Back to Long Tests report for BioC 3.22

This page was generated on 2025-10-25 23:55 -0400 (Sat, 25 Oct 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" 4901
lconwaymacOS 12.7.6 Montereyx86_644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4691
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 8/31HostnameOS / ArchCHECK
biodbNci 1.13.1  (landing page)
Pierrick Roger
Snapshot Date: 2025-10-25 09:55 -0400 (Sat, 25 Oct 2025)
git_url: https://git.bioconductor.org/packages/biodbNci
git_branch: devel
git_last_commit: 658b5cb
git_last_commit_date: 2025-07-24 10:46:27 -0400 (Thu, 24 Jul 2025)
nebbiolo2Linux (Ubuntu 24.04.3 LTS) / x86_64  ERROR  
lconwaymacOS 12.7.6 Monterey / x86_64  ERROR  

CHECK results for biodbNci on nebbiolo2

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

raw results


Summary

Package: biodbNci
Version: 1.13.1
Command: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --test-dir=longtests --no-stop-on-test-error --no-codoc --no-examples --no-manual --ignore-vignettes --check-subdirs=no biodbNci_1.13.1.tar.gz
StartedAt: 2025-10-25 16:02:33 -0400 (Sat, 25 Oct 2025)
EndedAt: 2025-10-25 16:03:36 -0400 (Sat, 25 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 [2025-10-25 16:03:33.275][biodb::testContext]
biodb.INFO [2025-10-25 16:03:33.277][biodb::testContext] ********************************************************************************
biodb.INFO [2025-10-25 16:03:33.277][biodb::testContext] Test context - Generic long tests
biodb.INFO [2025-10-25 16:03:33.278][biodb::testContext] ********************************************************************************
biodb.INFO [2025-10-25 16:03:33.279][biodb::testContext]
biodb.INFO [2025-10-25 16:03:33.285][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.17.2.
biodb.DEBUG[2025-10-25 16:03:33.287][self$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.22-bioc/R/site-library/biodb/definitions.yml".
biodb.DEBUG[2025-10-25 16:03:33.294][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-10-25 16:03:33.295][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-10-25 16:03:33.296][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-10-25 16:03:33.297][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-25 16:03:33.298][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-25 16:03:33.299][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-25 16:03:33.300][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-10-25 16:03:33.317][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-10-25 16:03:33.318][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-25 16:03:33.326][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-25 16:03:33.327][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-25 16:03:33.328][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-10-25 16:03:33.329][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-10-25 16:03:33.330][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-25 16:03:33.331][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-25 16:03:33.331][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-25 16:03:33.332][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-10-25 16:03:33.333][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-10-25 16:03:33.334][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-10-25 16:03:33.335][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-25 16:03:33.336][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-25 16:03:33.337][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-25 16:03:33.337][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-10-25 16:03:33.338][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-10-25 16:03:33.339][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-10-25 16:03:33.340][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-25 16:03:33.341][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-25 16:03:33.342][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-25 16:03:33.343][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-10-25 16:03:33.344][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-10-25 16:03:33.344][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-25 16:03:33.345][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-25 16:03:33.346][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-25 16:03:33.347][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-10-25 16:03:33.348][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-10-25 16:03:33.349][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-10-25 16:03:33.350][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-25 16:03:33.351][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-25 16:03:33.351][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-25 16:03:33.352][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-10-25 16:03:33.353][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-10-25 16:03:33.354][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-25 16:03:33.355][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-25 16:03:33.356][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-25 16:03:33.356][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-10-25 16:03:33.357][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-10-25 16:03:33.358][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-10-25 16:03:33.359][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-25 16:03:33.360][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-25 16:03:33.361][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-25 16:03:33.362][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-10-25 16:03:33.363][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-10-25 16:03:33.364][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-10-25 16:03:33.364][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-10-25 16:03:33.365][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-10-25 16:03:33.366][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-10-25 16:03:33.367][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-25 16:03:33.368][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-25 16:03:33.369][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-25 16:03:33.370][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-10-25 16:03:33.371][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-10-25 16:03:33.371][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-25 16:03:33.372][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-25 16:03:33.373][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-25 16:03:33.374][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-10-25 16:03:33.375][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-10-25 16:03:33.376][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-25 16:03:33.377][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-25 16:03:33.377][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-25 16:03:33.378][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-10-25 16:03:33.379][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-10-25 16:03:33.380][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-25 16:03:33.381][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-25 16:03:33.382][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-25 16:03:33.383][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-10-25 16:03:33.383][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-10-25 16:03:33.384][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-10-25 16:03:33.385][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-25 16:03:33.386][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-25 16:03:33.387][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-25 16:03:33.388][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-10-25 16:03:33.389][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-10-25 16:03:33.393][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-10-25 16:03:33.394][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-25 16:03:33.395][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-25 16:03:33.395][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-25 16:03:33.396][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-10-25 16:03:33.397][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-10-25 16:03:33.398][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-10-25 16:03:33.399][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-25 16:03:33.400][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-25 16:03:33.401][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-25 16:03:33.404][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-10-25 16:03:33.434][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-10-25 16:03:33.448][self$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[2025-10-25 16:03:33.449][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-10-25 16:03:33.450][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-10-25 16:03:33.451][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-10-25 16:03:33.452][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-10-25 16:03:33.453][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-10-25 16:03:33.454][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-10-25 16:03:33.455][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-10-25 16:03:33.456][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-10-25 16:03:33.457][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-10-25 16:03:33.457][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-10-25 16:03:33.458][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-10-25 16:03:33.459][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-10-25 16:03:33.460][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-10-25 16:03:33.461][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-10-25 16:03:33.461][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-10-25 16:03:33.461][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-10-25 16:03:33.461][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-10-25 16:03:33.461][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-10-25 16:03:33.462][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-10-25 16:03:33.463][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-25 16:03:33.464][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-25 16:03:33.465][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-10-25 16:03:33.466][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-25 16:03:33.466][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-25 16:03:33.467][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-10-25 16:03:33.468][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-10-25 16:03:33.469][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-10-25 16:03:33.470][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-10-25 16:03:33.471][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-10-25 16:03:33.472][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-10-25 16:03:33.473][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-10-25 16:03:33.479][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-10-25 16:03:33.479][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-10-25 16:03:33.480][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-10-25 16:03:33.481][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-10-25 16:03:33.482][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-10-25 16:03:33.483][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-10-25 16:03:33.484][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-10-25 16:03:33.485][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-10-25 16:03:33.486][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-10-25 16:03:33.487][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-10-25 16:03:33.488][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-10-25 16:03:33.489][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-10-25 16:03:33.489][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-10-25 16:03:33.490][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-10-25 16:03:33.491][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-10-25 16:03:33.492][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-10-25 16:03:33.492][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-10-25 16:03:33.492][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-10-25 16:03:33.492][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-10-25 16:03:33.492][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-10-25 16:03:33.493][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-10-25 16:03:33.494][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-25 16:03:33.495][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-25 16:03:33.496][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-10-25 16:03:33.497][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-25 16:03:33.498][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-25 16:03:33.498][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-10-25 16:03:33.499][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-10-25 16:03:33.500][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-10-25 16:03:33.501][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-10-25 16:03:33.502][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-10-25 16:03:33.503][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-10-25 16:03:33.504][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-10-25 16:03:33.506][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-10-25 16:03:33.507][self$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[2025-10-25 16:03:33.507][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-10-25 16:03:33.508][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-10-25 16:03:33.509][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-10-25 16:03:33.510][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-10-25 16:03:33.511][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-10-25 16:03:33.512][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-10-25 16:03:33.513][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-10-25 16:03:33.514][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-10-25 16:03:33.515][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-10-25 16:03:33.516][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-10-25 16:03:33.517][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-10-25 16:03:33.518][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-10-25 16:03:33.519][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-10-25 16:03:33.519][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-10-25 16:03:33.520][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-10-25 16:03:33.521][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-25 16:03:33.522][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-25 