Back to Long Tests report for BioC 3.22

This page was generated on 2025-10-04 23:55 -0400 (Sat, 04 Oct 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" 4853
lconwaymacOS 12.7.1 Montereyx86_644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4640
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 8/29HostnameOS / ArchCHECK
biodbNci 1.13.1  (landing page)
Pierrick Roger
Snapshot Date: 2025-10-04 09:55 -0400 (Sat, 04 Oct 2025)
git_url: https://git.bioconductor.org/packages/biodbNci
git_branch: devel
git_last_commit: 658b5cb
git_last_commit_date: 2025-07-24 10:46:27 -0400 (Thu, 24 Jul 2025)
nebbiolo2Linux (Ubuntu 24.04.3 LTS) / x86_64  ERROR  
lconwaymacOS 12.7.1 Monterey / x86_64  ERROR  

CHECK results for biodbNci on nebbiolo2

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

raw results


Summary

Package: biodbNci
Version: 1.13.1
Command: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --test-dir=longtests --no-stop-on-test-error --no-codoc --no-examples --no-manual --ignore-vignettes --check-subdirs=no biodbNci_1.13.1.tar.gz
StartedAt: 2025-10-04 16:02:38 -0400 (Sat, 04 Oct 2025)
EndedAt: 2025-10-04 16:03:41 -0400 (Sat, 04 Oct 2025)
EllapsedTime: 63.0 seconds
RetCode: 1
Status:   ERROR  
CheckDir: biodbNci.Rcheck
Warnings: NA

