.443][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:03:33.444][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:03:33.445][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-11-01 16:03:33.446][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-11-01 16:03:33.447][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:03:33.448][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:03:33.449][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-11-01 16:03:33.451][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-11-01 16:03:33.452][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:03:33.452][ef$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:03:33.453][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-11-01 16:03:33.455][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-11-01 16:03:33.456][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:03:33.457][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:03:33.465][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-11-01 16:03:33.466][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-11-01 16:03:33.467][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:03:33.468][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:03:33.469][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-11-01 16:03:33.470][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-11-01 16:03:33.471][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:03:33.472][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:03:33.473][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-11-01 16:03:33.474][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-11-01 16:03:33.475][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:03:33.476][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:03:33.477][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-11-01 16:03:33.478][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-11-01 16:03:33.479][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:03:33.480][ef$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:03:33.481][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-11-01 16:03:33.482][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-11-01 16:03:33.488][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:03:33.489][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:03:33.497][ef$get] Asked field names are: accession.
biodb.TRACE[2025-11-01 16:03:33.498][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-01 16:03:33.499][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:03:33.500][ef$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:03:33.505][ef$get] Asked field names are: cas.id.
biodb.TRACE[2025-11-01 16:03:33.506][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-11-01 16:03:33.507][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:03:33.508][ef$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:03:33.512][ef$get] Asked field names are: formula.
biodb.TRACE[2025-11-01 16:03:33.513][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-11-01 16:03:33.514][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:03:33.515][ef$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:03:33.519][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-11-01 16:03:33.520][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-11-01 16:03:33.521][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:03:33.522][ef$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:03:33.526][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-11-01 16:03:33.527][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-11-01 16:03:33.528][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:03:33.529][ef$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:03:33.533][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-11-01 16:03:33.534][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-11-01 16:03:33.535][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:03:33.536][ef$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:03:33.540][ef$get] Asked field names are: name.
biodb.TRACE[2025-11-01 16:03:33.542][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-11-01 16:03:33.543][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:03:33.544][ef$get] fields variable is a list.
biodb.INFO [2025-11-01 16:03:33.550][biodb::testThat]
biodb.INFO [2025-11-01 16:03:33.551][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2025-11-01 16:03:33.552][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-11-01 16:03:33.553][biodb::testThat]
biodb.DEBUG[2025-11-01 16:03:33.556][private$loadEntries] Creating entries from ids [2]: "749674, 750690".
biodb.DEBUG[2025-11-01 16:03:33.558][conn$getEntryContent] Get NCI CACTUS entry content(s) for 2 id(s)...
biodb.DEBUG[2025-11-01 16:03:33.562][self$isDownloaded] Database nci.cactus has already been downloaded.
biodb.DEBUG[2025-11-01 16:03:33.592][self$isDownloaded] Database nci.cactus has already been downloaded.
biodb.INFO [2025-11-01 16:03:33.594][self$download] Extract whole database of nci.cactus.
biodb.INFO [2025-11-01 16:03:33.595][private$doExtractDownload] Extracting content of downloaded biodbNci, a library for connecting to the National Cancer Institute (USA) CACTUS Database....
biodb.INFO [2025-11-01 16:03:33.645][biodb::testThat]
biodb.INFO [2025-11-01 16:03:33.646][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2025-11-01 16:03:33.647][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-11-01 16:03:33.648][biodb::testThat]
biodb.INFO [2025-11-01 16:03:33.654][biodb::testThat]
biodb.INFO [2025-11-01 16:03:33.655][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2025-11-01 16:03:33.656][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-11-01 16:03:33.657][biodb::testThat]
biodb.WARN [2025-11-01 16:03:33.678][self$searchForEntries] This database is not searchable by field "name".
biodb.WARN [2025-11-01 16:03:33.697][self$searchForEntries] This database is not searchable by field "name".
