Back to Long Tests report for BioC 3.22

This page was generated on 2025-11-22 23:55 -0500 (Sat, 22 Nov 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 4873
merida1macOS 12.7.6 Montereyx86_644.5.2 Patched (2025-11-05 r88990) -- "[Not] Part in a Rumble" 4654
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 8/31HostnameOS / ArchCHECK
biodbNci 1.14.0  (landing page)
Pierrick Roger
Snapshot Date: 2025-11-22 09:55 -0500 (Sat, 22 Nov 2025)
git_url: https://git.bioconductor.org/packages/biodbNci
git_branch: RELEASE_3_22
git_last_commit: 4ce22d8
git_last_commit_date: 2025-10-29 11:15:34 -0500 (Wed, 29 Oct 2025)
nebbiolo2Linux (Ubuntu 24.04.3 LTS) / x86_64  ERROR  
merida1macOS 12.7.6 Monterey / x86_64  ERROR  

CHECK results for biodbNci on nebbiolo2

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

raw results


Summary

Package: biodbNci
Version: 1.14.0
Command: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --test-dir=longtests --no-stop-on-test-error --no-codoc --no-examples --no-manual --ignore-vignettes --check-subdirs=no biodbNci_1.14.0.tar.gz
StartedAt: 2025-11-22 16:02:17 -0500 (Sat, 22 Nov 2025)
EndedAt: 2025-11-22 16:03:21 -0500 (Sat, 22 Nov 2025)
EllapsedTime: 64.0 seconds
RetCode: 1
Status:   ERROR  
CheckDir: biodbNci.Rcheck
Warnings: NA

Tests output

biodbNci.Rcheck/tests/testthat.Rout.fail


R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

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> # Script needed to run testthat automatically from ‘R CMD check’. See
> # testthat::test_dir documentation.
> library(testthat)
> library(biodbNci)
Warning message:
In fun(libname, pkgname) :
  Package 'biodbNci' is deprecated and will be removed from Bioconductor
  version 3.23
> Sys.setenv(TESTTHAT_REPORTER="summary")
> Sys.setenv(BIODB_LOG_DST="console")
> test_check("biodbNci")
biodb.INFO [2025-11-22 16:03:17.775][biodb::testContext]
biodb.INFO [2025-11-22 16:03:17.777][biodb::testContext] ********************************************************************************
biodb.INFO [2025-11-22 16:03:17.778][biodb::testContext] Test context - Generic long tests
biodb.INFO [2025-11-22 16:03:17.779][biodb::testContext] ********************************************************************************
biodb.INFO [2025-11-22 16:03:17.780][biodb::testContext]
biodb.INFO [2025-11-22 16:03:17.786][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.18.0.
biodb.DEBUG[2025-11-22 16:03:17.788][self$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.22-bioc/R/site-library/biodb/definitions.yml".