Tests output

biodbNci.Rcheck/tests/testthat.Rout.fail


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

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> # Script needed to run testthat automatically from ‘R CMD check’. See
> # testthat::test_dir documentation.
> library(testthat)
> library(biodbNci)
Warning message:
In fun(libname, pkgname) :
  Package 'biodbNci' is deprecated and will be removed from Bioconductor
  version 3.23
> Sys.setenv(TESTTHAT_REPORTER="summary")
> Sys.setenv(BIODB_LOG_DST="console")
> test_check("biodbNci")
biodb.INFO [2025-10-04 16:03:38.196][biodb::testContext]
biodb.INFO [2025-10-04 16:03:38.198][biodb::testContext] ********************************************************************************
biodb.INFO [2025-10-04 16:03:38.199][biodb::testContext] Test context - Generic long tests
biodb.INFO [2025-10-04 16:03:38.200][biodb::testContext] ********************************************************************************
biodb.INFO [2025-10-04 16:03:38.201][biodb::testContext]
biodb.INFO [2025-10-04 16:03:38.207][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.17.2.
biodb.DEBUG[2025-10-04 16:03:38.209][self$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.22-bioc/R/site-library/biodb/definitions.yml".
biodb.DEBUG[2025-10-04 16:03:38.215][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-10-04 16:03:38.216][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-10-04 16:03:38.217][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-10-04 16:03:38.218][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:03:38.219][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:03:38.220][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:03:38.221][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-10-04 16:03:38.238][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-10-04 16:03:38.239][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:03:38.240][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:03:38.241][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:03:38.241][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-10-04 16:03:38.242][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-10-04 16:03:38.243][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:03:38.244][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:03:38.253][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:03:38.254][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-10-04 16:03:38.255][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-10-04 16:03:38.256][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-10-04 16:03:38.256][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:03:38.257][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:03:38.258][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:03:38.259][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-10-04 16:03:38.260][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-10-04 16:03:38.261][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-10-04 16:03:38.262][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:03:38.262][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:03:38.263][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:03:38.264][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-10-04 16:03:38.265][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-10-04 16:03:38.266][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:03:38.267][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:03:38.268][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:03:38.269][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-10-04 16:03:38.269][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-10-04 16:03:38.270][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-10-04 16:03:38.271][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:03:38.272][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:03:38.273][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:03:38.274][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-10-04 16:03:38.275][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-10-04 16:03:38.276][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:03:38.276][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:03:38.277][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:03:38.278][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-10-04 16:03:38.279][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-10-04 16:03:38.280][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-10-04 16:03:38.281][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:03:38.282][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:03:38.282][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:03:38.283][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-10-04 16:03:38.284][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-10-04 16:03:38.285][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-10-04 16:03:38.286][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-10-04 16:03:38.287][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-10-04 16:03:38.288][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-10-04 16:03:38.289][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:03:38.290][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:03:38.290][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:03:38.291][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-10-04 16:03:38.292][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-10-04 16:03:38.293][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:03:38.294][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:03:38.295][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:03:38.296][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-10-04 16:03:38.297][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-10-04 16:03:38.297][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:03:38.298][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:03:38.299][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:03:38.300][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-10-04 16:03:38.301][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-10-04 16:03:38.302][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:03:38.302][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:03:38.303][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:03:38.304][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-10-04 16:03:38.305][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-10-04 16:03:38.306][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-10-04 16:03:38.307][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:03:38.308][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:03:38.309][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:03:38.309][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-10-04 16:03:38.310][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-10-04 16:03:38.313][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-10-04 16:03:38.314][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:03:38.315][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:03:38.316][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:03:38.317][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-10-04 16:03:38.318][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-10-04 16:03:38.319][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-10-04 16:03:38.320][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:03:38.320][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:03:38.321][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:03:38.324][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-10-04 16:03:38.355][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-10-04 16:03:38.369][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2025-10-04 16:03:38.370][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-10-04 16:03:38.371][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-10-04 16:03:38.372][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-10-04 16:03:38.373][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-10-04 16:03:38.374][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-10-04 16:03:38.375][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-10-04 16:03:38.375][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-10-04 16:03:38.376][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-10-04 16:03:38.377][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-10-04 16:03:38.378][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-10-04 16:03:38.379][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-10-04 16:03:38.380][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-10-04 16:03:38.381][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-10-04 16:03:38.382][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-10-04 16:03:38.382][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-10-04 16:03:38.382][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-10-04 16:03:38.382][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-10-04 16:03:38.382][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-10-04 16:03:38.383][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-10-04 16:03:38.384][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-04 16:03:38.385][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-04 16:03:38.385][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-10-04 16:03:38.386][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-04 16:03:38.387][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-04 16:03:38.388][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-10-04 16:03:38.389][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-10-04 16:03:38.390][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-10-04 16:03:38.391][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-10-04 16:03:38.391][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-10-04 16:03:38.392][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-10-04 16:03:38.393][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-10-04 16:03:38.395][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-10-04 16:03:38.396][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-10-04 16:03:38.397][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-10-04 16:03:38.398][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-10-04 16:03:38.399][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-10-04 16:03:38.400][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-10-04 16:03:38.405][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-10-04 16:03:38.406][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-10-04 16:03:38.406][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-10-04 16:03:38.407][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-10-04 16:03:38.408][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-10-04 16:03:38.409][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-10-04 16:03:38.410][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-10-04 16:03:38.411][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-10-04 16:03:38.412][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-10-04 16:03:38.413][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-10-04 16:03:38.413][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-10-04 16:03:38.413][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-10-04 16:03:38.413][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-10-04 16:03:38.413][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-10-04 16:03:38.414][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-10-04 16:03:38.415][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-04 16:03:38.416][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-04 16:03:38.417][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-10-04 16:03:38.417][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-04 16:03:38.418][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-04 16:03:38.419][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-10-04 16:03:38.420][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-10-04 16:03:38.421][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-10-04 16:03:38.422][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-10-04 16:03:38.423][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-10-04 16:03:38.424][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-10-04 16:03:38.425][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-10-04 16:03:38.426][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-10-04 16:03:38.427][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2025-10-04 16:03:38.428][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-10-04 16:03:38.429][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-10-04 16:03:38.430][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-10-04 16:03:38.431][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-10-04 16:03:38.432][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-10-04 16:03:38.433][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-10-04 16:03:38.434][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-10-04 16:03:38.435][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-10-04 16:03:38.436][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-10-04 16:03:38.437][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-10-04 16:03:38.438][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-10-04 16:03:38.439][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-10-04 16:03:38.440][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-10-04 16:03:38.441][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-10-04 16:03:38.441][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-10-04 16:03:38.442][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-04 16:03:38.443][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-04 16:03:38.444][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-10-04 16:03:38.445][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-04 16:03:38.446][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-04 16:03:38.447][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-10-04 16:03:38.448][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-10-04 16:03:38.449][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-10-04 16:03:38.449][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-10-04 16:03:38.450][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-10-04 16:03:38.451][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-10-04 16:03:38.452][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-10-04 16:03:38.454][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-10-04 16:03:38.455][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-10-04 16:03:38.456][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-10-04 16:03:38.457][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-10-04 16:03:38.458][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-10-04 16:03:38.459][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-10-04 16:03:38.460][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-10-04 16:03:38.460][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-10-04 16:03:38.461][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-10-04 16:03:38.462][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-10-04 16:03:38.463][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-10-04 16:03:38.464][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-10-04 16:03:38.465][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-10-04 16:03:38.466][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-10-04 16:03:38.467][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-10-04 16:03:38.468][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-10-04 16:03:38.469][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-10-04 16:03:38.470][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-04 16:03:38.471][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-04 16:03:38.472][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-10-04 16:03:38.472][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-04 16:03:38.473][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-04 16:03:38.474][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-10-04 16:03:38.475][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-10-04 16:03:38.476][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-10-04 16:03:38.477][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-10-04 16:03:38.478][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-10-04 16:03:38.479][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-10-04 16:03:38.482][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-10-04 16:03:38.483][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:03:38.484][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:03:38.485][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:03:38.486][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-04 16:03:38.486][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-04 16:03:38.487][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:03:38.488][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:03:38.489][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:03:38.490][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-04 16:03:38.491][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-04 16:03:38.491][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:03:38.492][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:03:38.493][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:03:38.494][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-04 16:03:38.495][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-04 16:03:38.495][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:03:38.496][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:03:38.497][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:03:38.498][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-04 16:03:38.499][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-04 16:03:38.500][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:03:38.500][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:03:38.501][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:03:38.502][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-04 16:03:38.503][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-04 16:03:38.504][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:03:38.505][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:03:38.505][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:03:38.506][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-04 16:03:38.507][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-04 16:03:38.508][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:03:38.509][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:03:38.509][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:03:38.510][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-04 16:03:38.511][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-04 16:03:38.512][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:03:38.513][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:03:38.514][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:03:38.514][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-04 16:03:38.515][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-04 16:03:38.516][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:03:38.517][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:03:38.518][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:03:38.519][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-04 16:03:38.519][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-04 16:03:38.520][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:03:38.521][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:03:38.522][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:03:38.523][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-04 16:03:38.523][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-04 16:03:38.524][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:03:38.525][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:03:38.526][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:03:38.527][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-04 16:03:38.528][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-04 16:03:38.528][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:03:38.529][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:03:38.530][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:03:38.531][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-04 16:03:38.532][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-04 16:03:38.533][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:03:38.533][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:03:38.534][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:03:38.535][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-04 16:03:38.536][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-04 16:03:38.537][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:03:38.537][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:03:38.538][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:03:38.539][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-04 16:03:38.540][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-04 