biodb.INFO [2025-11-01 16:03:33.706][biodb::testThat]
biodb.INFO [2025-11-01 16:03:33.707][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2025-11-01 16:03:33.708][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-11-01 16:03:33.709][biodb::testThat]
biodb.DEBUG[2025-11-01 16:03:33.727][private$loadEntries] Creating entries from ids [1]: "749674".
biodb.DEBUG[2025-11-01 16:03:33.785][conn$getEntryContent] Get NCI CACTUS entry content(s) for 1 id(s)...
biodb.DEBUG[2025-11-01 16:03:33.787][self$isDownloaded] Database nci.cactus has already been downloaded.
biodb.DEBUG[2025-11-01 16:03:33.788][self$isDownloaded] Database nci.cactus has already been downloaded.
biodb.INFO [2025-11-01 16:03:33.789][self$download] Extract whole database of nci.cactus.
biodb.INFO [2025-11-01 16:03:33.802][private$doExtractDownload] Extracting content of downloaded biodbNci, a library for connecting to the National Cancer Institute (USA) CACTUS Database....
biodb.INFO [2025-11-01 16:03:33.828][biodb::testThat]
biodb.INFO [2025-11-01 16:03:33.829][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2025-11-01 16:03:33.830][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-11-01 16:03:33.831][biodb::testThat]
biodb.INFO [2025-11-01 16:03:33.838][biodb::testThat]
biodb.INFO [2025-11-01 16:03:33.839][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2025-11-01 16:03:33.845][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-11-01 16:03:33.846][biodb::testThat]
biodb.INFO [2025-11-01 16:03:33.853][biodb::testThat]
biodb.INFO [2025-11-01 16:03:33.854][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2025-11-01 16:03:33.855][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-11-01 16:03:33.856][biodb::testThat]
biodb.INFO [2025-11-01 16:03:33.862][biodb::testThat]
biodb.INFO [2025-11-01 16:03:33.863][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2025-11-01 16:03:33.864][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-11-01 16:03:33.865][biodb::testThat]
biodb.INFO [2025-11-01 16:03:33.870][biodb$terminate] Closing BiodbMain instance...
biodb.INFO [2025-11-01 16:03:33.872][self$deleteConn] Connector "nci.cactus" deleted.
biodb.DEBUG[2025-11-01 16:03:33.873][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-11-01 16:03:33.873][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-01 16:03:33.874][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-01 16:03:33.875][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-01 16:03:33.876][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-01 16:03:33.877][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:03:33.878][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2025-11-01 16:03:33.888][biodb::testContext]
biodb.INFO [2025-11-01 16:03:33.889][biodb::testContext] ********************************************************************************
biodb.INFO [2025-11-01 16:03:33.890][biodb::testContext] Test context - Example long tests
biodb.INFO [2025-11-01 16:03:33.891][biodb::testContext] ********************************************************************************
biodb.INFO [2025-11-01 16:03:33.891][biodb::testContext]
biodb.INFO [2025-11-01 16:03:33.894][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.18.0.
biodb.DEBUG[2025-11-01 16:03:33.895][self$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.22-bioc/R/site-library/biodb/definitions.yml".