biodb.DEBUG[2025-11-22 16:03:17.795][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-11-22 16:03:17.796][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-11-22 16:03:17.797][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-11-22 16:03:17.798][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:03:17.798][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:03:17.799][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:03:17.800][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-11-22 16:03:17.817][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-11-22 16:03:17.818][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:03:17.819][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:03:17.819][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:03:17.820][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-11-22 16:03:17.821][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-11-22 16:03:17.822][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:03:17.832][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:03:17.833][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:03:17.834][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-11-22 16:03:17.834][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-11-22 16:03:17.835][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-11-22 16:03:17.836][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:03:17.837][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:03:17.838][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:03:17.839][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-11-22 16:03:17.840][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-11-22 16:03:17.841][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-11-22 16:03:17.841][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:03:17.842][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:03:17.843][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:03:17.844][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-11-22 16:03:17.845][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-11-22 16:03:17.846][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:03:17.847][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:03:17.847][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[2025-11-22 16:03:17.848][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-11-22 16:03:17.849][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-11-22 16:03:17.850][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-11-22 16:03:17.851][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:03:17.852][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:03:17.853][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:03:17.854][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-11-22 16:03:17.855][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-11-22 16:03:17.856][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:03:17.856][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:03:17.857][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:03:17.858][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-11-22 16:03:17.859][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-11-22 16:03:17.860][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-11-22 16:03:17.861][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:03:17.862][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:03:17.862][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:03:17.863][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-11-22 16:03:17.864][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-11-22 16:03:17.865][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-11-22 16:03:17.866][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-11-22 16:03:17.867][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-11-22 16:03:17.868][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-11-22 16:03:17.869][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:03:17.870][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:03:17.870][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:03:17.871][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-11-22 16:03:17.872][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-11-22 16:03:17.873][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:03:17.874][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:03:17.875][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:03:17.876][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-11-22 16:03:17.877][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-11-22 16:03:17.877][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:03:17.878][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:03:17.879][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[2025-11-22 16:03:17.880][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-11-22 16:03:17.881][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-11-22 16:03:17.882][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:03:17.883][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:03:17.883][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:03:17.884][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-11-22 16:03:17.885][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-11-22 16:03:17.886][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-11-22 16:03:17.887][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:03:17.888][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:03:17.889][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:03:17.890][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-11-22 16:03:17.891][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-11-22 16:03:17.894][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-11-22 16:03:17.895][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:03:17.896][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:03:17.897][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:03:17.897][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-11-22 16:03:17.898][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-11-22 16:03:17.899][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-11-22 16:03:17.900][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:03:17.901][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:03:17.902][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:03:17.905][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-11-22 16:03:17.936][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-11-22 16:03:17.951][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2025-11-22 16:03:17.952][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-11-22 16:03:17.953][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-11-22 16:03:17.954][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-11-22 16:03:17.955][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-11-22 16:03:17.956][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-11-22 16:03:17.956][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-11-22 16:03:17.957][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-11-22 16:03:17.958][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-11-22 16:03:17.959][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-11-22 16:03:17.960][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-11-22 16:03:17.961][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-11-22 16:03:17.962][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-11-22 16:03:17.963][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-11-22 16:03:17.964][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-11-22 16:03:17.964][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-11-22 16:03:17.964][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-11-22 16:03:17.964][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-11-22 16:03:17.964][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-11-22 16:03:17.965][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-11-22 16:03:17.966][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-11-22 16:03:17.967][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-11-22 16:03:17.967][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-11-22 16:03:17.968][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-11-22 16:03:17.969][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-11-22 16:03:17.970][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-11-22 16:03:17.971][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-11-22 16:03:17.972][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-11-22 16:03:17.973][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-11-22 16:03:17.974][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-11-22 16:03:17.975][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-11-22 16:03:17.976][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-11-22 16:03:17.977][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-11-22 16:03:17.978][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-11-22 16:03:17.979][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-11-22 