16:03:33.523][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-10-25 16:03:33.524][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-25 16:03:33.525][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-25 16:03:33.526][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-10-25 16:03:33.526][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-10-25 16:03:33.527][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-10-25 16:03:33.528][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-10-25 16:03:33.529][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-10-25 16:03:33.530][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-10-25 16:03:33.531][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-10-25 16:03:33.533][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-10-25 16:03:33.534][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-10-25 16:03:33.534][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-10-25 16:03:33.535][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-10-25 16:03:33.536][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-10-25 16:03:33.537][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-10-25 16:03:33.538][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-10-25 16:03:33.539][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-10-25 16:03:33.540][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-10-25 16:03:33.541][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-10-25 16:03:33.542][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-10-25 16:03:33.543][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-10-25 16:03:33.544][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-10-25 16:03:33.545][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-10-25 16:03:33.545][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-10-25 16:03:33.546][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-10-25 16:03:33.547][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-10-25 16:03:33.548][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-25 16:03:33.549][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-25 16:03:33.550][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-10-25 16:03:33.551][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-25 16:03:33.552][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-25 16:03:33.553][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-10-25 16:03:33.553][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-10-25 16:03:33.554][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-10-25 16:03:33.555][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-10-25 16:03:33.556][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-10-25 16:03:33.557][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-10-25 16:03:33.560][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-10-25 16:03:33.561][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-10-25 16:03:33.562][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-25 16:03:33.563][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-25 16:03:33.564][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-25 16:03:33.565][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-25 16:03:33.565][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-25 16:03:33.566][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-25 16:03:33.567][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-25 16:03:33.568][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-25 16:03:33.569][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-25 16:03:33.570][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-25 16:03:33.570][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-25 16:03:33.571][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-25 16:03:33.572][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-25 16:03:33.573][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-25 16:03:33.574][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-25 16:03:33.574][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-25 16:03:33.575][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-25 16:03:33.576][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-25 16:03:33.577][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-25 16:03:33.578][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-25 16:03:33.579][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-25 16:03:33.579][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-25 16:03:33.580][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-25 16:03:33.581][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-25 16:03:33.582][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-25 16:03:33.583][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-25 16:03:33.583][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-25 16:03:33.584][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-25 16:03:33.585][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-25 16:03:33.586][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-25 16:03:33.587][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-25 16:03:33.588][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-25 16:03:33.588][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-25 16:03:33.589][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-25 16:03:33.590][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-25 16:03:33.591][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-25 16:03:33.592][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-25 16:03:33.592][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-25 16:03:33.593][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-25 16:03:33.594][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-25 16:03:33.595][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-25 16:03:33.596][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-25 16:03:33.597][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-25 16:03:33.597][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-25 16:03:33.598][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-25 16:03:33.599][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-25 16:03:33.600][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-25 16:03:33.601][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-25 16:03:33.602][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-25 16:03:33.602][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-25 16:03:33.603][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-25 16:03:33.604][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-25 16:03:33.605][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-25 16:03:33.606][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-25 16:03:33.606][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-25 16:03:33.607][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-25 16:03:33.608][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-25 16:03:33.609][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-25 16:03:33.610][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-25 16:03:33.611][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-25 16:03:33.611][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-25 16:03:33.612][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-25 16:03:33.613][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-25 16:03:33.614][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-25 16:03:33.615][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-25 16:03:33.615][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-25 16:03:33.616][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-25 16:03:33.617][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-25 16:03:33.618][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-25 16:03:33.619][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-25 16:03:33.620][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-25 16:03:33.620][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-25 16:03:33.621][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-25 16:03:33.622][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-25 16:03:33.623][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-25 16:03:33.624][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-25 16:03:33.624][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-25 16:03:33.625][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-25 16:03:33.630][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-25 16:03:33.630][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-25 16:03:33.631][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-25 16:03:33.632][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-10-25 16:03:33.636][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-10-25 16:03:33.638][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-10-25 16:03:33.639][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-10-25 16:03:33.640][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-10-25 16:03:33.642][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-10-25 16:03:33.643][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-10-25 16:03:33.644][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-10-25 16:03:33.645][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-10-25 16:03:33.647][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-10-25 16:03:33.648][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-10-25 16:03:33.649][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-10-25 16:03:33.651][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-10-25 16:03:33.652][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-10-25 16:03:33.653][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-10-25 16:03:33.654][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-10-25 16:03:33.656][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-10-25 16:03:33.657][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-10-25 16:03:33.658][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-10-25 16:03:33.660][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-10-25 16:03:33.661][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-10-25 16:03:33.662][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-10-25 16:03:33.663][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-10-25 16:03:33.665][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-10-25 16:03:33.666][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-10-25 16:03:33.667][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-10-25 16:03:33.669][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-10-25 16:03:33.670][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-10-25 16:03:33.671][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-10-25 16:03:33.672][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-10-25 16:03:33.674][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-10-25 16:03:33.675][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-10-25 16:03:33.676][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-10-25 16:03:33.678][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-10-25 16:03:33.679][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-10-25 16:03:33.680][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-10-25 16:03:33.681][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-10-25 16:03:33.683][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-10-25 16:03:33.684][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-10-25 16:03:33.685][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-10-25 16:03:33.687][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-10-25 16:03:33.688][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-10-25 16:03:33.689][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-10-25 16:03:33.690][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-10-25 16:03:33.692][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-10-25 16:03:33.693][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-10-25 16:03:33.694][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-10-25 16:03:33.696][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-10-25 16:03:33.697][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-10-25 16:03:33.698][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-10-25 16:03:33.699][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-10-25 16:03:33.701][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-10-25 16:03:33.702][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-10-25 16:03:33.703][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-10-25 16:03:33.705][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-10-25 16:03:33.706][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-10-25 16:03:33.707][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-10-25 16:03:33.708][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-10-25 16:03:33.710][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-10-25 16:03:33.711][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-10-25 16:03:33.712][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-10-25 16:03:33.714][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-10-25 16:03:33.715][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-10-25 16:03:33.716][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-10-25 16:03:33.717][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-10-25 16:03:33.719][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-10-25 16:03:33.720][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-10-25 16:03:33.721][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-10-25 16:03:33.722][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-10-25 16:03:33.724][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-10-25 16:03:33.725][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-10-25 16:03:33.726][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-10-25 16:03:33.728][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-10-25 16:03:33.729][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-10-25 16:03:33.730][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-10-25 16:03:33.731][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-10-25 16:03:33.740][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-10-25 16:03:33.741][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-10-25 16:03:33.743][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-10-25 16:03:33.744][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-10-25 16:03:33.746][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-10-25 16:03:33.747][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-10-25 16:03:33.749][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-10-25 16:03:33.756][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-10-25 16:03:33.758][initialize] This is biodb version 1.17.2.