16:03:38.541][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:03:38.542][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:03:38.542][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:03:38.543][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-04 16:03:38.544][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-04 16:03:38.545][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:03:38.546][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:03:38.546][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:03:38.547][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-04 16:03:38.548][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-04 16:03:38.549][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:03:38.550][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:03:38.551][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-10-04 16:03:38.555][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-10-04 16:03:38.560][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-10-04 16:03:38.561][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-10-04 16:03:38.562][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-10-04 16:03:38.564][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-10-04 16:03:38.565][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-10-04 16:03:38.566][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-10-04 16:03:38.567][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-10-04 16:03:38.569][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-10-04 16:03:38.570][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-10-04 16:03:38.571][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-10-04 16:03:38.573][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-10-04 16:03:38.574][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-10-04 16:03:38.575][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-10-04 16:03:38.576][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-10-04 16:03:38.578][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-10-04 16:03:38.579][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-10-04 16:03:38.580][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-10-04 16:03:38.582][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-10-04 16:03:38.583][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-10-04 16:03:38.584][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-10-04 16:03:38.585][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-10-04 16:03:38.587][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-10-04 16:03:38.588][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-10-04 16:03:38.589][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-10-04 16:03:38.591][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-10-04 16:03:38.592][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-10-04 16:03:38.593][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-10-04 16:03:38.594][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-10-04 16:03:38.596][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-10-04 16:03:38.597][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-10-04 16:03:38.598][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-10-04 16:03:38.600][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-10-04 16:03:38.601][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-10-04 16:03:38.602][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-10-04 16:03:38.603][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-10-04 16:03:38.605][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-10-04 16:03:38.606][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-10-04 16:03:38.607][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-10-04 16:03:38.608][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-10-04 16:03:38.610][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-10-04 16:03:38.611][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-10-04 16:03:38.612][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-10-04 16:03:38.614][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-10-04 16:03:38.615][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-10-04 16:03:38.616][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-10-04 16:03:38.618][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-10-04 16:03:38.619][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-10-04 16:03:38.620][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-10-04 16:03:38.621][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-10-04 16:03:38.623][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-10-04 16:03:38.624][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-10-04 16:03:38.625][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-10-04 16:03:38.627][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-10-04 16:03:38.628][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-10-04 16:03:38.629][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-10-04 16:03:38.630][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-10-04 16:03:38.632][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-10-04 16:03:38.633][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-10-04 16:03:38.634][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-10-04 16:03:38.636][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-10-04 16:03:38.637][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-10-04 16:03:38.638][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-10-04 16:03:38.640][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-10-04 16:03:38.641][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-10-04 16:03:38.642][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-10-04 16:03:38.643][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-10-04 16:03:38.645][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-10-04 16:03:38.646][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-10-04 16:03:38.647][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-10-04 16:03:38.649][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-10-04 16:03:38.650][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-10-04 16:03:38.651][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-10-04 16:03:38.652][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-10-04 16:03:38.654][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-10-04 16:03:38.655][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-10-04 16:03:38.656][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-10-04 16:03:38.657][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-10-04 16:03:38.659][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-10-04 16:03:38.660][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-10-04 16:03:38.661][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-10-04 16:03:38.663][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-10-04 16:03:38.675][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-10-04 16:03:38.678][initialize] This is biodb version 1.17.2.
biodb.DEBUG[2025-10-04 16:03:38.682][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-10-04 16:03:38.683][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-10-04 16:03:38.684][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-04 16:03:38.684][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:03:38.685][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:03:38.691][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:03:38.692][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-04 16:03:38.693][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-04 16:03:38.694][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-04 16:03:38.694][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-04 16:03:38.695][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:03:38.696][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:03:38.697][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:03:38.698][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-04 16:03:38.699][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-04 16:03:38.700][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-04 16:03:38.701][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-04 16:03:38.702][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:03:38.703][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:03:38.704][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:03:38.705][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-04 16:03:38.706][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-04 16:03:38.707][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-04 16:03:38.707][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-04 16:03:38.708][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:03:38.709][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:03:38.710][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:03:38.711][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-04 16:03:38.712][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-04 16:03:38.713][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-04 16:03:38.714][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-04 16:03:38.715][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:03:38.716][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:03:38.731][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:03:38.732][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-04 16:03:38.733][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-04 16:03:38.734][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-04 16:03:38.735][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-04 16:03:38.736][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:03:38.737][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:03:38.738][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:03:38.739][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-04 16:03:38.740][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-04 16:03:38.741][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-04 16:03:38.741][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-04 16:03:38.742][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:03:38.743][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:03:38.744][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:03:38.745][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-04 16:03:38.746][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-04 16:03:38.747][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-04 16:03:38.748][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-04 16:03:38.749][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:03:38.750][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:03:38.751][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:03:38.752][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-04 16:03:38.753][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-04 16:03:38.753][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-04 16:03:38.754][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-04 16:03:38.755][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:03:38.756][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:03:38.757][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:03:38.758][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-04 16:03:38.759][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-04 16:03:38.760][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-04 16:03:38.761][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-04 16:03:38.762][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:03:38.763][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:03:38.763][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:03:38.764][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-04 16:03:38.765][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-04 16:03:38.766][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-04 16:03:38.767][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-04 16:03:38.768][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:03:38.769][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:03:38.770][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:03:38.771][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-04 16:03:38.772][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-04 16:03:38.772][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-04 16:03:38.773][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-04 16:03:38.774][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:03:38.775][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:03:38.776][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:03:38.777][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-04 16:03:38.778][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-04 16:03:38.779][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-04 16:03:38.780][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-04 16:03:38.780][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:03:38.781][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:03:38.782][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:03:38.783][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-04 16:03:38.784][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-04 16:03:38.785][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-04 16:03:38.786][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-04 16:03:38.787][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:03:38.788][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:03:38.789][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:03:38.789][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-04 16:03:38.790][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-04 16:03:38.791][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-04 16:03:38.792][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-04 16:03:38.793][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:03:38.794][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:03:38.795][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:03:38.796][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-04 16:03:38.797][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-04 16:03:38.797][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-04 16:03:38.798][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-04 16:03:38.799][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:03:38.800][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:03:38.801][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:03:38.802][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-04 16:03:38.803][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-04 16:03:38.804][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-04 16:03:38.805][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-04 16:03:38.806][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:03:38.806][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:03:38.808][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNci.Rcheck/biodbNci/definitions.yml".
biodb.DEBUG[2025-10-04 16:03:38.818][self$getDbsInfo()$define] Define connector nci.cactus.
biodb.DEBUG[2025-10-04 16:03:38.820][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-10-04 16:03:38.821][self$setPropertyValue] Setting property "description" to "National Cancer Institute (USA) CACTUS Database.".
biodb.DEBUG[2025-10-04 16:03:38.822][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-10-04 16:03:38.823][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-10-04 16:03:38.824][self$setPropertyValue] Setting property "downloadable" to "TRUE".
biodb.DEBUG[2025-10-04 16:03:38.825][self$setPropertyValue] Setting property "dwnld.ext" to "gz".
biodb.DEBUG[2025-10-04 16:03:38.826][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-10-04 16:03:38.827][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-10-04 16:03:38.828][self$setPropertyValue] Setting property "entry.content.type" to "sdf".
biodb.DEBUG[2025-10-04 16:03:38.829][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-10-04 16:03:38.830][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-10-04 16:03:38.831][self$setPropertyValue] Setting property "name" to "NCI CACTUS".
biodb.DEBUG[2025-10-04 16:03:38.832][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-10-04 16:03:38.833][self$setPropertyValue] Setting property "parsing.expr" to "NSC".
biodb.DEBUG[2025-10-04 16:03:38.833][self$setPropertyValue] Setting property "parsing.expr" to "DTP names".
biodb.DEBUG[2025-10-04 16:03:38.833][self$setPropertyValue] Setting property "parsing.expr" to "Standard InChI".
biodb.DEBUG[2025-10-04 16:03:38.833][self$setPropertyValue] Setting property "parsing.expr" to "c("Standard InChIKey", "^InChIKey=(.*)$")".
biodb.DEBUG[2025-10-04 16:03:38.833][self$setPropertyValue] Setting property "parsing.expr" to "Formula".
biodb.DEBUG[2025-10-04 16:03:38.833][self$setPropertyValue] Setting property "parsing.expr" to "Molecular Weight".
biodb.DEBUG[2025-10-04 16:03:38.833][self$setPropertyValue] Setting property "parsing.expr" to "CAS".
biodb.DEBUG[2025-10-04 16:03:38.834][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-10-04 16:03:38.835][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-10-04 16:03:38.836][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-10-04 16:03:38.837][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-04 16:03:38.838][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-04 16:03:38.839][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-10-04 16:03:38.840][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-04 16:03:38.840][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-04 16:03:38.841][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-10-04 16:03:38.842][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/".
biodb.DEBUG[2025-10-04 16:03:38.842][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/".
biodb.DEBUG[2025-10-04 16:03:38.842][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/download/nci/".
biodb.DEBUG[2025-10-04 16:03:38.842][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/download/nci/NCI-Open_2012-05-01.sdf.gz".
biodb.DEBUG[2025-10-04 16:03:38.843][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-10-04 16:03:38.844][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-10-04 16:03:38.845][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-10-04 16:03:38.846][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-10-04 16:03:38.852][self$getEntryFields()$define] Define field nci.cactus.id.
biodb.DEBUG[2025-10-04 16:03:38.872][super$initialize] Initialize connector nci.cactus.
biodb.DEBUG[2025-10-04 16:03:38.887][biodb$getFactory()$createConn] Creating new connector nci.cactus for database class nci.cactus .
biodb.INFO [2025-10-04 16:03:38.895][biodb::testThat]
biodb.INFO [2025-10-04 16:03:38.902][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2025-10-04 16:03:38.903][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-10-04 16:03:38.904][biodb::testThat]
biodb.TRACE[2025-10-04 16:03:38.907][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNci.Rcheck/biodbNci/testref/entry-nci.cactus-749674-content.sdf".
biodb.DEBUG[2025-10-04 16:03:38.908][biodb$getFactory()$createEntryFromCo ...] Creating NCI CACTUS entries from 1 content(s).
biodb.DEBUG[2025-10-04 16:03:38.911][biodb$getFactory()$createEntryFromCo ...] Parsing 1 NCI CACTUS entries.