biodb.DEBUG[2025-11-01 16:03:33.899][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-11-01 16:03:33.900][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-11-01 16:03:33.901][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-11-01 16:03:33.902][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:03:33.903][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:03:33.904][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:03:33.905][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-11-01 16:03:33.906][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-11-01 16:03:33.907][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:03:33.908][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:03:33.909][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:03:33.910][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-11-01 16:03:33.911][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-11-01 16:03:33.912][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:03:33.913][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:03:33.913][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:03:33.914][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-11-01 16:03:33.915][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-11-01 16:03:33.916][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-11-01 16:03:33.917][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:03:33.918][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:03:33.919][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:03:33.920][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-11-01 16:03:33.921][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-11-01 16:03:33.922][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-11-01 16:03:33.923][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:03:33.924][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:03:33.925][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:03:33.926][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-11-01 16:03:33.927][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-11-01 16:03:33.928][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:03:33.929][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:03:33.930][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:03:33.931][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-11-01 16:03:33.932][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-11-01 16:03:33.933][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-11-01 16:03:33.934][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:03:33.934][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:03:33.935][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:03:33.936][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-11-01 16:03:33.937][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-11-01 16:03:33.938][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:03:33.939][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:03:33.940][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:03:33.941][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-11-01 16:03:33.942][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-11-01 16:03:33.943][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-11-01 16:03:33.944][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:03:33.945][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:03:33.946][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:03:33.947][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-11-01 16:03:33.948][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-11-01 16:03:33.949][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-11-01 16:03:33.950][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-11-01 16:03:33.951][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-11-01 16:03:33.952][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-11-01 16:03:33.953][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:03:33.954][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:03:33.955][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:03:33.956][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-11-01 16:03:33.957][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-11-01 16:03:33.957][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:03:33.958][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:03:33.959][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:03:33.960][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-11-01 16:03:33.967][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-11-01 16:03:33.968][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:03:33.969][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:03:33.970][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:03:33.971][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-11-01 16:03:33.972][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-11-01 16:03:33.973][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:03:33.973][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:03:33.974][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:03:33.975][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-11-01 16:03:33.976][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-11-01 16:03:33.977][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-11-01 16:03:33.978][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:03:33.979][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:03:33.980][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:03:33.981][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-11-01 16:03:33.982][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-11-01 16:03:33.986][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-11-01 16:03:33.987][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:03:33.988][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:03:33.989][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:03:33.990][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-11-01 16:03:33.991][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-11-01 16:03:33.992][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-11-01 16:03:33.993][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:03:33.994][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:03:33.994][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:03:33.996][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-11-01 16:03:33.998][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-11-01 16:03:33.999][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2025-11-01 16:03:34.000][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-11-01 16:03:34.001][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-11-01 16:03:34.002][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-11-01 16:03:34.003][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-11-01 16:03:34.004][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-11-01 16:03:34.005][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-11-01 16:03:34.006][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-11-01 16:03:34.007][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-11-01 16:03:34.008][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-11-01 16:03:34.009][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-11-01 16:03:34.010][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-11-01 16:03:34.011][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-11-01 16:03:34.012][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-11-01 16:03:34.013][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-11-01 16:03:34.013][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-11-01 16:03:34.013][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-11-01 16:03:34.013][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-11-01 16:03:34.013][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-11-01 16:03:34.014][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-11-01 16:03:34.015][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-11-01 16:03:34.016][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-11-01 16:03:34.017][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-11-01 16:03:34.018][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-11-01 16:03:34.019][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-11-01 16:03:34.019][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-11-01 16:03:34.020][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-11-01 16:03:34.021][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-11-01 16:03:34.022][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-11-01 16:03:34.023][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-11-01 16:03:34.024][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-11-01 16:03:34.026][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-11-01 16:03:34.027][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-11-01 16:03:34.028][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-11-01 16:03:34.029][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-11-01 