biodb.DEBUG[2025-10-25 16:03:33.762][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-10-25 16:03:33.763][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-10-25 16:03:33.764][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-25 16:03:33.764][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-10-25 16:03:33.765][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-25 16:03:33.770][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-25 16:03:33.771][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-25 16:03:33.772][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-25 16:03:33.773][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-25 16:03:33.774][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-25 16:03:33.775][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-25 16:03:33.776][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-25 16:03:33.777][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-25 16:03:33.778][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-25 16:03:33.779][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-25 16:03:33.779][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-25 16:03:33.780][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-25 16:03:33.781][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-25 16:03:33.782][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-25 16:03:33.783][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-25 16:03:33.784][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-25 16:03:33.785][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-25 16:03:33.786][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-25 16:03:33.787][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-25 16:03:33.802][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-25 16:03:33.803][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-25 16:03:33.804][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-25 16:03:33.805][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-25 16:03:33.806][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-25 16:03:33.807][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-25 16:03:33.808][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-25 16:03:33.809][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-25 16:03:33.810][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-25 16:03:33.811][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-25 16:03:33.812][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-25 16:03:33.812][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-25 16:03:33.813][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-25 16:03:33.814][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-25 16:03:33.815][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-25 16:03:33.816][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-25 16:03:33.817][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-25 16:03:33.818][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-25 16:03:33.819][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-25 16:03:33.820][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-25 16:03:33.821][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-25 16:03:33.822][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-25 16:03:33.822][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-25 16:03:33.823][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-25 16:03:33.824][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-25 16:03:33.825][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-25 16:03:33.826][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-25 16:03:33.827][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-25 16:03:33.828][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-25 16:03:33.829][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-25 16:03:33.830][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-25 16:03:33.831][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-25 16:03:33.831][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-25 16:03:33.832][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-25 16:03:33.833][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-25 16:03:33.834][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-25 16:03:33.835][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-25 16:03:33.836][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-25 16:03:33.837][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-25 16:03:33.838][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-25 16:03:33.839][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-25 16:03:33.839][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-25 16:03:33.840][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-25 16:03:33.841][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-25 16:03:33.842][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-25 16:03:33.843][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-25 16:03:33.844][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-25 16:03:33.845][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-25 16:03:33.846][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-25 16:03:33.847][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-25 16:03:33.847][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-25 16:03:33.848][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-25 16:03:33.849][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-25 16:03:33.850][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-25 16:03:33.851][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-25 16:03:33.852][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-25 16:03:33.853][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-25 16:03:33.854][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-25 16:03:33.855][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-25 16:03:33.856][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-25 16:03:33.856][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-25 16:03:33.857][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-25 16:03:33.858][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-25 16:03:33.859][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-25 16:03:33.860][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-25 16:03:33.861][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-25 16:03:33.862][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-25 16:03:33.863][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-25 16:03:33.864][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-25 16:03:33.864][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-25 16:03:33.865][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-25 16:03:33.866][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-25 16:03:33.867][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-25 16:03:33.868][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-25 16:03:33.869][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-25 16:03:33.870][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-25 16:03:33.871][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-25 16:03:33.872][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-25 16:03:33.872][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-25 16:03:33.873][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-25 16:03:33.874][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-25 16:03:33.875][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-25 16:03:33.876][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-25 16:03:33.877][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-25 16:03:33.878][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-25 16:03:33.879][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-25 16:03:33.880][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-25 16:03:33.880][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-25 16:03:33.881][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-25 16:03:33.882][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-25 16:03:33.883][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-25 16:03:33.884][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-25 16:03:33.885][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-25 16:03:33.887][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNci.Rcheck/biodbNci/definitions.yml".
biodb.DEBUG[2025-10-25 16:03:33.896][self$getDbsInfo()$define] Define connector nci.cactus.
biodb.DEBUG[2025-10-25 16:03:33.898][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-10-25 16:03:33.899][self$setPropertyValue] Setting property "description" to "National Cancer Institute (USA) CACTUS Database.".
biodb.DEBUG[2025-10-25 16:03:33.900][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-10-25 16:03:33.901][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-10-25 16:03:33.902][self$setPropertyValue] Setting property "downloadable" to "TRUE".
biodb.DEBUG[2025-10-25 16:03:33.903][self$setPropertyValue] Setting property "dwnld.ext" to "gz".
biodb.DEBUG[2025-10-25 16:03:33.904][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-10-25 16:03:33.905][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-10-25 16:03:33.906][self$setPropertyValue] Setting property "entry.content.type" to "sdf".
biodb.DEBUG[2025-10-25 16:03:33.907][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-10-25 16:03:33.908][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-10-25 16:03:33.909][self$setPropertyValue] Setting property "name" to "NCI CACTUS".
biodb.DEBUG[2025-10-25 16:03:33.910][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-10-25 16:03:33.911][self$setPropertyValue] Setting property "parsing.expr" to "NSC".
biodb.DEBUG[2025-10-25 16:03:33.911][self$setPropertyValue] Setting property "parsing.expr" to "DTP names".
biodb.DEBUG[2025-10-25 16:03:33.911][self$setPropertyValue] Setting property "parsing.expr" to "Standard InChI".
biodb.DEBUG[2025-10-25 16:03:33.911][self$setPropertyValue] Setting property "parsing.expr" to "c("Standard InChIKey", "^InChIKey=(.*)$")".
biodb.DEBUG[2025-10-25 16:03:33.911][self$setPropertyValue] Setting property "parsing.expr" to "Formula".
biodb.DEBUG[2025-10-25 16:03:33.911][self$setPropertyValue] Setting property "parsing.expr" to "Molecular Weight".
biodb.DEBUG[2025-10-25 16:03:33.911][self$setPropertyValue] Setting property "parsing.expr" to "CAS".
biodb.DEBUG[2025-10-25 16:03:33.912][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-10-25 16:03:33.913][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-10-25 16:03:33.914][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-10-25 16:03:33.915][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-25 16:03:33.916][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-25 16:03:33.917][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-10-25 16:03:33.918][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-25 16:03:33.918][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-25 16:03:33.919][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-10-25 16:03:33.920][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/".
biodb.DEBUG[2025-10-25 16:03:33.920][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/".
biodb.DEBUG[2025-10-25 16:03:33.920][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/download/nci/".
biodb.DEBUG[2025-10-25 16:03:33.920][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/download/nci/NCI-Open_2012-05-01.sdf.gz".
biodb.DEBUG[2025-10-25 16:03:33.921][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-10-25 16:03:33.922][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-10-25 16:03:33.923][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-10-25 16:03:33.924][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-10-25 16:03:33.929][self$getEntryFields()$define] Define field nci.cactus.id.
biodb.DEBUG[2025-10-25 16:03:33.950][super$initialize] Initialize connector nci.cactus.
biodb.DEBUG[2025-10-25 16:03:33.971][biodb$getFactory()$createConn] Creating new connector nci.cactus for database class nci.cactus .
biodb.INFO [2025-10-25 16:03:33.979][biodb::testThat]
biodb.INFO [2025-10-25 16:03:33.980][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2025-10-25 16:03:33.981][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-10-25 16:03:33.982][biodb::testThat]
biodb.TRACE[2025-10-25 16:03:33.985][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNci.Rcheck/biodbNci/testref/entry-nci.cactus-749674-content.sdf".
biodb.DEBUG[2025-10-25 16:03:33.987][biodb$getFactory()$createEntryFromCo ...] Creating NCI CACTUS entries from 1 content(s).
biodb.DEBUG[2025-10-25 16:03:33.990][biodb$getFactory()$createEntryFromCo ...] Parsing 1 NCI CACTUS entries.
biodb.DEBUG[2025-10-25 16:03:33.997][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-10-25 16:03:33.997][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-25 16:03:33.998][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-25 16:03:34.009][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-10-25 16:03:34.010][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-25 16:03:34.011][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-10-25 16:03:34.012][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-10-25 16:03:34.028][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-25 16:03:34.029][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-25 16:03:34.030][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:03:34.031][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:03:34.032][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-25 16:03:34.043][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-25 16:03:34.044][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:03:34.045][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:03:34.047][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-10-25 16:03:34.048][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-10-25 16:03:34.049][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:03:34.050][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:03:34.074][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-10-25 16:03:34.075][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-10-25 16:03:34.076][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:03:34.077][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:03:34.078][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-10-25 16:03:34.079][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-10-25 16:03:34.080][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:03:34.081][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:03:34.082][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-10-25 16:03:34.083][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-10-25 16:03:34.084][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:03:34.085][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:03:34.087][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-10-25 16:03:34.088][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-10-25 16:03:34.089][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:03:34.090][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:03:34.091][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-10-25 16:03:34.092][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-10-25 16:03:34.093][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:03:34.093][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:03:34.095][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-10-25 16:03:34.096][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-10-25 16:03:34.097][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:03:34.098][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:03:34.099][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-10-25 16:03:34.100][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-10-25 16:03:34.101][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:03:34.102][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:03:34.103][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-10-25 16:03:34.111][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-10-25 16:03:34.112][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:03:34.113][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:03:34.114][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-10-25 16:03:34.115][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-10-25 16:03:34.115][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:03:34.116][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:03:34.117][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-25 16:03:34.118][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-25 16:03:34.119][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:03:34.120][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:03:34.121][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-10-25 16:03:34.122][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-10-25 16:03:34.123][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:03:34.124][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:03:34.125][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-25 16:03:34.126][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-25 16:03:34.127][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:03:34.128][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:03:34.129][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-25 16:03:34.129][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-25 16:03:34.130][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:03:34.131][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:03:34.132][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-25 16:03:34.133][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-25 16:03:34.134][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:03:34.135][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:03:34.166][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-25 16:03:34.167][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-25 16:03:34.168][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:03:34.169][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:03:34.170][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-25 16:03:34.171][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-25 16:03:34.172][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:03:34.173][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:03:34.173][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-25 16:03:34.174][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-25 16:03:34.175][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:03:34.176][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-10-25 16:03:34.177][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 749674.