biodb.DEBUG[2025-10-04 16:03:38.919][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-10-04 16:03:38.919][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-04 16:03:38.920][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-04 16:03:38.931][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-10-04 16:03:38.932][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-04 16:03:38.933][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:03:38.934][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-10-04 16:03:38.949][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-04 16:03:38.950][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-04 16:03:38.951][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:03:38.952][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:03:38.953][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-04 16:03:38.965][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-04 16:03:38.966][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:03:38.966][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:03:38.969][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-10-04 16:03:38.970][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-10-04 16:03:38.971][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:03:38.971][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:03:38.995][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-10-04 16:03:38.996][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-10-04 16:03:38.997][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:03:38.998][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:03:38.999][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-10-04 16:03:39.000][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-10-04 16:03:39.001][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:03:39.002][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:03:39.003][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-10-04 16:03:39.004][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-10-04 16:03:39.005][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:03:39.006][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:03:39.007][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-10-04 16:03:39.008][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-10-04 16:03:39.009][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:03:39.010][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:03:39.011][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-10-04 16:03:39.012][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-10-04 16:03:39.013][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:03:39.014][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:03:39.015][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-10-04 16:03:39.016][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-10-04 16:03:39.017][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:03:39.018][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:03:39.019][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-10-04 16:03:39.020][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-10-04 16:03:39.021][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:03:39.022][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:03:39.023][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-10-04 16:03:39.024][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-10-04 16:03:39.025][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:03:39.026][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:03:39.027][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-10-04 16:03:39.028][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-10-04 16:03:39.029][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:03:39.030][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:03:39.031][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-04 16:03:39.037][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-04 16:03:39.038][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:03:39.039][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:03:39.040][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-10-04 16:03:39.041][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-10-04 16:03:39.042][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:03:39.043][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:03:39.044][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-04 16:03:39.045][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-04 16:03:39.046][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:03:39.046][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:03:39.047][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-04 16:03:39.048][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-04 16:03:39.049][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:03:39.050][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:03:39.051][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-04 16:03:39.052][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-04 16:03:39.053][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:03:39.054][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:03:39.085][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-04 16:03:39.086][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-04 16:03:39.087][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:03:39.088][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:03:39.089][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-04 16:03:39.090][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-04 16:03:39.091][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:03:39.092][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:03:39.092][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-04 16:03:39.093][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-04 16:03:39.094][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:03:39.095][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-10-04 16:03:39.096][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 749674.
biodb.TRACE[2025-10-04 16:03:39.098][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-10-04 16:03:39.099][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-10-04 16:03:39.100][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:03:39.101][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:03:39.102][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-10-04 16:03:39.103][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-10-04 16:03:39.104][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:03:39.105][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:03:39.106][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-10-04 16:03:39.107][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-10-04 16:03:39.108][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:03:39.108][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:03:39.109][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-10-04 16:03:39.110][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-10-04 16:03:39.111][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:03:39.112][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:03:39.114][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-04 16:03:39.115][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-04 16:03:39.116][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:03:39.117][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:03:39.129][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-10-04 16:03:39.130][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-10-04 16:03:39.131][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:03:39.132][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:03:39.136][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-04 16:03:39.137][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-04 16:03:39.138][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:03:39.138][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:03:39.139][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-04 16:03:39.140][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-04 16:03:39.180][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:03:39.181][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:03:39.182][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-04 16:03:39.183][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-04 16:03:39.184][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:03:39.185][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:03:39.187][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-04 16:03:39.188][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-04 16:03:39.189][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:03:39.190][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:03:39.191][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-04 16:03:39.192][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-04 16:03:39.193][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:03:39.194][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:03:39.194][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-04 16:03:39.195][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-04 16:03:39.196][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:03:39.197][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:03:39.198][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-10-04 16:03:39.199][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-10-04 16:03:39.200][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:03:39.201][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:03:39.202][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-10-04 16:03:39.203][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-10-04 16:03:39.204][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:03:39.205][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:03:39.206][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-10-04 16:03:39.207][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-10-04 16:03:39.208][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:03:39.208][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:03:39.215][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-04 16:03:39.216][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-04 16:03:39.217][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:03:39.217][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:03:39.218][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-04 16:03:39.219][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-04 16:03:39.220][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:03:39.221][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:03:39.222][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-04 16:03:39.223][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-04 16:03:39.224][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:03:39.225][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:03:39.226][ef$get] Asked field names are: accession.
biodb.TRACE[2025-10-04 16:03:39.227][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-04 16:03:39.228][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:03:39.228][ef$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:03:39.229][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-04 16:03:39.230][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-04 16:03:39.231][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:03:39.232][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:03:39.240][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-10-04 16:03:39.241][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-10-04 16:03:39.241][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:03:39.242][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:03:39.243][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-10-04 16:03:39.244][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-10-04 16:03:39.245][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:03:39.246][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:03:39.247][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-10-04 16:03:39.248][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-10-04 16:03:39.249][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:03:39.250][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:03:39.251][ef$get] Asked field names are: formula.
biodb.TRACE[2025-10-04 16:03:39.252][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-10-04 16:03:39.252][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:03:39.253][ef$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:03:39.254][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-10-04 16:03:39.255][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-10-04 16:03:39.256][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:03:39.257][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:03:39.264][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-10-04 16:03:39.265][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-10-04 16:03:39.266][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:03:39.267][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:03:39.268][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-10-04 16:03:39.269][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-10-04 16:03:39.269][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:03:39.270][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:03:39.271][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-10-04 16:03:39.272][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-10-04 16:03:39.273][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:03:39.274][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:03:39.275][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-10-04 16:03:39.276][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-10-04 16:03:39.277][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:03:39.278][ef$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:03:39.279][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-10-04 16:03:39.280][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-10-04 16:03:39.280][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:03:39.281][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:03:39.288][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-10-04 16:03:39.289][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-10-04 16:03:39.290][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:03:39.291][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:03:39.292][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-10-04 16:03:39.293][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-10-04 16:03:39.297][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:03:39.298][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:03:39.299][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-10-04 16:03:39.300][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-10-04 16:03:39.301][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:03:39.302][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:03:39.303][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-10-04 16:03:39.304][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-10-04 16:03:39.305][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:03:39.306][ef$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:03:39.307][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-10-04 16:03:39.308][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-10-04 16:03:39.309][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:03:39.309][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:03:39.316][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-10-04 16:03:39.317][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-10-04 16:03:39.318][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:03:39.319][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:03:39.320][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-10-04 16:03:39.321][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-10-04 16:03:39.322][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:03:39.323][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:03:39.324][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-10-04 16:03:39.325][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-10-04 16:03:39.326][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:03:39.327][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:03:39.327][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-10-04 16:03:39.328][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-10-04 16:03:39.329][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:03:39.330][ef$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:03:39.331][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-10-04 16:03:39.332][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-10-04 16:03:39.333][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:03:39.334][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:03:39.341][ef$get] Asked field names are: accession.
biodb.TRACE[2025-10-04 16:03:39.342][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-04 16:03:39.343][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:03:39.344][ef$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:03:39.347][ef$get] Asked field names are: formula.
biodb.TRACE[2025-10-04 16:03:39.348][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-10-04 16:03:39.349][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:03:39.350][ef$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:03:39.354][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-10-04 16:03:39.355][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-10-04 16:03:39.356][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:03:39.357][ef$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:03:39.360][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-10-04 16:03:39.361][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-10-04 16:03:39.362][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:03:39.363][ef$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:03:39.367][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-10-04 16:03:39.368][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-10-04 16:03:39.369][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:03:39.369][ef$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:03:39.387][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNci.Rcheck/biodbNci/testref/entry-nci.cactus-750690-content.sdf".
biodb.DEBUG[2025-10-04 16:03:39.423][biodb$getFactory()$createEntryFromCo ...] Creating NCI CACTUS entries from 1 content(s).
biodb.DEBUG[2025-10-04 16:03:39.424][biodb$getFactory()$createEntryFromCo ...] Parsing 1 NCI CACTUS entries.
biodb.DEBUG[2025-10-04 16:03:39.426][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-10-04 16:03:39.427][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-04 16:03:39.428][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-04 16:03:39.432][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-10-04 16:03:39.433][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-04 16:03:39.434][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:03:39.434][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-10-04 16:03:39.443][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-04 16:03:39.444][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-04 16:03:39.445][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:03:39.446][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:03:39.447][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-04 16:03:39.448][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-04 16:03:39.449][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:03:39.450][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:03:39.467][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-10-04 16:03:39.468][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-10-04 16:03:39.469][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:03:39.470][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:03:39.471][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-10-04 16:03:39.472][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-10-04 16:03:39.473][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:03:39.474][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:03:39.475][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-10-04 16:03:39.476][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-10-04 16:03:39.477][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:03:39.478][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:03:39.479][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-10-04 16:03:39.480][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-10-04 16:03:39.481][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:03:39.482][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:03:39.483][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-10-04 16:03:39.484][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-10-04 16:03:39.485][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:03:39.486][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:03:39.487][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-10-04 16:03:39.488][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-10-04 16:03:39.489][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:03:39.489][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:03:39.491][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-10-04 16:03:39.492][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-10-04 16:03:39.493][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:03:39.493][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:03:39.494][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-10-04 16:03:39.495][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-10-04 16:03:39.496][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:03:39.497][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:03:39.498][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-10-04 16:03:39.499][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-10-04 16:03:39.500][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:03:39.501][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:03:39.502][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-10-04 16:03:39.503][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-10-04 16:03:39.504][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:03:39.505][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:03:39.506][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-10-04 16:03:39.507][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-10-04 16:03:39.508][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:03:39.509][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:03:39.509][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-10-04 16:03:39.510][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-10-04 16:03:39.511][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:03:39.512][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:03:39.513][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-10-04 16:03:39.514][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-10-04 16:03:39.515][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:03:39.516][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:03:39.521][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-10-04 