16:03:17.980][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-11-22 16:03:17.981][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-11-22 16:03:17.982][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-11-22 16:03:17.983][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-11-22 16:03:17.984][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-11-22 16:03:17.989][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-11-22 16:03:17.990][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-11-22 16:03:17.991][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-11-22 16:03:17.992][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-11-22 16:03:17.993][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-11-22 16:03:17.994][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-11-22 16:03:17.995][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-11-22 16:03:17.996][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-11-22 16:03:17.996][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-11-22 16:03:17.996][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-11-22 16:03:17.996][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-11-22 16:03:17.996][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-11-22 16:03:17.997][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-11-22 16:03:17.998][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-11-22 16:03:17.998][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-11-22 16:03:17.999][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-11-22 16:03:18.000][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-11-22 16:03:18.001][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-11-22 16:03:18.002][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-11-22 16:03:18.003][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-11-22 16:03:18.004][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-11-22 16:03:18.005][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-11-22 16:03:18.006][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-11-22 16:03:18.007][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-11-22 16:03:18.008][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-11-22 16:03:18.009][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-11-22 16:03:18.010][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2025-11-22 16:03:18.011][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-11-22 16:03:18.012][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-11-22 16:03:18.013][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-11-22 16:03:18.014][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-11-22 16:03:18.015][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-11-22 16:03:18.016][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-11-22 16:03:18.017][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-11-22 16:03:18.018][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-11-22 16:03:18.019][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-11-22 16:03:18.019][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-11-22 16:03:18.020][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-11-22 16:03:18.021][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-11-22 16:03:18.022][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-11-22 16:03:18.023][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-11-22 16:03:18.024][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-11-22 16:03:18.025][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-11-22 16:03:18.026][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-11-22 16:03:18.027][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-11-22 16:03:18.028][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-11-22 16:03:18.028][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-11-22 16:03:18.029][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-11-22 16:03:18.030][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-11-22 16:03:18.031][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-11-22 16:03:18.032][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-11-22 16:03:18.033][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-11-22 16:03:18.034][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-11-22 16:03:18.035][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-11-22 16:03:18.036][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-11-22 16:03:18.037][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-11-22 16:03:18.038][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-11-22 16:03:18.039][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-11-22 16:03:18.040][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-11-22 16:03:18.041][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-11-22 16:03:18.042][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-11-22 16:03:18.043][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-11-22 16:03:18.044][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-11-22 16:03:18.045][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-11-22 16:03:18.046][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-11-22 16:03:18.047][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-11-22 16:03:18.048][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-11-22 16:03:18.049][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-11-22 16:03:18.049][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-11-22 16:03:18.050][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-11-22 16:03:18.051][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-11-22 16:03:18.052][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-11-22 16:03:18.053][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-11-22 16:03:18.054][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-11-22 16:03:18.055][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-11-22 16:03:18.056][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-11-22 16:03:18.056][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-11-22 16:03:18.057][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-11-22 16:03:18.058][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-11-22 16:03:18.059][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-11-22 16:03:18.060][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-11-22 16:03:18.061][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-11-22 16:03:18.065][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-11-22 16:03:18.065][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:03:18.066][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:03:18.067][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:03:18.068][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-22 16:03:18.069][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-22 16:03:18.070][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:03:18.070][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:03:18.071][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:03:18.072][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-22 16:03:18.073][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-22 16:03:18.074][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:03:18.075][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:03:18.075][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:03:18.076][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-22 16:03:18.077][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-22 16:03:18.078][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:03:18.079][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:03:18.080][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:03:18.080][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-22 16:03:18.081][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-22 16:03:18.082][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:03:18.083][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:03:18.084][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:03:18.085][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-22 16:03:18.085][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-22 16:03:18.086][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:03:18.087][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:03:18.088][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:03:18.089][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-22 16:03:18.089][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-22 16:03:18.090][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:03:18.091][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:03:18.092][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:03:18.093][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-22 16:03:18.094][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-22 16:03:18.094][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:03:18.095][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:03:18.096][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:03:18.097][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-22 