biodb.TRACE[2025-10-25 16:03:34.179][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-10-25 16:03:34.180][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-10-25 16:03:34.181][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:03:34.182][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:03:34.183][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-10-25 16:03:34.184][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-10-25 16:03:34.185][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:03:34.186][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:03:34.187][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-10-25 16:03:34.188][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-10-25 16:03:34.189][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:03:34.190][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:03:34.190][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-10-25 16:03:34.191][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-10-25 16:03:34.192][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:03:34.193][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:03:34.195][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-25 16:03:34.196][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-25 16:03:34.197][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:03:34.198][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:03:34.210][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-10-25 16:03:34.211][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-10-25 16:03:34.212][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:03:34.213][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:03:34.259][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-25 16:03:34.260][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-25 16:03:34.261][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:03:34.262][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:03:34.263][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-25 16:03:34.264][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-25 16:03:34.265][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:03:34.266][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:03:34.267][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-25 16:03:34.268][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-25 16:03:34.269][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:03:34.270][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:03:34.272][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-25 16:03:34.273][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-25 16:03:34.274][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:03:34.275][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:03:34.276][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-25 16:03:34.277][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-25 16:03:34.278][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:03:34.279][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:03:34.280][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-25 16:03:34.281][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-25 16:03:34.281][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:03:34.282][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:03:34.284][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-10-25 16:03:34.285][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-10-25 16:03:34.285][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:03:34.286][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:03:34.287][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-10-25 16:03:34.288][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-10-25 16:03:34.289][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:03:34.290][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:03:34.291][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-10-25 16:03:34.292][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-10-25 16:03:34.293][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:03:34.294][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:03:34.301][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-25 16:03:34.302][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-25 16:03:34.303][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:03:34.304][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:03:34.305][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-25 16:03:34.306][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-25 16:03:34.306][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:03:34.307][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:03:34.308][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-25 16:03:34.309][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-25 16:03:34.310][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:03:34.311][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:03:34.312][ef$get] Asked field names are: accession.
biodb.TRACE[2025-10-25 16:03:34.313][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-25 16:03:34.314][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:03:34.315][ef$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:03:34.316][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-25 16:03:34.317][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-25 16:03:34.318][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:03:34.319][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:03:34.326][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-10-25 16:03:34.327][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-10-25 16:03:34.328][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:03:34.329][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:03:34.330][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-10-25 16:03:34.331][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-10-25 16:03:34.332][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:03:34.333][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:03:34.334][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-10-25 16:03:34.335][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-10-25 16:03:34.336][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:03:34.337][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:03:34.337][ef$get] Asked field names are: formula.
biodb.TRACE[2025-10-25 16:03:34.338][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-10-25 16:03:34.339][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:03:34.340][ef$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:03:34.341][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-10-25 16:03:34.342][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-10-25 16:03:34.343][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:03:34.344][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:03:34.351][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-10-25 16:03:34.352][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-10-25 16:03:34.353][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:03:34.354][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:03:34.355][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-10-25 16:03:34.356][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-10-25 16:03:34.357][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:03:34.358][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:03:34.359][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-10-25 16:03:34.360][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-10-25 16:03:34.361][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:03:34.361][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:03:34.362][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-10-25 16:03:34.363][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-10-25 16:03:34.364][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:03:34.365][ef$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:03:34.366][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-10-25 16:03:34.367][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-10-25 16:03:34.368][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:03:34.369][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:03:34.380][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-10-25 16:03:34.381][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-10-25 16:03:34.382][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:03:34.383][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:03:34.384][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-10-25 16:03:34.385][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-10-25 16:03:34.386][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:03:34.387][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:03:34.388][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-10-25 16:03:34.389][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-10-25 16:03:34.390][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:03:34.390][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:03:34.391][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-10-25 16:03:34.392][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-10-25 16:03:34.393][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:03:34.394][ef$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:03:34.395][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-10-25 16:03:34.396][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-10-25 16:03:34.397][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:03:34.398][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:03:34.405][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-10-25 16:03:34.406][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-10-25 16:03:34.407][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:03:34.408][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:03:34.409][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-10-25 16:03:34.410][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-10-25 16:03:34.411][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:03:34.411][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:03:34.412][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-10-25 16:03:34.413][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-10-25 16:03:34.414][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:03:34.415][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:03:34.416][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-10-25 16:03:34.417][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-10-25 16:03:34.418][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:03:34.419][ef$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:03:34.420][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-10-25 16:03:34.421][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-10-25 16:03:34.422][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:03:34.422][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:03:34.430][ef$get] Asked field names are: accession.
biodb.TRACE[2025-10-25 16:03:34.431][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-25 16:03:34.431][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:03:34.432][ef$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:03:34.436][ef$get] Asked field names are: formula.
biodb.TRACE[2025-10-25 16:03:34.437][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-10-25 16:03:34.438][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:03:34.439][ef$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:03:34.442][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-10-25 16:03:34.443][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-10-25 16:03:34.444][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:03:34.445][ef$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:03:34.449][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-10-25 16:03:34.450][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-10-25 16:03:34.451][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:03:34.452][ef$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:03:34.455][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-10-25 16:03:34.456][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-10-25 16:03:34.457][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:03:34.458][ef$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:03:34.473][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNci.Rcheck/biodbNci/testref/entry-nci.cactus-750690-content.sdf".
biodb.DEBUG[2025-10-25 16:03:34.509][biodb$getFactory()$createEntryFromCo ...] Creating NCI CACTUS entries from 1 content(s).
biodb.DEBUG[2025-10-25 16:03:34.511][biodb$getFactory()$createEntryFromCo ...] Parsing 1 NCI CACTUS entries.
biodb.DEBUG[2025-10-25 16:03:34.512][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-10-25 16:03:34.513][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-25 16:03:34.514][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-25 16:03:34.518][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-10-25 16:03:34.518][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-25 16:03:34.519][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-10-25 16:03:34.520][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-10-25 16:03:34.529][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-25 16:03:34.530][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-25 16:03:34.531][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:03:34.532][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:03:34.533][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-25 16:03:34.534][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-25 16:03:34.535][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:03:34.535][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:03:34.553][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-10-25 16:03:34.554][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-10-25 16:03:34.555][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:03:34.555][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:03:34.556][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-10-25 16:03:34.557][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-10-25 16:03:34.558][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:03:34.559][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:03:34.561][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-10-25 16:03:34.562][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-10-25 16:03:34.563][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:03:34.563][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:03:34.564][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-10-25 16:03:34.565][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-10-25 16:03:34.566][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:03:34.567][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:03:34.568][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-10-25 16:03:34.569][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-10-25 16:03:34.570][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:03:34.571][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:03:34.572][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-10-25 16:03:34.573][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-10-25 16:03:34.574][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:03:34.575][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:03:34.576][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-10-25 16:03:34.577][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-10-25 16:03:34.578][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:03:34.579][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:03:34.580][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-10-25 16:03:34.581][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-10-25 16:03:34.582][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:03:34.582][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:03:34.584][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-10-25 16:03:34.585][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-10-25 16:03:34.585][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:03:34.586][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:03:34.587][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-10-25 16:03:34.588][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-10-25 16:03:34.593][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:03:34.593][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:03:34.594][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-10-25 16:03:34.595][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-10-25 16:03:34.596][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:03:34.597][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:03:34.598][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-10-25 16:03:34.599][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-10-25 16:03:34.600][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:03:34.601][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:03:34.602][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-10-25 16:03:34.603][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-10-25 16:03:34.604][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:03:34.604][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:03:34.606][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-10-25 16:03:34.607][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-10-25 16:03:34.608][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:03:34.609][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:03:34.610][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-10-25 16:03:34.611][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-10-25 16:03:34.612][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:03:34.613][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:03:34.614][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-10-25 16:03:34.615][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-10-25 16:03:34.616][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:03:34.617][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:03:34.618][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-10-25 16:03:34.619][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-10-25 16:03:34.620][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:03:34.620][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:03:34.622][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-10-25 16:03:34.623][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-10-25 16:03:34.624][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:03:34.625][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:03:34.626][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-10-25 16:03:34.627][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-10-25 16:03:34.628][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:03:34.628][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:03:34.629][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-25 16:03:34.630][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-25 16:03:34.631][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:03:34.632][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:03:34.633][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-10-25 16:03:34.634][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-10-25 16:03:34.635][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:03:34.636][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:03:34.637][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-25 16:03:34.638][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-25 16:03:34.639][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:03:34.639][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:03:34.640][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-25 16:03:34.641][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-25 16:03:34.642][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:03:34.643][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:03:34.644][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-25 16:03:34.645][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-25 16:03:34.646][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:03:34.647][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:03:34.648][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-25 16:03:34.649][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-25 16:03:34.650][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:03:34.651][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:03:34.651][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-25 16:03:34.652][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-25 16:03:34.653][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:03:34.654][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:03:34.655][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-25 16:03:34.656][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-25 16:03:34.657][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:03:34.658][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-10-25 16:03:34.659][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 750690.