16:03:39.522][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-10-04 16:03:39.523][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:03:39.524][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:03:39.525][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-10-04 16:03:39.526][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-10-04 16:03:39.527][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:03:39.528][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:03:39.529][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-10-04 16:03:39.530][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-10-04 16:03:39.531][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:03:39.532][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:03:39.533][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-10-04 16:03:39.534][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-10-04 16:03:39.535][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:03:39.535][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:03:39.537][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-10-04 16:03:39.538][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-10-04 16:03:39.539][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:03:39.540][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:03:39.541][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-10-04 16:03:39.542][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-10-04 16:03:39.543][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:03:39.543][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:03:39.544][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-04 16:03:39.545][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-04 16:03:39.546][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:03:39.547][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:03:39.548][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-10-04 16:03:39.549][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-10-04 16:03:39.550][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:03:39.551][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:03:39.552][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-04 16:03:39.553][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-04 16:03:39.554][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:03:39.555][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:03:39.555][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-04 16:03:39.556][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-04 16:03:39.557][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:03:39.558][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:03:39.559][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-04 16:03:39.560][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-04 16:03:39.561][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:03:39.562][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:03:39.563][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-04 16:03:39.564][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-04 16:03:39.565][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:03:39.566][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:03:39.567][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-04 16:03:39.568][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-04 16:03:39.568][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:03:39.569][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:03:39.570][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-04 16:03:39.571][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-04 16:03:39.572][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:03:39.573][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-10-04 16:03:39.574][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 750690.
biodb.TRACE[2025-10-04 16:03:39.593][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-10-04 16:03:39.594][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-10-04 16:03:39.595][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:03:39.596][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:03:39.597][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-10-04 16:03:39.598][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-10-04 16:03:39.598][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:03:39.599][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:03:39.600][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-10-04 16:03:39.601][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-10-04 16:03:39.602][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:03:39.603][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:03:39.604][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-10-04 16:03:39.605][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-10-04 16:03:39.606][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:03:39.607][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:03:39.608][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-04 16:03:39.609][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-04 16:03:39.610][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:03:39.611][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:03:39.615][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-10-04 16:03:39.616][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-10-04 16:03:39.617][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:03:39.618][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:03:39.622][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-04 16:03:39.623][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-04 16:03:39.624][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:03:39.625][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:03:39.626][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-04 16:03:39.627][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-04 16:03:39.628][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:03:39.629][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:03:39.630][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-04 16:03:39.634][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-04 16:03:39.635][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:03:39.636][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:03:39.638][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-04 16:03:39.639][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-04 16:03:39.640][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:03:39.641][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:03:39.642][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-04 16:03:39.643][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-04 16:03:39.644][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:03:39.645][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:03:39.646][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-04 16:03:39.647][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-04 16:03:39.647][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:03:39.648][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:03:39.649][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-10-04 16:03:39.650][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-10-04 16:03:39.651][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:03:39.652][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:03:39.653][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-10-04 16:03:39.654][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-10-04 16:03:39.655][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:03:39.656][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:03:39.657][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-10-04 16:03:39.658][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-10-04 16:03:39.659][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:03:39.660][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:03:39.675][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-04 16:03:39.676][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-04 16:03:39.677][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:03:39.678][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:03:39.678][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-04 16:03:39.679][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-04 16:03:39.680][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:03:39.681][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:03:39.682][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-04 16:03:39.683][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-04 16:03:39.684][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:03:39.685][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:03:39.686][ef$get] Asked field names are: accession.
biodb.TRACE[2025-10-04 16:03:39.687][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-04 16:03:39.688][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:03:39.689][ef$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:03:39.690][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-04 16:03:39.691][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-04 16:03:39.691][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:03:39.692][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:03:39.699][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-10-04 16:03:39.700][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-10-04 16:03:39.701][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:03:39.702][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:03:39.703][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-10-04 16:03:39.704][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-10-04 16:03:39.705][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:03:39.706][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:03:39.707][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-10-04 16:03:39.708][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-10-04 16:03:39.709][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:03:39.710][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:03:39.711][ef$get] Asked field names are: cas.id.
biodb.TRACE[2025-10-04 16:03:39.712][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-10-04 16:03:39.712][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:03:39.713][ef$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:03:39.714][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-10-04 16:03:39.715][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-10-04 16:03:39.716][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:03:39.717][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:03:39.724][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-10-04 16:03:39.725][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-10-04 16:03:39.726][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:03:39.727][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:03:39.728][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-10-04 16:03:39.729][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-10-04 16:03:39.730][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:03:39.731][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:03:39.732][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-10-04 16:03:39.733][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-10-04 16:03:39.733][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:03:39.734][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:03:39.735][ef$get] Asked field names are: name.
biodb.TRACE[2025-10-04 16:03:39.736][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-10-04 16:03:39.737][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:03:39.738][ef$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:03:39.739][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-10-04 16:03:39.740][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-10-04 16:03:39.741][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:03:39.742][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:03:39.753][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-10-04 16:03:39.754][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-10-04 16:03:39.754][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:03:39.755][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:03:39.756][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-10-04 16:03:39.757][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-10-04 16:03:39.758][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:03:39.759][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:03:39.760][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-10-04 16:03:39.761][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-10-04 16:03:39.762][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:03:39.763][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:03:39.764][ef$get] Asked field names are: formula.
biodb.TRACE[2025-10-04 16:03:39.765][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-10-04 16:03:39.766][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:03:39.767][ef$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:03:39.767][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-10-04 16:03:39.768][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-10-04 16:03:39.769][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:03:39.770][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:03:39.777][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-10-04 16:03:39.778][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-10-04 16:03:39.779][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:03:39.780][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:03:39.781][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-10-04 16:03:39.782][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-10-04 16:03:39.783][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:03:39.784][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:03:39.785][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-10-04 16:03:39.786][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-10-04 16:03:39.787][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:03:39.788][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:03:39.789][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-10-04 16:03:39.790][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-10-04 16:03:39.790][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:03:39.791][ef$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:03:39.792][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-10-04 16:03:39.793][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-10-04 16:03:39.794][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:03:39.795][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:03:39.802][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-10-04 16:03:39.803][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-10-04 16:03:39.804][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:03:39.805][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:03:39.806][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-10-04 16:03:39.807][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-10-04 16:03:39.808][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:03:39.809][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:03:39.810][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-10-04 16:03:39.811][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-10-04 16:03:39.812][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:03:39.812][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:03:39.813][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-10-04 16:03:39.814][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-10-04 16:03:39.815][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:03:39.816][ef$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:03:39.817][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-10-04 16:03:39.818][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-10-04 16:03:39.819][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:03:39.820][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:03:39.827][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-10-04 16:03:39.828][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-10-04 16:03:39.829][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:03:39.830][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:03:39.831][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-10-04 16:03:39.832][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-10-04 16:03:39.833][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:03:39.834][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:03:39.834][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-10-04 16:03:39.835][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-10-04 16:03:39.836][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:03:39.837][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:03:39.838][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-10-04 16:03:39.839][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-10-04 16:03:39.840][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:03:39.841][ef$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:03:39.842][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-10-04 16:03:39.843][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-10-04 16:03:39.844][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:03:39.845][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:03:39.852][ef$get] Asked field names are: accession.
biodb.TRACE[2025-10-04 16:03:39.853][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-04 16:03:39.854][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:03:39.855][ef$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:03:39.858][ef$get] Asked field names are: cas.id.
biodb.TRACE[2025-10-04 16:03:39.859][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-10-04 16:03:39.860][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:03:39.865][ef$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:03:39.869][ef$get] Asked field names are: formula.
biodb.TRACE[2025-10-04 16:03:39.870][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-10-04 16:03:39.871][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:03:39.872][ef$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:03:39.876][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-10-04 16:03:39.877][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-10-04 16:03:39.877][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:03:39.878][ef$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:03:39.882][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-10-04 16:03:39.883][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-10-04 16:03:39.884][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:03:39.885][ef$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:03:39.889][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-10-04 16:03:39.890][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-10-04 16:03:39.891][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:03:39.892][ef$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:03:39.895][ef$get] Asked field names are: name.
biodb.TRACE[2025-10-04 16:03:39.897][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-10-04 16:03:39.897][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:03:39.898][ef$get] fields variable is a list.
biodb.INFO [2025-10-04 16:03:39.905][biodb::testThat]
biodb.INFO [2025-10-04 16:03:39.906][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2025-10-04 16:03:39.907][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-10-04 16:03:39.908][biodb::testThat]
biodb.DEBUG[2025-10-04 16:03:39.910][private$loadEntries] Creating entries from ids [2]: "749674, 750690".
biodb.DEBUG[2025-10-04 16:03:39.912][conn$getEntryContent] Get NCI CACTUS entry content(s) for 2 id(s)...
biodb.DEBUG[2025-10-04 16:03:39.914][self$isDownloaded] Database nci.cactus has already been downloaded.
biodb.DEBUG[2025-10-04 16:03:39.943][self$isDownloaded] Database nci.cactus has already been downloaded.
biodb.INFO [2025-10-04 16:03:39.944][self$download] Extract whole database of nci.cactus.
biodb.INFO [2025-10-04 16:03:39.945][private$doExtractDownload] Extracting content of downloaded biodbNci, a library for connecting to the National Cancer Institute (USA) CACTUS Database....
biodb.INFO [2025-10-04 16:03:39.987][biodb::testThat]
biodb.INFO [2025-10-04 16:03:39.988][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2025-10-04 16:03:39.989][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-10-04 16:03:39.989][biodb::testThat]
biodb.INFO [2025-10-04 16:03:39.995][biodb::testThat]
biodb.INFO [2025-10-04 16:03:39.995][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2025-10-04 16:03:39.996][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-10-04 16:03:39.997][biodb::testThat]
biodb.WARN [2025-10-04 16:03:40.015][self$searchForEntries] This database is not searchable by field "name".
biodb.WARN [2025-10-04 16:03:40.033][self$searchForEntries] This database is not searchable by field "name".
biodb.INFO [2025-10-04 16:03:40.041][biodb::testThat]