16:03:18.098][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-22 16:03:18.099][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:03:18.099][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:03:18.100][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:03:18.101][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-22 16:03:18.102][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-22 16:03:18.103][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:03:18.104][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:03:18.104][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:03:18.105][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-22 16:03:18.106][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-22 16:03:18.107][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:03:18.108][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:03:18.109][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:03:18.109][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-22 16:03:18.110][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-22 16:03:18.111][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:03:18.112][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:03:18.113][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:03:18.114][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-22 16:03:18.114][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-22 16:03:18.115][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:03:18.116][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:03:18.117][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:03:18.118][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-22 16:03:18.119][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-22 16:03:18.119][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:03:18.120][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:03:18.121][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:03:18.122][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-22 16:03:18.123][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-22 16:03:18.123][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:03:18.124][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:03:18.125][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:03:18.126][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-22 16:03:18.127][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-22 16:03:18.128][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:03:18.128][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:03:18.129][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:03:18.130][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-22 16:03:18.131][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-22 16:03:18.132][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:03:18.133][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:03:18.134][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-11-22 16:03:18.138][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-11-22 16:03:18.139][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-11-22 16:03:18.141][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-11-22 16:03:18.142][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-11-22 16:03:18.148][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-11-22 16:03:18.154][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-11-22 16:03:18.158][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-11-22 16:03:18.160][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-11-22 16:03:18.161][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-11-22 16:03:18.163][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-11-22 16:03:18.165][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-11-22 16:03:18.166][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-11-22 16:03:18.168][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-11-22 16:03:18.170][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-11-22 16:03:18.171][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-11-22 16:03:18.173][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-11-22 16:03:18.175][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-11-22 16:03:18.177][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-11-22 16:03:18.179][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-11-22 16:03:18.180][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-11-22 16:03:18.182][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-11-22 16:03:18.183][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-11-22 16:03:18.185][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-11-22 16:03:18.186][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-11-22 16:03:18.188][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-11-22 16:03:18.189][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-11-22 16:03:18.191][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-11-22 16:03:18.193][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-11-22 16:03:18.194][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-11-22 16:03:18.195][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-11-22 16:03:18.197][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-11-22 16:03:18.198][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-11-22 16:03:18.200][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-11-22 16:03:18.201][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-11-22 16:03:18.203][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-11-22 16:03:18.204][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-11-22 16:03:18.206][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-11-22 16:03:18.207][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-11-22 16:03:18.209][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-11-22 16:03:18.210][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-11-22 16:03:18.212][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-11-22 16:03:18.213][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-11-22 16:03:18.215][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-11-22 16:03:18.216][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-11-22 16:03:18.217][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-11-22 16:03:18.219][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-11-22 16:03:18.220][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-11-22 16:03:18.222][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-11-22 16:03:18.223][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-11-22 16:03:18.225][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-11-22 16:03:18.226][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-11-22 16:03:18.228][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-11-22 16:03:18.229][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-11-22 16:03:18.231][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-11-22 16:03:18.232][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-11-22 16:03:18.233][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-11-22 16:03:18.235][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-11-22 16:03:18.236][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-11-22 16:03:18.238][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-11-22 16:03:18.239][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-11-22 16:03:18.241][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-11-22 16:03:18.242][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-11-22 16:03:18.243][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-11-22 16:03:18.245][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-11-22 16:03:18.246][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-11-22 16:03:18.248][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-11-22 16:03:18.249][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-11-22 16:03:18.251][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-11-22 16:03:18.252][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-11-22 16:03:18.254][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-11-22 16:03:18.255][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-11-22 16:03:18.257][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-11-22 16:03:18.258][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-11-22 16:03:18.259][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-11-22 16:03:18.261][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-11-22 16:03:18.262][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-11-22 16:03:18.264][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-11-22 16:03:18.265][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-11-22 16:03:18.267][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-11-22 16:03:18.268][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-11-22 16:03:18.270][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-11-22 16:03:18.271][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-11-22 16:03:18.278][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-11-22 16:03:18.281][initialize] This is biodb version 1.18.0.