biodb.TRACE[2025-10-25 16:03:34.678][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-10-25 16:03:34.679][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-10-25 16:03:34.680][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:03:34.681][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:03:34.682][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-10-25 16:03:34.683][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-10-25 16:03:34.684][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:03:34.684][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:03:34.685][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-10-25 16:03:34.686][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-10-25 16:03:34.687][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:03:34.688][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:03:34.689][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-10-25 16:03:34.690][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-10-25 16:03:34.691][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:03:34.692][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:03:34.694][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-25 16:03:34.694][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-25 16:03:34.695][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:03:34.696][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:03:34.700][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-10-25 16:03:34.705][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-10-25 16:03:34.706][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:03:34.707][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:03:34.711][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-25 16:03:34.712][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-25 16:03:34.712][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:03:34.713][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:03:34.714][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-25 16:03:34.715][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-25 16:03:34.716][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:03:34.717][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:03:34.718][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-25 16:03:34.719][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-25 16:03:34.720][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:03:34.721][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:03:34.723][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-25 16:03:34.724][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-25 16:03:34.725][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:03:34.726][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:03:34.727][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-25 16:03:34.728][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-25 16:03:34.729][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:03:34.729][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:03:34.730][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-25 16:03:34.731][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-25 16:03:34.732][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:03:34.733][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:03:34.734][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-10-25 16:03:34.735][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-10-25 16:03:34.736][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:03:34.737][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:03:34.738][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-10-25 16:03:34.739][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-10-25 16:03:34.740][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:03:34.741][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:03:34.742][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-10-25 16:03:34.742][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-10-25 16:03:34.743][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:03:34.744][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:03:34.759][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-25 16:03:34.760][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-25 16:03:34.761][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:03:34.762][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:03:34.763][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-25 16:03:34.764][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-25 16:03:34.765][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:03:34.766][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:03:34.767][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-25 16:03:34.768][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-25 16:03:34.768][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:03:34.769][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:03:34.770][ef$get] Asked field names are: accession.
biodb.TRACE[2025-10-25 16:03:34.771][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-25 16:03:34.772][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:03:34.773][ef$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:03:34.774][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-25 16:03:34.775][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-25 16:03:34.776][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:03:34.777][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:03:34.784][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-10-25 16:03:34.785][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-10-25 16:03:34.786][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:03:34.787][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:03:34.787][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-10-25 16:03:34.788][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-10-25 16:03:34.789][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:03:34.790][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:03:34.791][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-10-25 16:03:34.792][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-10-25 16:03:34.793][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:03:34.794][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:03:34.795][ef$get] Asked field names are: cas.id.
biodb.TRACE[2025-10-25 16:03:34.796][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-10-25 16:03:34.797][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:03:34.798][ef$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:03:34.798][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-10-25 16:03:34.799][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-10-25 16:03:34.800][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:03:34.801][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:03:34.808][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-10-25 16:03:34.809][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-10-25 16:03:34.810][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:03:34.811][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:03:34.812][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-10-25 16:03:34.816][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-10-25 16:03:34.817][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:03:34.818][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:03:34.819][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-10-25 16:03:34.820][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-10-25 16:03:34.821][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:03:34.822][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:03:34.823][ef$get] Asked field names are: name.
biodb.TRACE[2025-10-25 16:03:34.824][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-10-25 16:03:34.825][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:03:34.826][ef$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:03:34.827][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-10-25 16:03:34.828][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-10-25 16:03:34.828][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:03:34.829][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:03:34.837][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-10-25 16:03:34.838][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-10-25 16:03:34.838][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:03:34.839][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:03:34.840][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-10-25 16:03:34.841][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-10-25 16:03:34.842][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:03:34.843][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:03:34.844][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-10-25 16:03:34.845][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-10-25 16:03:34.846][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:03:34.847][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:03:34.848][ef$get] Asked field names are: formula.
biodb.TRACE[2025-10-25 16:03:34.849][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-10-25 16:03:34.849][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:03:34.850][ef$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:03:34.851][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-10-25 16:03:34.852][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-10-25 16:03:34.853][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:03:34.854][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:03:34.861][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-10-25 16:03:34.862][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-10-25 16:03:34.863][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:03:34.864][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:03:34.865][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-10-25 16:03:34.866][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-10-25 16:03:34.867][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:03:34.867][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:03:34.868][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-10-25 16:03:34.869][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-10-25 16:03:34.870][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:03:34.871][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:03:34.872][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-10-25 16:03:34.873][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-10-25 16:03:34.874][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:03:34.875][ef$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:03:34.876][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-10-25 16:03:34.877][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-10-25 16:03:34.878][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:03:34.878][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:03:34.886][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-10-25 16:03:34.887][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-10-25 16:03:34.887][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:03:34.888][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:03:34.889][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-10-25 16:03:34.890][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-10-25 16:03:34.891][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:03:34.892][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:03:34.893][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-10-25 16:03:34.894][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-10-25 16:03:34.895][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:03:34.896][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:03:34.897][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-10-25 16:03:34.898][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-10-25 16:03:34.898][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:03:34.899][ef$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:03:34.900][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-10-25 16:03:34.901][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-10-25 16:03:34.902][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:03:34.903][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:03:34.910][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-10-25 16:03:34.911][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-10-25 16:03:34.912][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:03:34.913][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:03:34.914][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-10-25 16:03:34.915][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-10-25 16:03:34.916][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:03:34.917][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:03:34.917][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-10-25 16:03:34.918][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-10-25 16:03:34.919][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:03:34.920][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:03:34.921][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-10-25 16:03:34.922][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-10-25 16:03:34.923][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:03:34.924][ef$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:03:34.925][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-10-25 16:03:34.926][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-10-25 16:03:34.930][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:03:34.931][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:03:34.938][ef$get] Asked field names are: accession.
biodb.TRACE[2025-10-25 16:03:34.939][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-25 16:03:34.940][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:03:34.941][ef$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:03:34.945][ef$get] Asked field names are: cas.id.
biodb.TRACE[2025-10-25 16:03:34.946][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-10-25 16:03:34.947][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:03:34.948][ef$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:03:34.951][ef$get] Asked field names are: formula.
biodb.TRACE[2025-10-25 16:03:34.952][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-10-25 16:03:34.953][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:03:34.954][ef$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:03:34.958][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-10-25 16:03:34.959][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-10-25 16:03:34.960][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:03:34.961][ef$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:03:34.964][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-10-25 16:03:34.965][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-10-25 16:03:34.966][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:03:34.967][ef$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:03:34.971][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-10-25 16:03:34.972][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-10-25 16:03:34.973][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:03:34.974][ef$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:03:34.977][ef$get] Asked field names are: name.
biodb.TRACE[2025-10-25 16:03:34.978][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-10-25 16:03:34.979][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:03:34.980][ef$get] fields variable is a list.
biodb.INFO [2025-10-25 16:03:34.986][biodb::testThat]
biodb.INFO [2025-10-25 16:03:34.987][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2025-10-25 16:03:34.988][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-10-25 16:03:34.989][biodb::testThat]
biodb.DEBUG[2025-10-25 16:03:34.991][private$loadEntries] Creating entries from ids [2]: "749674, 750690".
biodb.DEBUG[2025-10-25 16:03:34.993][conn$getEntryContent] Get NCI CACTUS entry content(s) for 2 id(s)...