biodb.INFO [2025-10-04 16:03:40.042][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2025-10-04 16:03:40.043][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-10-04 16:03:40.044][biodb::testThat]
biodb.DEBUG[2025-10-04 16:03:40.059][private$loadEntries] Creating entries from ids [1]: "749674".
biodb.DEBUG[2025-10-04 16:03:40.108][conn$getEntryContent] Get NCI CACTUS entry content(s) for 1 id(s)...
biodb.DEBUG[2025-10-04 16:03:40.110][self$isDownloaded] Database nci.cactus has already been downloaded.
biodb.DEBUG[2025-10-04 16:03:40.111][self$isDownloaded] Database nci.cactus has already been downloaded.
biodb.INFO [2025-10-04 16:03:40.112][self$download] Extract whole database of nci.cactus.
biodb.INFO [2025-10-04 16:03:40.124][private$doExtractDownload] Extracting content of downloaded biodbNci, a library for connecting to the National Cancer Institute (USA) CACTUS Database....
biodb.INFO [2025-10-04 16:03:40.147][biodb::testThat]
biodb.INFO [2025-10-04 16:03:40.148][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2025-10-04 16:03:40.149][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-10-04 16:03:40.150][biodb::testThat]
biodb.INFO [2025-10-04 16:03:40.156][biodb::testThat]
biodb.INFO [2025-10-04 16:03:40.157][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2025-10-04 16:03:40.158][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-10-04 16:03:40.159][biodb::testThat]
biodb.INFO [2025-10-04 16:03:40.165][biodb::testThat]
biodb.INFO [2025-10-04 16:03:40.166][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2025-10-04 16:03:40.167][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-10-04 16:03:40.168][biodb::testThat]
biodb.INFO [2025-10-04 16:03:40.173][biodb::testThat]
biodb.INFO [2025-10-04 16:03:40.174][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2025-10-04 16:03:40.175][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-10-04 16:03:40.176][biodb::testThat]
biodb.INFO [2025-10-04 16:03:40.185][biodb$terminate] Closing BiodbMain instance...
biodb.INFO [2025-10-04 16:03:40.186][self$deleteConn] Connector "nci.cactus" deleted.
biodb.DEBUG[2025-10-04 16:03:40.187][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-10-04 16:03:40.188][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-04 16:03:40.189][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-04 16:03:40.189][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-04 16:03:40.190][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-04 16:03:40.191][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:03:40.192][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2025-10-04 16:03:40.201][biodb::testContext]
biodb.INFO [2025-10-04 16:03:40.202][biodb::testContext] ********************************************************************************
biodb.INFO [2025-10-04 16:03:40.203][biodb::testContext] Test context - Example long tests
biodb.INFO [2025-10-04 16:03:40.204][biodb::testContext] ********************************************************************************
biodb.INFO [2025-10-04 16:03:40.205][biodb::testContext]
biodb.INFO [2025-10-04 16:03:40.206][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.17.2.
biodb.DEBUG[2025-10-04 16:03:40.208][self$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.22-bioc/R/site-library/biodb/definitions.yml".
biodb.DEBUG[2025-10-04 16:03:40.212][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-10-04 16:03:40.213][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-10-04 16:03:40.214][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-10-04 16:03:40.214][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:03:40.215][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:03:40.216][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:03:40.217][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-10-04 16:03:40.218][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-10-04 16:03:40.219][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:03:40.220][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:03:40.220][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:03:40.221][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-10-04 16:03:40.222][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-10-04 16:03:40.223][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:03:40.224][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:03:40.225][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:03:40.226][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-10-04 16:03:40.227][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-10-04 16:03:40.228][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-10-04 16:03:40.228][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:03:40.229][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:03:40.230][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:03:40.231][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-10-04 16:03:40.232][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-10-04 16:03:40.233][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-10-04 16:03:40.234][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:03:40.235][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:03:40.235][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:03:40.236][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-10-04 16:03:40.237][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-10-04 16:03:40.238][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:03:40.239][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:03:40.240][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:03:40.241][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-10-04 16:03:40.242][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-10-04 16:03:40.243][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-10-04 16:03:40.243][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:03:40.244][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:03:40.245][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:03:40.246][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-10-04 16:03:40.247][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-10-04 16:03:40.248][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:03:40.249][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:03:40.249][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:03:40.250][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-10-04 16:03:40.251][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-10-04 16:03:40.252][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-10-04 16:03:40.253][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:03:40.254][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:03:40.255][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:03:40.256][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-10-04 16:03:40.257][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-10-04 16:03:40.257][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-10-04 16:03:40.258][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-10-04 16:03:40.259][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-10-04 16:03:40.260][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-10-04 16:03:40.261][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:03:40.262][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:03:40.263][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:03:40.264][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-10-04 16:03:40.265][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-10-04 16:03:40.266][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:03:40.266][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:03:40.267][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:03:40.268][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-10-04 16:03:40.269][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-10-04 16:03:40.270][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:03:40.271][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:03:40.272][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:03:40.272][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-10-04 16:03:40.273][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-10-04 16:03:40.274][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:03:40.275][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:03:40.276][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:03:40.277][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-10-04 16:03:40.278][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-10-04 16:03:40.279][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-10-04 16:03:40.280][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:03:40.280][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:03:40.281][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:03:40.282][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-10-04 16:03:40.283][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-10-04 16:03:40.288][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-10-04 16:03:40.288][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:03:40.289][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:03:40.290][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:03:40.291][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-10-04 16:03:40.292][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-10-04 16:03:40.297][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-10-04 16:03:40.298][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:03:40.299][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:03:40.299][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:03:40.300][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-10-04 16:03:40.302][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-10-04 16:03:40.303][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2025-10-04 16:03:40.304][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-10-04 16:03:40.305][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-10-04 16:03:40.306][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-10-04 16:03:40.307][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-10-04 16:03:40.308][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-10-04 16:03:40.309][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-10-04 16:03:40.310][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-10-04 16:03:40.311][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-10-04 16:03:40.311][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-10-04 16:03:40.312][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-10-04 16:03:40.313][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-10-04 16:03:40.314][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-10-04 16:03:40.315][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-10-04 16:03:40.316][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-10-04 16:03:40.316][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-10-04 16:03:40.316][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-10-04 16:03:40.316][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-10-04 16:03:40.316][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-10-04 16:03:40.317][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-10-04 16:03:40.318][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-04 16:03:40.319][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-04 16:03:40.320][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-10-04 16:03:40.321][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-04 16:03:40.321][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-04 16:03:40.322][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-10-04 16:03:40.323][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-10-04 16:03:40.324][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-10-04 16:03:40.325][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-10-04 16:03:40.326][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-10-04 16:03:40.327][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-10-04 16:03:40.328][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-10-04 16:03:40.330][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-10-04 16:03:40.331][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-10-04 16:03:40.332][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-10-04 16:03:40.332][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-10-04 16:03:40.333][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-10-04 16:03:40.334][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-10-04 16:03:40.335][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-10-04 16:03:40.336][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-10-04 16:03:40.337][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-10-04 16:03:40.338][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-10-04 16:03:40.339][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-10-04 16:03:40.340][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-10-04 16:03:40.341][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-10-04 16:03:40.342][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-10-04 16:03:40.343][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-10-04 16:03:40.344][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-10-04 16:03:40.344][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-10-04 16:03:40.344][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-10-04 16:03:40.344][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-10-04 16:03:40.344][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-10-04 16:03:40.345][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-10-04 16:03:40.345][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-04 16:03:40.346][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-04 16:03:40.347][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-10-04 16:03:40.348][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-04 16:03:40.349][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-04 16:03:40.350][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-10-04 16:03:40.351][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-10-04 16:03:40.352][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-10-04 16:03:40.352][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-10-04 16:03:40.353][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-10-04 16:03:40.354][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-10-04 16:03:40.355][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-10-04 16:03:40.357][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-10-04 16:03:40.358][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2025-10-04 16:03:40.359][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-10-04 16:03:40.360][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-10-04 16:03:40.361][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-10-04 16:03:40.362][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-10-04 16:03:40.363][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-10-04 16:03:40.364][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-10-04 16:03:40.364][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-10-04 16:03:40.365][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-10-04 16:03:40.366][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-10-04 16:03:40.367][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-10-04 16:03:40.368][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-10-04 16:03:40.369][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-10-04 16:03:40.370][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-10-04 16:03:40.371][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-10-04 16:03:40.372][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-10-04 16:03:40.373][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-04 16:03:40.374][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-04 16:03:40.375][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-10-04 16:03:40.375][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-04 16:03:40.376][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-04 16:03:40.377][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-10-04 16:03:40.378][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-10-04 16:03:40.379][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-10-04 16:03:40.380][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-10-04 16:03:40.381][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-10-04 16:03:40.382][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-10-04 16:03:40.383][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-10-04 16:03:40.384][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-10-04 16:03:40.385][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-10-04 16:03:40.386][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-10-04 16:03:40.387][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-10-04 16:03:40.388][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-10-04 16:03:40.389][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-10-04 16:03:40.390][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-10-04 16:03:40.391][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-10-04 16:03:40.392][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-10-04 16:03:40.393][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-10-04 16:03:40.394][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-10-04 16:03:40.395][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-10-04 16:03:40.396][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-10-04 16:03:40.397][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-10-04 16:03:40.397][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-10-04 16:03:40.398][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-10-04 16:03:40.399][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-10-04 16:03:40.400][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-04 16:03:40.401][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-04 16:03:40.402][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-10-04 16:03:40.407][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-04 16:03:40.407][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-04 16:03:40.408][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-10-04 16:03:40.409][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-10-04 16:03:40.410][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-10-04 16:03:40.411][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-10-04 16:03:40.412][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-10-04 16:03:40.413][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-10-04 16:03:40.414][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-10-04 16:03:40.415][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:03:40.416][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:03:40.417][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:03:40.417][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-04 16:03:40.418][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-04 16:03:40.419][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:03:40.420][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:03:40.421][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:03:40.422][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-04 16:03:40.422][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-04 16:03:40.423][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:03:40.424][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:03:40.425][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:03:40.426][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-04 16:03:40.427][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-04 16:03:40.427][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:03:40.428][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:03:40.429][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:03:40.430][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-04 16:03:40.431][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-04 16:03:40.432][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:03:40.432][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[2025-10-04 16:03:40.433][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:03:40.434][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-04 16:03:40.435][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-04 16:03:40.436][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:03:40.437][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:03:40.437][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:03:40.438][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-04 16:03:40.439][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-04 16:03:40.440][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:03:40.441][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:03:40.442][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:03:40.442][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-04 16:03:40.443][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-04 16:03:40.444][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:03:40.445][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:03:40.446][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:03:40.447][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-04 16:03:40.447][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-04 