16:03:34.030][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-11-01 16:03:34.031][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-11-01 16:03:34.032][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-11-01 16:03:34.033][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-11-01 16:03:34.034][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-11-01 16:03:34.035][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-11-01 16:03:34.036][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-11-01 16:03:34.038][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-11-01 16:03:34.039][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-11-01 16:03:34.040][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-11-01 16:03:34.041][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-11-01 16:03:34.042][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-11-01 16:03:34.043][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-11-01 16:03:34.043][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-11-01 16:03:34.043][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-11-01 16:03:34.043][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-11-01 16:03:34.043][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-11-01 16:03:34.044][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-11-01 16:03:34.045][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-11-01 16:03:34.045][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-11-01 16:03:34.046][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-11-01 16:03:34.047][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-11-01 16:03:34.048][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-11-01 16:03:34.049][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-11-01 16:03:34.050][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-11-01 16:03:34.051][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-11-01 16:03:34.052][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-11-01 16:03:34.053][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-11-01 16:03:34.054][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-11-01 16:03:34.055][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-11-01 16:03:34.057][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-11-01 16:03:34.058][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2025-11-01 16:03:34.059][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-11-01 16:03:34.060][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-11-01 16:03:34.061][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-11-01 16:03:34.062][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-11-01 16:03:34.063][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-11-01 16:03:34.064][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-11-01 16:03:34.065][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-11-01 16:03:34.066][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-11-01 16:03:34.067][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-11-01 16:03:34.068][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-11-01 16:03:34.069][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-11-01 16:03:34.070][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-11-01 16:03:34.071][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-11-01 16:03:34.072][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-11-01 16:03:34.073][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-11-01 16:03:34.074][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-11-01 16:03:34.075][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-11-01 16:03:34.076][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-11-01 16:03:34.077][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-11-01 16:03:34.078][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-11-01 16:03:34.079][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-11-01 16:03:34.080][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-11-01 16:03:34.081][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-11-01 16:03:34.082][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-11-01 16:03:34.088][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-11-01 16:03:34.089][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-11-01 16:03:34.090][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-11-01 16:03:34.092][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-11-01 16:03:34.093][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-11-01 16:03:34.094][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-11-01 16:03:34.095][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-11-01 16:03:34.096][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-11-01 16:03:34.097][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-11-01 16:03:34.098][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-11-01 16:03:34.099][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-11-01 16:03:34.100][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-11-01 16:03:34.101][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-11-01 16:03:34.102][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-11-01 16:03:34.103][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-11-01 16:03:34.104][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-11-01 16:03:34.105][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-11-01 16:03:34.106][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-11-01 16:03:34.107][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-11-01 16:03:34.108][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-11-01 16:03:34.109][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-11-01 16:03:34.110][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-11-01 16:03:34.111][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-11-01 16:03:34.112][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-11-01 16:03:34.113][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-11-01 16:03:34.114][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-11-01 16:03:34.115][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-11-01 16:03:34.116][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-11-01 16:03:34.117][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-11-01 16:03:34.118][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-11-01 16:03:34.119][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-11-01 16:03:34.120][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-11-01 16:03:34.121][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:03:34.122][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[2025-11-01 16:03:34.123][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:03:34.124][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-01 16:03:34.125][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-01 16:03:34.126][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:03:34.126][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:03:34.127][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:03:34.128][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-01 16:03:34.129][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-01 16:03:34.130][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:03:34.131][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:03:34.132][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:03:34.133][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-01 16:03:34.134][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-01 16:03:34.135][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:03:34.136][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:03:34.136][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:03:34.137][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-01 16:03:34.138][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-01 16:03:34.139][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:03:34.140][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:03:34.141][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:03:34.142][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-01 16:03:34.143][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-01 16:03:34.144][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:03:34.145][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:03:34.146][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:03:34.146][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-01 16:03:34.147][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-01 16:03:34.148][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:03:34.149][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:03:34.150][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:03:34.151][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-01 16:03:34.152][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-01 16:03:34.153][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:03:34.154][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:03:34.155][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:03:34.155][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-01 