biodb.DEBUG[2025-10-25 16:03:34.996][self$isDownloaded] Database nci.cactus has already been downloaded.
biodb.DEBUG[2025-10-25 16:03:35.023][self$isDownloaded] Database nci.cactus has already been downloaded.
biodb.INFO [2025-10-25 16:03:35.024][self$download] Extract whole database of nci.cactus.
biodb.INFO [2025-10-25 16:03:35.025][private$doExtractDownload] Extracting content of downloaded biodbNci, a library for connecting to the National Cancer Institute (USA) CACTUS Database....
biodb.INFO [2025-10-25 16:03:35.066][biodb::testThat]
biodb.INFO [2025-10-25 16:03:35.067][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2025-10-25 16:03:35.068][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-10-25 16:03:35.069][biodb::testThat]
biodb.INFO [2025-10-25 16:03:35.074][biodb::testThat]
biodb.INFO [2025-10-25 16:03:35.075][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2025-10-25 16:03:35.076][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-10-25 16:03:35.076][biodb::testThat]
biodb.WARN [2025-10-25 16:03:35.094][self$searchForEntries] This database is not searchable by field "name".
biodb.WARN [2025-10-25 16:03:35.112][self$searchForEntries] This database is not searchable by field "name".
biodb.INFO [2025-10-25 16:03:35.119][biodb::testThat]
biodb.INFO [2025-10-25 16:03:35.120][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2025-10-25 16:03:35.121][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-10-25 16:03:35.122][biodb::testThat]
biodb.DEBUG[2025-10-25 16:03:35.138][private$loadEntries] Creating entries from ids [1]: "749674".
biodb.DEBUG[2025-10-25 16:03:35.187][conn$getEntryContent] Get NCI CACTUS entry content(s) for 1 id(s)...
biodb.DEBUG[2025-10-25 16:03:35.189][self$isDownloaded] Database nci.cactus has already been downloaded.
biodb.DEBUG[2025-10-25 16:03:35.190][self$isDownloaded] Database nci.cactus has already been downloaded.
biodb.INFO [2025-10-25 16:03:35.192][self$download] Extract whole database of nci.cactus.
biodb.INFO [2025-10-25 16:03:35.203][private$doExtractDownload] Extracting content of downloaded biodbNci, a library for connecting to the National Cancer Institute (USA) CACTUS Database....
biodb.INFO [2025-10-25 16:03:35.225][biodb::testThat]
biodb.INFO [2025-10-25 16:03:35.226][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2025-10-25 16:03:35.227][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-10-25 16:03:35.228][biodb::testThat]
biodb.INFO [2025-10-25 16:03:35.234][biodb::testThat]
biodb.INFO [2025-10-25 16:03:35.235][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2025-10-25 16:03:35.240][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-10-25 16:03:35.240][biodb::testThat]
biodb.INFO [2025-10-25 16:03:35.246][biodb::testThat]
biodb.INFO [2025-10-25 16:03:35.247][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2025-10-25 16:03:35.248][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-10-25 16:03:35.249][biodb::testThat]
biodb.INFO [2025-10-25 16:03:35.254][biodb::testThat]
biodb.INFO [2025-10-25 16:03:35.255][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2025-10-25 16:03:35.256][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-10-25 16:03:35.257][biodb::testThat]
biodb.INFO [2025-10-25 16:03:35.262][biodb$terminate] Closing BiodbMain instance...
biodb.INFO [2025-10-25 16:03:35.263][self$deleteConn] Connector "nci.cactus" deleted.
biodb.DEBUG[2025-10-25 16:03:35.264][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-10-25 16:03:35.264][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-25 16:03:35.265][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-25 16:03:35.266][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-25 16:03:35.267][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-25 16:03:35.268][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-10-25 16:03:35.269][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2025-10-25 16:03:35.277][biodb::testContext]
biodb.INFO [2025-10-25 16:03:35.278][biodb::testContext] ********************************************************************************
biodb.INFO [2025-10-25 16:03:35.279][biodb::testContext] Test context - Example long tests
biodb.INFO [2025-10-25 16:03:35.280][biodb::testContext] ********************************************************************************
biodb.INFO [2025-10-25 16:03:35.280][biodb::testContext]
biodb.INFO [2025-10-25 16:03:35.282][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.17.2.
biodb.DEBUG[2025-10-25 16:03:35.284][self$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.22-bioc/R/site-library/biodb/definitions.yml".
biodb.DEBUG[2025-10-25 16:03:35.287][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-10-25 16:03:35.288][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-10-25 16:03:35.289][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-10-25 16:03:35.290][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-25 16:03:35.291][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-25 16:03:35.292][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-25 16:03:35.292][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-10-25 16:03:35.293][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-10-25 16:03:35.294][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-25 16:03:35.295][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-25 16:03:35.296][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-25 16:03:35.297][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-10-25 16:03:35.298][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-10-25 16:03:35.299][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-25 16:03:35.299][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-25 16:03:35.300][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-25 16:03:35.301][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-10-25 16:03:35.302][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-10-25 16:03:35.303][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-10-25 16:03:35.304][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-25 16:03:35.305][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-25 16:03:35.305][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-25 16:03:35.306][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-10-25 16:03:35.307][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-10-25 16:03:35.308][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-10-25 16:03:35.309][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-25 16:03:35.310][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-25 16:03:35.311][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-25 16:03:35.312][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-10-25 16:03:35.313][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-10-25 16:03:35.313][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-25 16:03:35.314][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-25 16:03:35.315][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-25 16:03:35.316][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-10-25 16:03:35.317][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-10-25 16:03:35.318][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-10-25 16:03:35.319][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-25 16:03:35.319][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-25 16:03:35.320][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-25 16:03:35.321][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-10-25 16:03:35.322][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-10-25 16:03:35.323][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-25 16:03:35.324][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-25 16:03:35.324][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-25 16:03:35.325][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-10-25 16:03:35.326][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-10-25 16:03:35.327][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-10-25 16:03:35.328][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-25 16:03:35.329][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-25 16:03:35.330][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-25 16:03:35.331][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-10-25 16:03:35.332][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-10-25 16:03:35.333][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-10-25 16:03:35.333][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-10-25 16:03:35.334][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-10-25 16:03:35.335][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-10-25 16:03:35.336][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-25 16:03:35.337][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-25 16:03:35.338][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-25 16:03:35.339][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-10-25 16:03:35.340][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-10-25 16:03:35.340][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-25 16:03:35.341][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-25 16:03:35.342][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-25 16:03:35.343][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-10-25 16:03:35.348][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-10-25 16:03:35.349][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-25 16:03:35.349][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-25 16:03:35.350][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-25 16:03:35.351][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-10-25 16:03:35.352][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-10-25 16:03:35.353][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-25 16:03:35.354][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-25 16:03:35.355][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-25 16:03:35.355][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-10-25 16:03:35.356][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-10-25 16:03:35.357][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-10-25 16:03:35.358][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-25 16:03:35.359][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-25 16:03:35.360][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-25 16:03:35.361][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-10-25 16:03:35.362][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-10-25 16:03:35.366][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-10-25 16:03:35.367][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-25 16:03:35.367][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-25 16:03:35.368][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-25 16:03:35.369][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-10-25 16:03:35.370][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-10-25 16:03:35.371][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-10-25 16:03:35.372][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-25 16:03:35.373][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-25 16:03:35.373][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-25 16:03:35.375][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-10-25 16:03:35.376][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-10-25 16:03:35.377][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2025-10-25 16:03:35.378][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-10-25 16:03:35.379][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-10-25 16:03:35.380][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-10-25 16:03:35.381][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-10-25 16:03:35.382][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-10-25 16:03:35.383][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-10-25 16:03:35.384][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-10-25 16:03:35.384][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-10-25 16:03:35.385][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-10-25 16:03:35.386][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-10-25 16:03:35.387][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-10-25 16:03:35.388][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-10-25 16:03:35.389][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-10-25 16:03:35.390][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-10-25 16:03:35.390][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-10-25 16:03:35.390][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-10-25 16:03:35.390][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-10-25 16:03:35.390][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-10-25 16:03:35.391][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-10-25 16:03:35.392][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-25 16:03:35.393][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-25 16:03:35.394][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-10-25 16:03:35.395][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-25 16:03:35.395][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-25 16:03:35.396][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-10-25 16:03:35.397][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-10-25 16:03:35.398][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-10-25 16:03:35.399][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-10-25 16:03:35.400][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-10-25 16:03:35.401][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-10-25 16:03:35.402][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-10-25 16:03:35.403][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-10-25 16:03:35.404][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-10-25 16:03:35.405][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-10-25 16:03:35.406][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-10-25 16:03:35.407][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-10-25 16:03:35.408][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-10-25 16:03:35.409][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-10-25 16:03:35.410][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-10-25 16:03:35.411][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-10-25 16:03:35.412][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-10-25 16:03:35.413][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-10-25 16:03:35.414][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-10-25 16:03:35.415][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-10-25 16:03:35.415][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-10-25 16:03:35.416][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-10-25 16:03:35.417][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-10-25 16:03:35.417][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-10-25 16:03:35.417][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-10-25 16:03:35.417][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-10-25 16:03:35.417][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-10-25 16:03:35.418][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-10-25 16:03:35.419][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-25 16:03:35.420][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-25 16:03:35.421][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-10-25 16:03:35.422][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-25 16:03:35.423][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-25 16:03:35.423][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-10-25 16:03:35.424][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-10-25 16:03:35.425][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-10-25 16:03:35.426][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-10-25 16:03:35.427][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-10-25 16:03:35.428][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-10-25 16:03:35.429][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-10-25 16:03:35.431][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-10-25 