biodb.DEBUG[2025-11-22 16:03:18.284][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-11-22 16:03:18.285][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-11-22 16:03:18.286][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-22 16:03:18.287][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:03:18.288][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:03:18.293][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:03:18.294][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-22 16:03:18.295][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-22 16:03:18.296][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-22 16:03:18.297][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-22 16:03:18.298][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:03:18.299][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[2025-11-22 16:03:18.300][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:03:18.301][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-22 16:03:18.302][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-22 16:03:18.303][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-22 16:03:18.303][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-22 16:03:18.304][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:03:18.305][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[2025-11-22 16:03:18.306][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:03:18.307][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-22 16:03:18.308][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-22 16:03:18.309][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-22 16:03:18.310][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-22 16:03:18.311][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:03:18.312][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:03:18.313][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:03:18.314][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-22 16:03:18.314][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-22 16:03:18.315][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-22 16:03:18.316][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-22 16:03:18.317][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:03:18.318][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:03:18.319][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:03:18.320][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-22 16:03:18.321][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-22 16:03:18.322][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-22 16:03:18.323][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-22 16:03:18.323][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:03:18.324][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[2025-11-22 16:03:18.325][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:03:18.339][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-22 16:03:18.340][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-22 16:03:18.340][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-22 16:03:18.341][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-22 16:03:18.342][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:03:18.343][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:03:18.344][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:03:18.344][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-22 16:03:18.345][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-22 16:03:18.346][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-22 16:03:18.347][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-22 16:03:18.348][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:03:18.349][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:03:18.349][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:03:18.350][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-22 16:03:18.351][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-22 16:03:18.352][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-22 16:03:18.353][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-22 16:03:18.354][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:03:18.354][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:03:18.355][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:03:18.356][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-22 16:03:18.357][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-22 16:03:18.358][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-22 16:03:18.359][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-22 16:03:18.359][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:03:18.360][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[2025-11-22 16:03:18.361][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:03:18.362][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-22 16:03:18.363][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-22 16:03:18.364][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-22 16:03:18.364][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-22 16:03:18.365][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:03:18.366][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:03:18.367][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:03:18.368][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-22 16:03:18.368][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-22 16:03:18.369][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-22 16:03:18.370][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-22 16:03:18.371][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:03:18.372][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:03:18.373][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:03:18.373][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-22 16:03:18.374][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-22 16:03:18.375][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-22 16:03:18.376][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-22 16:03:18.377][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:03:18.378][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:03:18.378][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:03:18.379][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-22 16:03:18.380][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-22 16:03:18.381][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-22 16:03:18.382][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-22 16:03:18.382][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:03:18.383][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:03:18.384][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:03:18.385][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-22 16:03:18.386][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-22 16:03:18.387][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-22 16:03:18.387][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-22 16:03:18.388][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:03:18.389][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:03:18.390][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:03:18.391][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-22 16:03:18.392][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-22 16:03:18.392][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-22 16:03:18.393][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-22 16:03:18.394][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:03:18.395][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[2025-11-22 16:03:18.396][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:03:18.396][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-22 16:03:18.397][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-22 16:03:18.398][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-22 16:03:18.399][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-22 16:03:18.400][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:03:18.401][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[2025-11-22 16:03:18.402][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNci.Rcheck/biodbNci/definitions.yml".
biodb.DEBUG[2025-11-22 16:03:18.411][self$getDbsInfo()$define] Define connector nci.cactus.
biodb.DEBUG[2025-11-22 16:03:18.413][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-11-22 16:03:18.414][self$setPropertyValue] Setting property "description" to "National Cancer Institute (USA) CACTUS Database.".
biodb.DEBUG[2025-11-22 16:03:18.415][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-11-22 16:03:18.416][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-11-22 16:03:18.417][self$setPropertyValue] Setting property "downloadable" to "TRUE".
biodb.DEBUG[2025-11-22 16:03:18.418][self$setPropertyValue] Setting property "dwnld.ext" to "gz".
biodb.DEBUG[2025-11-22 16:03:18.419][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-11-22 16:03:18.420][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-11-22 16:03:18.421][self$setPropertyValue] Setting property "entry.content.type" to "sdf".
biodb.DEBUG[2025-11-22 16:03:18.422][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-11-22 16:03:18.422][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-11-22 16:03:18.423][self$setPropertyValue] Setting property "name" to "NCI CACTUS".
biodb.DEBUG[2025-11-22 16:03:18.424][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-11-22 16:03:18.425][self$setPropertyValue] Setting property "parsing.expr" to "NSC".