16:03:34.156][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-01 16:03:34.157][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:03:34.158][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:03:34.159][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:03:34.160][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-01 16:03:34.161][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-01 16:03:34.162][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:03:34.163][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:03:34.163][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:03:34.164][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-01 16:03:34.165][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-01 16:03:34.166][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:03:34.167][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:03:34.168][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:03:34.169][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-01 16:03:34.170][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-01 16:03:34.171][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:03:34.172][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:03:34.172][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:03:34.173][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-01 16:03:34.174][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-01 16:03:34.175][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:03:34.176][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:03:34.177][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:03:34.178][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-01 16:03:34.179][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-01 16:03:34.180][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:03:34.181][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:03:34.182][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:03:34.182][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-01 16:03:34.183][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-01 16:03:34.184][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:03:34.185][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:03:34.186][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:03:34.187][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-01 16:03:34.188][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-01 16:03:34.189][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:03:34.190][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:03:34.191][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:03:34.191][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-01 16:03:34.192][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-01 16:03:34.193][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:03:34.194][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:03:34.195][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-11-01 16:03:34.197][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-11-01 16:03:34.198][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-11-01 16:03:34.200][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-11-01 16:03:34.206][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-11-01 16:03:34.208][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-11-01 16:03:34.209][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-11-01 16:03:34.211][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-11-01 16:03:34.212][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-11-01 16:03:34.213][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-11-01 16:03:34.215][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-11-01 16:03:34.216][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-11-01 16:03:34.218][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-11-01 16:03:34.219][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-11-01 16:03:34.221][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-11-01 16:03:34.222][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-11-01 16:03:34.223][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-11-01 16:03:34.225][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-11-01 16:03:34.226][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-11-01 16:03:34.228][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-11-01 16:03:34.229][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-11-01 16:03:34.231][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-11-01 16:03:34.232][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-11-01 16:03:34.233][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-11-01 16:03:34.235][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-11-01 16:03:34.236][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-11-01 16:03:34.238][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-11-01 16:03:34.239][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-11-01 16:03:34.240][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-11-01 16:03:34.242][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-11-01 16:03:34.243][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-11-01 16:03:34.245][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-11-01 16:03:34.246][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-11-01 16:03:34.248][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-11-01 16:03:34.249][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-11-01 16:03:34.250][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-11-01 16:03:34.252][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-11-01 16:03:34.253][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-11-01 16:03:34.255][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-11-01 16:03:34.256][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-11-01 16:03:34.257][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-11-01 16:03:34.259][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-11-01 16:03:34.260][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-11-01 16:03:34.262][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-11-01 16:03:34.263][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-11-01 16:03:34.265][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-11-01 16:03:34.266][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-11-01 16:03:34.268][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-11-01 16:03:34.269][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-11-01 16:03:34.270][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-11-01 16:03:34.272][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-11-01 16:03:34.273][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-11-01 16:03:34.275][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-11-01 16:03:34.276][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-11-01 16:03:34.277][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-11-01 16:03:34.279][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-11-01 16:03:34.280][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-11-01 16:03:34.282][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-11-01 16:03:34.283][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-11-01 16:03:34.284][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-11-01 16:03:34.286][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-11-01 16:03:34.287][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-11-01 16:03:34.289][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-11-01 16:03:34.290][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-11-01 16:03:34.291][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-11-01 16:03:34.293][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-11-01 16:03:34.294][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-11-01 16:03:34.296][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-11-01 16:03:34.297][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-11-01 16:03:34.298][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-11-01 16:03:34.300][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-11-01 16:03:34.301][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-11-01 16:03:34.303][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-11-01 16:03:34.304][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-11-01 16:03:34.306][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-11-01 16:03:34.307][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-11-01 16:03:34.308][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-11-01 16:03:34.310][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-11-01 16:03:34.311][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-11-01 16:03:34.313][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-11-01 16:03:34.314][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-11-01 16:03:34.316][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-11-01 16:03:34.323][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-11-01 16:03:34.324][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-11-01 16:03:34.326][initialize] This is biodb version 1.18.0.