16:03:35.432][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2025-10-25 16:03:35.432][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-10-25 16:03:35.433][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-10-25 16:03:35.434][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-10-25 16:03:35.435][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-10-25 16:03:35.436][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-10-25 16:03:35.437][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-10-25 16:03:35.438][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-10-25 16:03:35.439][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-10-25 16:03:35.440][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-10-25 16:03:35.441][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-10-25 16:03:35.442][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-10-25 16:03:35.443][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-10-25 16:03:35.444][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-10-25 16:03:35.444][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-10-25 16:03:35.445][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-10-25 16:03:35.446][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-25 16:03:35.447][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-25 16:03:35.448][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-10-25 16:03:35.449][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-25 16:03:35.450][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-25 16:03:35.451][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-10-25 16:03:35.452][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-10-25 16:03:35.452][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-10-25 16:03:35.453][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-10-25 16:03:35.458][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-10-25 16:03:35.459][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-10-25 16:03:35.460][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-10-25 16:03:35.461][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-10-25 16:03:35.462][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-10-25 16:03:35.463][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-10-25 16:03:35.464][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-10-25 16:03:35.465][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-10-25 16:03:35.466][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-10-25 16:03:35.467][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-10-25 16:03:35.468][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-10-25 16:03:35.469][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-10-25 16:03:35.470][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-10-25 16:03:35.471][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-10-25 16:03:35.472][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-10-25 16:03:35.473][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-10-25 16:03:35.473][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-10-25 16:03:35.474][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-10-25 16:03:35.475][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-10-25 16:03:35.476][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-10-25 16:03:35.477][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-25 16:03:35.478][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-25 16:03:35.479][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-10-25 16:03:35.480][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-25 16:03:35.481][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-25 16:03:35.481][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-10-25 16:03:35.482][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-10-25 16:03:35.483][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-10-25 16:03:35.484][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-10-25 16:03:35.485][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-10-25 16:03:35.486][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-10-25 16:03:35.487][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-10-25 16:03:35.488][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-10-25 16:03:35.489][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-25 16:03:35.490][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-25 16:03:35.490][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-25 16:03:35.491][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-25 16:03:35.492][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-25 16:03:35.493][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-25 16:03:35.494][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-25 16:03:35.495][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-25 16:03:35.495][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-25 16:03:35.496][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-25 16:03:35.497][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-25 16:03:35.498][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-25 16:03:35.499][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-25 16:03:35.500][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-25 16:03:35.500][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-25 16:03:35.501][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-25 16:03:35.502][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-25 16:03:35.503][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-25 16:03:35.504][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-25 16:03:35.504][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-25 16:03:35.505][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[2025-10-25 16:03:35.506][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-25 16:03:35.507][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-25 16:03:35.508][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-25 16:03:35.509][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-25 16:03:35.509][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[2025-10-25 16:03:35.510][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-25 16:03:35.511][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-25 16:03:35.512][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-25 16:03:35.513][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-25 16:03:35.514][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-25 16:03:35.514][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-25 16:03:35.515][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-25 16:03:35.516][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-25 16:03:35.517][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-25 16:03:35.518][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-25 16:03:35.518][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-25 16:03:35.519][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-25 16:03:35.520][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-25 16:03:35.521][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-25 16:03:35.522][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-25 16:03:35.523][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-25 16:03:35.523][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-25 16:03:35.524][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-25 16:03:35.525][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-25 16:03:35.526][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-25 16:03:35.527][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-25 16:03:35.528][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-25 16:03:35.528][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-25 16:03:35.529][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-25 16:03:35.530][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-25 16:03:35.531][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-25 16:03:35.532][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-25 16:03:35.532][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-25 16:03:35.533][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-25 16:03:35.534][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-25 16:03:35.535][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-25 16:03:35.536][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-25 16:03:35.537][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-25 16:03:35.537][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-25 16:03:35.538][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-25 16:03:35.539][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-25 16:03:35.540][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-25 16:03:35.541][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-25 16:03:35.542][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-25 16:03:35.542][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[2025-10-25 16:03:35.543][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-25 16:03:35.544][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-25 16:03:35.545][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-25 16:03:35.546][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-25 16:03:35.547][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-25 16:03:35.547][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-25 16:03:35.548][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-25 16:03:35.549][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-25 16:03:35.550][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-25 16:03:35.551][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-25 16:03:35.552][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-25 16:03:35.552][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-25 16:03:35.553][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-25 16:03:35.554][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-25 16:03:35.555][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-25 16:03:35.556][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-10-25 16:03:35.557][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-10-25 16:03:35.559][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-10-25 16:03:35.560][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-10-25 16:03:35.565][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-10-25 16:03:35.566][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-10-25 16:03:35.567][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-10-25 16:03:35.569][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-10-25 16:03:35.570][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-10-25 16:03:35.571][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-10-25 16:03:35.572][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-10-25 16:03:35.574][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-10-25 16:03:35.575][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-10-25 16:03:35.576][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-10-25 16:03:35.578][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-10-25 16:03:35.579][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-10-25 16:03:35.580][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-10-25 16:03:35.582][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-10-25 16:03:35.583][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-10-25 16:03:35.584][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-10-25 16:03:35.585][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-10-25 16:03:35.587][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-10-25 16:03:35.588][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-10-25 16:03:35.589][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-10-25 16:03:35.591][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-10-25 16:03:35.592][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-10-25 16:03:35.593][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-10-25 16:03:35.594][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-10-25 16:03:35.596][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-10-25 16:03:35.597][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-10-25 16:03:35.598][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-10-25 16:03:35.600][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-10-25 16:03:35.601][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-10-25 16:03:35.602][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-10-25 16:03:35.603][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-10-25 16:03:35.605][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-10-25 16:03:35.606][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-10-25 16:03:35.607][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-10-25 16:03:35.609][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-10-25 16:03:35.610][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-10-25 16:03:35.611][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-10-25 16:03:35.612][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-10-25 16:03:35.614][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-10-25 16:03:35.615][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-10-25 16:03:35.616][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-10-25 16:03:35.618][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-10-25 16:03:35.619][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-10-25 16:03:35.620][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-10-25 16:03:35.622][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-10-25 16:03:35.623][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-10-25 16:03:35.624][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-10-25 16:03:35.625][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-10-25 16:03:35.627][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-10-25 16:03:35.628][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-10-25 16:03:35.629][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-10-25 16:03:35.631][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-10-25 16:03:35.632][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-10-25 16:03:35.633][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-10-25 16:03:35.634][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-10-25 16:03:35.636][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-10-25 16:03:35.637][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-10-25 16:03:35.638][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-10-25 16:03:35.640][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-10-25 16:03:35.641][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-10-25 16:03:35.642][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-10-25 16:03:35.643][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-10-25 16:03:35.645][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-10-25 16:03:35.646][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-10-25 16:03:35.647][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-10-25 16:03:35.649][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-10-25 16:03:35.650][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-10-25 16:03:35.651][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-10-25 16:03:35.652][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-10-25 16:03:35.654][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-10-25 16:03:35.655][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-10-25 16:03:35.656][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-10-25 16:03:35.658][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-10-25 16:03:35.659][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-10-25 16:03:35.660][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-10-25 16:03:35.661][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-10-25 16:03:35.663][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-10-25 16:03:35.664][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-10-25 16:03:35.669][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-10-25 16:03:35.671][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-10-25 16:03:35.672][initialize] This is biodb version 1.17.2.