16:03:40.448][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:03:40.449][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:03:40.450][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:03:40.451][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-04 16:03:40.452][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-04 16:03:40.452][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:03:40.453][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:03:40.454][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:03:40.455][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-04 16:03:40.456][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-04 16:03:40.457][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:03:40.457][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:03:40.458][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:03:40.459][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-04 16:03:40.460][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-04 16:03:40.461][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:03:40.462][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:03:40.462][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:03:40.463][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-04 16:03:40.464][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-04 16:03:40.465][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:03:40.466][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:03:40.467][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:03:40.467][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-04 16:03:40.468][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-04 16:03:40.469][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:03:40.470][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:03:40.471][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:03:40.472][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-04 16:03:40.472][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-04 16:03:40.473][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:03:40.474][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:03:40.475][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:03:40.476][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-04 16:03:40.477][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-04 16:03:40.477][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:03:40.478][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:03:40.479][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:03:40.480][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-04 16:03:40.481][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-04 16:03:40.482][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:03:40.482][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:03:40.483][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-10-04 16:03:40.485][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-10-04 16:03:40.486][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-10-04 16:03:40.487][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-10-04 16:03:40.489][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-10-04 16:03:40.490][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-10-04 16:03:40.491][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-10-04 16:03:40.492][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-10-04 16:03:40.494][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-10-04 16:03:40.495][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-10-04 16:03:40.496][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-10-04 16:03:40.498][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-10-04 16:03:40.499][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-10-04 16:03:40.500][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-10-04 16:03:40.502][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-10-04 16:03:40.503][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-10-04 16:03:40.504][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-10-04 16:03:40.505][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-10-04 16:03:40.507][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-10-04 16:03:40.508][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-10-04 16:03:40.509][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-10-04 16:03:40.514][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-10-04 16:03:40.516][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-10-04 16:03:40.517][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-10-04 16:03:40.518][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-10-04 16:03:40.520][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-10-04 16:03:40.521][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-10-04 16:03:40.522][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-10-04 16:03:40.524][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-10-04 16:03:40.525][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-10-04 16:03:40.526][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-10-04 16:03:40.527][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-10-04 16:03:40.529][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-10-04 16:03:40.530][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-10-04 16:03:40.531][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-10-04 16:03:40.533][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-10-04 16:03:40.534][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-10-04 16:03:40.535][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-10-04 16:03:40.537][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-10-04 16:03:40.538][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-10-04 16:03:40.539][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-10-04 16:03:40.540][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-10-04 16:03:40.542][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-10-04 16:03:40.543][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-10-04 16:03:40.544][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-10-04 16:03:40.546][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-10-04 16:03:40.547][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-10-04 16:03:40.548][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-10-04 16:03:40.550][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-10-04 16:03:40.551][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-10-04 16:03:40.552][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-10-04 16:03:40.553][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-10-04 16:03:40.555][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-10-04 16:03:40.556][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-10-04 16:03:40.557][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-10-04 16:03:40.559][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-10-04 16:03:40.560][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-10-04 16:03:40.561][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-10-04 16:03:40.562][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-10-04 16:03:40.564][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-10-04 16:03:40.565][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-10-04 16:03:40.566][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-10-04 16:03:40.568][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-10-04 16:03:40.569][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-10-04 16:03:40.570][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-10-04 16:03:40.571][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-10-04 16:03:40.573][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-10-04 16:03:40.574][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-10-04 16:03:40.575][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-10-04 16:03:40.577][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-10-04 16:03:40.578][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-10-04 16:03:40.579][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-10-04 16:03:40.580][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-10-04 16:03:40.582][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-10-04 16:03:40.583][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-10-04 16:03:40.584][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-10-04 16:03:40.586][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-10-04 16:03:40.587][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-10-04 16:03:40.588][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-10-04 16:03:40.590][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-10-04 16:03:40.591][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-10-04 16:03:40.592][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-10-04 16:03:40.593][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-10-04 16:03:40.595][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-10-04 16:03:40.596][initialize] This is biodb version 1.17.2.
biodb.DEBUG[2025-10-04 16:03:40.597][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-10-04 16:03:40.598][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-10-04 16:03:40.599][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-04 16:03:40.600][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:03:40.601][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:03:40.601][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:03:40.602][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-04 16:03:40.603][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-04 16:03:40.604][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-04 16:03:40.605][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-04 16:03:40.606][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:03:40.606][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:03:40.607][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:03:40.608][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-04 16:03:40.609][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-04 16:03:40.610][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-04 16:03:40.611][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-04 16:03:40.611][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:03:40.612][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:03:40.613][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:03:40.614][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-04 16:03:40.615][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-04 16:03:40.616][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-04 16:03:40.616][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-04 16:03:40.621][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:03:40.622][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:03:40.623][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:03:40.624][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-04 16:03:40.625][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-04 16:03:40.626][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-04 16:03:40.626][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-04 16:03:40.627][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:03:40.628][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:03:40.629][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:03:40.630][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-04 16:03:40.631][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-04 16:03:40.632][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-04 16:03:40.632][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-04 16:03:40.633][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:03:40.634][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:03:40.635][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:03:40.636][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-04 16:03:40.637][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-04 16:03:40.637][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-04 16:03:40.638][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-04 16:03:40.639][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:03:40.640][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:03:40.641][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:03:40.642][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-04 16:03:40.643][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-04 16:03:40.643][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-04 16:03:40.644][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-04 16:03:40.645][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:03:40.646][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:03:40.647][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:03:40.648][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-04 16:03:40.648][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-04 16:03:40.649][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-04 16:03:40.650][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-04 16:03:40.651][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:03:40.652][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:03:40.653][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:03:40.653][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-04 16:03:40.654][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-04 16:03:40.655][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-04 16:03:40.656][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-04 16:03:40.657][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:03:40.657][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:03:40.658][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:03:40.659][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-04 16:03:40.660][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-04 16:03:40.661][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-04 16:03:40.662][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-04 16:03:40.662][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:03:40.663][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:03:40.664][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:03:40.665][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-04 16:03:40.666][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-04 16:03:40.667][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-04 16:03:40.667][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-04 16:03:40.668][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:03:40.669][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:03:40.670][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:03:40.671][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-04 16:03:40.672][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-04 16:03:40.672][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-04 16:03:40.673][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-04 16:03:40.674][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:03:40.675][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:03:40.676][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:03:40.677][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-04 16:03:40.677][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-04 16:03:40.678][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-04 16:03:40.679][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-04 16:03:40.680][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:03:40.681][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:03:40.682][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:03:40.682][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-04 16:03:40.683][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-04 16:03:40.684][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-04 16:03:40.685][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-04 16:03:40.686][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:03:40.687][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:03:40.687][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:03:40.688][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-04 16:03:40.689][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-04 16:03:40.690][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-04 16:03:40.691][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-04 16:03:40.692][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:03:40.692][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:03:40.693][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:03:40.694][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-04 16:03:40.695][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-04 16:03:40.696][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-04 16:03:40.697][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-04 16:03:40.697][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:03:40.698][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:03:40.700][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNci.Rcheck/biodbNci/definitions.yml".
biodb.DEBUG[2025-10-04 16:03:40.701][self$getDbsInfo()$define] Define connector nci.cactus.
biodb.DEBUG[2025-10-04 16:03:40.703][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-10-04 16:03:40.704][self$setPropertyValue] Setting property "description" to "National Cancer Institute (USA) CACTUS Database.".
biodb.DEBUG[2025-10-04 16:03:40.705][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-10-04 16:03:40.706][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-10-04 16:03:40.707][self$setPropertyValue] Setting property "downloadable" to "TRUE".
biodb.DEBUG[2025-10-04 16:03:40.707][self$setPropertyValue] Setting property "dwnld.ext" to "gz".
biodb.DEBUG[2025-10-04 16:03:40.708][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-10-04 16:03:40.709][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-10-04 16:03:40.710][self$setPropertyValue] Setting property "entry.content.type" to "sdf".
biodb.DEBUG[2025-10-04 16:03:40.711][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-10-04 16:03:40.712][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-10-04 16:03:40.713][self$setPropertyValue] Setting property "name" to "NCI CACTUS".
biodb.DEBUG[2025-10-04 16:03:40.714][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-10-04 16:03:40.715][self$setPropertyValue] Setting property "parsing.expr" to "NSC".
biodb.DEBUG[2025-10-04 16:03:40.715][self$setPropertyValue] Setting property "parsing.expr" to "DTP names".
biodb.DEBUG[2025-10-04 16:03:40.715][self$setPropertyValue] Setting property "parsing.expr" to "Standard InChI".
biodb.DEBUG[2025-10-04 16:03:40.715][self$setPropertyValue] Setting property "parsing.expr" to "c("Standard InChIKey", "^InChIKey=(.*)$")".
biodb.DEBUG[2025-10-04 16:03:40.715][self$setPropertyValue] Setting property "parsing.expr" to "Formula".
biodb.DEBUG[2025-10-04 16:03:40.715][self$setPropertyValue] Setting property "parsing.expr" to "Molecular Weight".
biodb.DEBUG[2025-10-04 16:03:40.715][self$setPropertyValue] Setting property "parsing.expr" to "CAS".
biodb.DEBUG[2025-10-04 16:03:40.716][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-10-04 16:03:40.717][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-10-04 16:03:40.718][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-10-04 16:03:40.719][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-04 16:03:40.720][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-04 16:03:40.721][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-10-04 16:03:40.721][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-04 16:03:40.722][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-04 16:03:40.723][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-10-04 16:03:40.724][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/".
biodb.DEBUG[2025-10-04 16:03:40.724][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/".
biodb.DEBUG[2025-10-04 16:03:40.724][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/download/nci/".
biodb.DEBUG[2025-10-04 16:03:40.724][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/download/nci/NCI-Open_2012-05-01.sdf.gz".
biodb.DEBUG[2025-10-04 16:03:40.725][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-10-04 16:03:40.730][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-10-04 16:03:40.731][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-10-04 16:03:40.732][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-10-04 16:03:40.733][self$getEntryFields()$define] Define field nci.cactus.id.
biodb.DEBUG[2025-10-04 16:03:40.736][super$initialize] Initialize connector nci.cactus.
biodb.DEBUG[2025-10-04 16:03:40.739][biodb$getFactory()$createConn] Creating new connector nci.cactus for database class nci.cactus .
biodb.INFO [2025-10-04 16:03:40.740][biodb$terminate] Closing BiodbMain instance...
biodb.INFO [2025-10-04 16:03:40.741][self$deleteConn] Connector "nci.cactus" deleted.
biodb.DEBUG[2025-10-04 16:03:40.742][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-10-04 16:03:40.743][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-04 16:03:40.743][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-04 16:03:40.744][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-04 16:03:40.745][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-04 16:03:40.746][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:03:40.747][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
[ FAIL 2 | WARN 0 | SKIP 0 | PASS 85 ]