biodb.DEBUG[2025-11-01 16:03:34.327][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-11-01 16:03:34.328][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-11-01 16:03:34.329][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-01 16:03:34.330][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:03:34.330][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:03:34.331][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:03:34.332][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-01 16:03:34.333][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-01 16:03:34.334][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-01 16:03:34.335][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-01 16:03:34.336][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:03:34.337][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:03:34.338][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:03:34.339][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-01 16:03:34.340][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-01 16:03:34.341][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-01 16:03:34.341][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-01 16:03:34.342][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:03:34.343][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:03:34.344][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:03:34.345][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-01 16:03:34.346][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-01 16:03:34.347][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-01 16:03:34.348][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-01 16:03:34.349][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:03:34.350][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:03:34.351][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:03:34.351][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-01 16:03:34.352][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-01 16:03:34.353][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-01 16:03:34.354][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-01 16:03:34.355][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:03:34.356][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:03:34.357][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:03:34.358][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-01 16:03:34.359][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-01 16:03:34.359][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-01 16:03:34.360][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-01 16:03:34.361][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:03:34.362][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:03:34.363][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:03:34.364][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-01 16:03:34.365][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-01 16:03:34.366][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-01 16:03:34.367][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-01 16:03:34.368][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:03:34.369][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:03:34.369][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:03:34.370][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-01 16:03:34.371][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-01 16:03:34.372][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-01 16:03:34.373][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-01 16:03:34.374][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:03:34.375][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:03:34.376][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:03:34.377][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-01 16:03:34.378][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-01 16:03:34.378][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-01 16:03:34.379][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-01 16:03:34.380][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:03:34.381][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:03:34.382][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:03:34.383][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-01 16:03:34.384][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-01 16:03:34.385][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-01 16:03:34.386][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-01 16:03:34.387][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:03:34.387][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:03:34.388][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:03:34.389][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-01 16:03:34.390][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-01 16:03:34.391][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-01 16:03:34.392][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-01 16:03:34.393][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:03:34.394][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:03:34.395][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:03:34.396][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-01 16:03:34.396][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-01 16:03:34.397][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-01 16:03:34.398][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-01 16:03:34.399][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:03:34.400][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:03:34.401][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:03:34.402][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-01 16:03:34.403][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-01 16:03:34.404][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-01 16:03:34.405][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-01 16:03:34.405][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:03:34.406][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:03:34.407][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:03:34.408][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-01 16:03:34.409][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-01 16:03:34.410][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-01 16:03:34.411][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-01 16:03:34.412][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:03:34.413][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:03:34.414][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:03:34.415][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-01 16:03:34.415][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-01 16:03:34.416][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-01 16:03:34.417][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-01 16:03:34.418][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:03:34.419][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:03:34.420][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:03:34.421][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-01 16:03:34.422][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-01 16:03:34.423][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-01 16:03:34.424][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-01 16:03:34.424][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:03:34.425][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:03:34.426][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:03:34.427][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-01 16:03:34.428][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-01 16:03:34.429][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-01 16:03:34.430][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-01 16:03:34.431][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:03:34.432][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:03:34.439][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNci.Rcheck/biodbNci/definitions.yml".
biodb.DEBUG[2025-11-01 16:03:34.440][self$getDbsInfo()$define] Define connector nci.cactus.
biodb.DEBUG[2025-11-01 16:03:34.442][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-11-01 16:03:34.443][self$setPropertyValue] Setting property "description" to "National Cancer Institute (USA) CACTUS Database.".
biodb.DEBUG[2025-11-01 16:03:34.444][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-11-01 16:03:34.445][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-11-01 16:03:34.447][self$setPropertyValue] Setting property "downloadable" to "TRUE".
biodb.DEBUG[2025-11-01 16:03:34.448][self$setPropertyValue] Setting property "dwnld.ext" to "gz".
biodb.DEBUG[2025-11-01 16:03:34.449][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-11-01 16:03:34.450][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-11-01 16:03:34.451][self$setPropertyValue] Setting property "entry.content.type" to "sdf".
biodb.DEBUG[2025-11-01 16:03:34.452][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-11-01 16:03:34.453][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-11-01 16:03:34.454][self$setPropertyValue] Setting property "name" to "NCI CACTUS".
biodb.DEBUG[2025-11-01 16:03:34.455][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-11-01 16:03:34.456][self$setPropertyValue] Setting property "parsing.expr" to "NSC".