biodb.DEBUG[2025-10-25 16:03:35.673][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-10-25 16:03:35.674][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-10-25 16:03:35.675][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-25 16:03:35.676][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-10-25 16:03:35.676][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-25 16:03:35.677][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-25 16:03:35.678][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-25 16:03:35.679][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-25 16:03:35.680][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-25 16:03:35.681][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-25 16:03:35.681][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-25 16:03:35.682][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-25 16:03:35.683][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-25 16:03:35.684][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-25 16:03:35.685][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-25 16:03:35.685][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-25 16:03:35.686][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-25 16:03:35.687][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-25 16:03:35.688][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-25 16:03:35.689][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-25 16:03:35.690][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-25 16:03:35.690][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-25 16:03:35.691][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-25 16:03:35.692][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-25 16:03:35.693][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-25 16:03:35.694][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-25 16:03:35.695][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-25 16:03:35.695][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-25 16:03:35.696][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-25 16:03:35.697][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-25 16:03:35.698][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-25 16:03:35.699][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-25 16:03:35.699][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-25 16:03:35.700][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-25 16:03:35.701][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-25 16:03:35.702][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-25 16:03:35.703][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-25 16:03:35.704][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-25 16:03:35.704][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-25 16:03:35.705][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-25 16:03:35.706][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-25 16:03:35.707][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-25 16:03:35.708][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-25 16:03:35.709][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-25 16:03:35.709][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-25 16:03:35.710][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-25 16:03:35.711][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-25 16:03:35.712][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-25 16:03:35.713][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-25 16:03:35.713][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-25 16:03:35.714][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-25 16:03:35.715][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-25 16:03:35.716][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-25 16:03:35.717][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-25 16:03:35.718][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-25 16:03:35.718][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-25 16:03:35.719][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-25 16:03:35.720][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-25 16:03:35.721][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-25 16:03:35.722][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-25 16:03:35.723][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-25 16:03:35.723][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-25 16:03:35.724][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-25 16:03:35.725][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-25 16:03:35.726][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-25 16:03:35.727][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-25 16:03:35.727][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-25 16:03:35.728][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-25 16:03:35.729][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-25 16:03:35.730][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-25 16:03:35.731][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-25 16:03:35.732][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-25 16:03:35.732][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-25 16:03:35.733][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-25 16:03:35.734][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-25 16:03:35.735][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-25 16:03:35.736][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-25 16:03:35.736][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-25 16:03:35.737][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-25 16:03:35.738][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-25 16:03:35.739][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-25 16:03:35.740][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-25 16:03:35.741][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-25 16:03:35.741][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-25 16:03:35.742][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-25 16:03:35.743][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-25 16:03:35.744][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-25 16:03:35.745][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-25 16:03:35.746][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-25 16:03:35.746][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-25 16:03:35.747][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-25 16:03:35.748][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-25 16:03:35.749][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-25 16:03:35.750][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-25 16:03:35.750][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-25 16:03:35.751][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-25 16:03:35.752][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-25 16:03:35.753][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-25 16:03:35.754][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-25 16:03:35.755][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-25 16:03:35.755][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-25 16:03:35.756][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-25 16:03:35.757][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-25 16:03:35.758][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-25 16:03:35.759][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-25 16:03:35.760][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-25 16:03:35.760][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-25 16:03:35.761][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-25 16:03:35.762][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-25 16:03:35.763][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[2025-10-25 16:03:35.764][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-25 16:03:35.764][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-25 16:03:35.765][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-25 16:03:35.766][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-25 16:03:35.767][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-25 16:03:35.768][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-25 16:03:35.769][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[2025-10-25 16:03:35.774][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNci.Rcheck/biodbNci/definitions.yml".
biodb.DEBUG[2025-10-25 16:03:35.775][self$getDbsInfo()$define] Define connector nci.cactus.
biodb.DEBUG[2025-10-25 16:03:35.777][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-10-25 16:03:35.778][self$setPropertyValue] Setting property "description" to "National Cancer Institute (USA) CACTUS Database.".
biodb.DEBUG[2025-10-25 16:03:35.779][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-10-25 16:03:35.780][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-10-25 16:03:35.781][self$setPropertyValue] Setting property "downloadable" to "TRUE".
biodb.DEBUG[2025-10-25 16:03:35.781][self$setPropertyValue] Setting property "dwnld.ext" to "gz".
biodb.DEBUG[2025-10-25 16:03:35.782][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-10-25 16:03:35.783][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-10-25 16:03:35.784][self$setPropertyValue] Setting property "entry.content.type" to "sdf".
biodb.DEBUG[2025-10-25 16:03:35.785][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-10-25 16:03:35.786][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-10-25 16:03:35.787][self$setPropertyValue] Setting property "name" to "NCI CACTUS".
biodb.DEBUG[2025-10-25 16:03:35.788][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-10-25 16:03:35.789][self$setPropertyValue] Setting property "parsing.expr" to "NSC".
biodb.DEBUG[2025-10-25 16:03:35.789][self$setPropertyValue] Setting property "parsing.expr" to "DTP names".
biodb.DEBUG[2025-10-25 16:03:35.789][self$setPropertyValue] Setting property "parsing.expr" to "Standard InChI".
biodb.DEBUG[2025-10-25 16:03:35.789][self$setPropertyValue] Setting property "parsing.expr" to "c("Standard InChIKey", "^InChIKey=(.*)$")".
biodb.DEBUG[2025-10-25 16:03:35.789][self$setPropertyValue] Setting property "parsing.expr" to "Formula".
biodb.DEBUG[2025-10-25 16:03:35.789][self$setPropertyValue] Setting property "parsing.expr" to "Molecular Weight".
biodb.DEBUG[2025-10-25 16:03:35.789][self$setPropertyValue] Setting property "parsing.expr" to "CAS".
biodb.DEBUG[2025-10-25 16:03:35.790][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-10-25 16:03:35.791][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-10-25 16:03:35.792][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-10-25 16:03:35.793][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-25 16:03:35.793][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-25 16:03:35.794][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-10-25 16:03:35.795][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-25 16:03:35.796][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-25 16:03:35.797][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-10-25 16:03:35.798][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/".
biodb.DEBUG[2025-10-25 16:03:35.798][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/".
biodb.DEBUG[2025-10-25 16:03:35.798][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/download/nci/".
biodb.DEBUG[2025-10-25 16:03:35.798][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/download/nci/NCI-Open_2012-05-01.sdf.gz".
biodb.DEBUG[2025-10-25 16:03:35.799][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-10-25 16:03:35.800][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-10-25 16:03:35.801][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-10-25 16:03:35.801][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-10-25 16:03:35.803][self$getEntryFields()$define] Define field nci.cactus.id.
biodb.DEBUG[2025-10-25 16:03:35.806][super$initialize] Initialize connector nci.cactus.
biodb.DEBUG[2025-10-25 16:03:35.809][biodb$getFactory()$createConn] Creating new connector nci.cactus for database class nci.cactus .
biodb.INFO [2025-10-25 16:03:35.810][biodb$terminate] Closing BiodbMain instance...
biodb.INFO [2025-10-25 16:03:35.811][self$deleteConn] Connector "nci.cactus" deleted.
biodb.DEBUG[2025-10-25 16:03:35.812][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-10-25 16:03:35.812][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-25 16:03:35.813][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-25 16:03:35.814][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-25 16:03:35.815][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-25 16:03:35.816][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-10-25 16:03:35.816][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
[ 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)