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

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

'R CMD check' output

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


* using log directory ‘/home/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNci.Rcheck’
* using R version 4.5.1 Patched (2025-08-23 r88802)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* using options ‘--no-codoc --no-examples --no-manual --ignore-vignettes --no-stop-on-test-error’
* checking for file ‘biodbNci/DESCRIPTION’ ... OK
* this is package ‘biodbNci’ version ‘1.13.1’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘biodbNci’ can be installed ... OK
* used C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
* checking installed package size ... INFO
  installed size is  6.1Mb
  sub-directories of 1Mb or more:
    libs   5.8Mb
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking whether startup messages can be suppressed ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  NciCactusConn.Rd: BiodbConn
  NciCactusEntry.Rd: BiodbSdfEntry
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... SKIPPED
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... OK
* checking files in ‘vignettes’ ... SKIPPED
* checking examples ... SKIPPED
* checking for unstated dependencies in ‘longtests’ ... OK
* checking tests in ‘longtests’ ...
  Running ‘testthat.R’
 ERROR
Running the tests in ‘longtests/testthat.R’ failed.
Last 13 lines of output:
  Backtrace:
      ▆
   1. ├─base::do.call(fct, params)
   2. └─biodb (local) `<fn>`(conn = `<NcCctsCn>`, opt = `<named list>`)
   3.   └─opt$refEntries$getRealEntry(id)
   4.     └─self$getRealEntries(ids = id)
   5.       └─private$bdb$getFactory()$getEntry(...)
   6.         └─private$loadEntries(conn$getId(), missing.ids, drop = FALSE)
   7.           └─conn$getEntryContent(ids)
   8.             └─self$download()
   9.               └─private$doExtractDownload()
  
  [ FAIL 2 | WARN 0 | SKIP 0 | PASS 85 ]
  Error: Test failures
  Execution halted
* DONE

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

Installation output

biodbNci.Rcheck/00install.out

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