biodb.DEBUG[2025-11-01 16:03:34.456][self$setPropertyValue] Setting property "parsing.expr" to "DTP names".
biodb.DEBUG[2025-11-01 16:03:34.456][self$setPropertyValue] Setting property "parsing.expr" to "Standard InChI".
biodb.DEBUG[2025-11-01 16:03:34.456][self$setPropertyValue] Setting property "parsing.expr" to "c("Standard InChIKey", "^InChIKey=(.*)$")".
biodb.DEBUG[2025-11-01 16:03:34.456][self$setPropertyValue] Setting property "parsing.expr" to "Formula".
biodb.DEBUG[2025-11-01 16:03:34.456][self$setPropertyValue] Setting property "parsing.expr" to "Molecular Weight".
biodb.DEBUG[2025-11-01 16:03:34.456][self$setPropertyValue] Setting property "parsing.expr" to "CAS".
biodb.DEBUG[2025-11-01 16:03:34.457][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-11-01 16:03:34.458][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-11-01 16:03:34.459][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-11-01 16:03:34.460][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-11-01 16:03:34.461][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-11-01 16:03:34.462][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-11-01 16:03:34.463][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-11-01 16:03:34.464][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-11-01 16:03:34.465][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-11-01 16:03:34.466][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/".
biodb.DEBUG[2025-11-01 16:03:34.466][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/".
biodb.DEBUG[2025-11-01 16:03:34.466][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/download/nci/".
biodb.DEBUG[2025-11-01 16:03:34.466][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/download/nci/NCI-Open_2012-05-01.sdf.gz".
biodb.DEBUG[2025-11-01 16:03:34.467][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-11-01 16:03:34.468][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-11-01 16:03:34.469][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-11-01 16:03:34.470][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-11-01 16:03:34.471][self$getEntryFields()$define] Define field nci.cactus.id.
biodb.DEBUG[2025-11-01 16:03:34.474][super$initialize] Initialize connector nci.cactus.
biodb.DEBUG[2025-11-01 16:03:34.478][biodb$getFactory()$createConn] Creating new connector nci.cactus for database class nci.cactus .
biodb.INFO [2025-11-01 16:03:34.479][biodb$terminate] Closing BiodbMain instance...
biodb.INFO [2025-11-01 16:03:34.480][self$deleteConn] Connector "nci.cactus" deleted.
biodb.DEBUG[2025-11-01 16:03:34.481][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-11-01 16:03:34.482][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-01 16:03:34.483][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-01 16:03:34.484][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-01 16:03:34.485][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-01 16:03:34.486][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:03:34.486][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
[ FAIL 2 | WARN 0 | SKIP 0 | PASS 85 ]

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

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

'R CMD check' output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --test-dir=longtests --no-stop-on-test-error --no-codoc --no-examples --no-manual --ignore-vignettes --check-subdirs=no biodbNci_1.14.0.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:
  Backtrace:
      ▆
   1. ├─base::do.call(fct, params)
   2. └─biodb (local) `<fn>`(conn = `<NcCctsCn>`, opt = `<named list>`)
   3.   └─opt$refEntries$getRealEntry(id)
   4.     └─self$getRealEntries(ids = id)
   5.       └─private$bdb$getFactory()$getEntry(...)
   6.         └─private$loadEntries(conn$getId(), missing.ids, drop = FALSE)
   7.           └─conn$getEntryContent(ids)
   8.             └─self$download()
   9.               └─private$doExtractDownload()
  
  [ FAIL 2 | WARN 0 | SKIP 0 | PASS 85 ]
  Error: Test failures
  Execution halted
* DONE

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

Installation output

biodbNci.Rcheck/00install.out

* installing *source* package ‘biodbNci’ ...
** this is package ‘biodbNci’ version ‘1.14.0’
** 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)