biodb.DEBUG[2025-11-22 16:03:18.425][self$setPropertyValue] Setting property "parsing.expr" to "DTP names".
biodb.DEBUG[2025-11-22 16:03:18.425][self$setPropertyValue] Setting property "parsing.expr" to "Standard InChI".
biodb.DEBUG[2025-11-22 16:03:18.425][self$setPropertyValue] Setting property "parsing.expr" to "c("Standard InChIKey", "^InChIKey=(.*)$")".
biodb.DEBUG[2025-11-22 16:03:18.425][self$setPropertyValue] Setting property "parsing.expr" to "Formula".
biodb.DEBUG[2025-11-22 16:03:18.425][self$setPropertyValue] Setting property "parsing.expr" to "Molecular Weight".
biodb.DEBUG[2025-11-22 16:03:18.425][self$setPropertyValue] Setting property "parsing.expr" to "CAS".
biodb.DEBUG[2025-11-22 16:03:18.426][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-11-22 16:03:18.427][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-11-22 16:03:18.428][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-11-22 16:03:18.429][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-11-22 16:03:18.430][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-11-22 16:03:18.431][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-11-22 16:03:18.432][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-11-22 16:03:18.432][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-11-22 16:03:18.433][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-11-22 16:03:18.434][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/".
biodb.DEBUG[2025-11-22 16:03:18.434][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/".
biodb.DEBUG[2025-11-22 16:03:18.434][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/download/nci/".
biodb.DEBUG[2025-11-22 16:03:18.434][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/download/nci/NCI-Open_2012-05-01.sdf.gz".
biodb.DEBUG[2025-11-22 16:03:18.435][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-11-22 16:03:18.436][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-11-22 16:03:18.437][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-11-22 16:03:18.438][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-11-22 16:03:18.443][self$getEntryFields()$define] Define field nci.cactus.id.
biodb.DEBUG[2025-11-22 16:03:18.464][super$initialize] Initialize connector nci.cactus.
biodb.DEBUG[2025-11-22 16:03:18.479][biodb$getFactory()$createConn] Creating new connector nci.cactus for database class nci.cactus .
biodb.INFO [2025-11-22 16:03:18.487][biodb::testThat]
biodb.INFO [2025-11-22 16:03:18.488][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2025-11-22 16:03:18.489][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-11-22 16:03:18.489][biodb::testThat]
biodb.TRACE[2025-11-22 16:03:18.493][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNci.Rcheck/biodbNci/testref/entry-nci.cactus-749674-content.sdf".
biodb.DEBUG[2025-11-22 16:03:18.494][biodb$getFactory()$createEntryFromCo ...] Creating NCI CACTUS entries from 1 content(s).
biodb.DEBUG[2025-11-22 16:03:18.497][biodb$getFactory()$createEntryFromCo ...] Parsing 1 NCI CACTUS entries.
biodb.DEBUG[2025-11-22 16:03:18.511][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-11-22 16:03:18.512][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-22 16:03:18.513][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-22 16:03:18.525][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-11-22 16:03:18.526][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-22 16:03:18.527][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:03:18.527][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-11-22 16:03:18.544][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-22 16:03:18.545][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-22 16:03:18.546][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:18.547][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:18.548][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-22 16:03:18.559][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-22 16:03:18.560][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:18.561][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:18.563][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-11-22 16:03:18.564][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-11-22 16:03:18.565][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:18.566][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:18.590][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-11-22 16:03:18.591][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-11-22 16:03:18.592][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:18.593][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:18.594][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-11-22 16:03:18.595][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-11-22 16:03:18.596][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:18.597][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:18.598][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-11-22 16:03:18.599][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-11-22 16:03:18.600][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:18.601][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:18.603][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-11-22 16:03:18.604][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-11-22 16:03:18.605][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:18.606][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:18.606][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-11-22 16:03:18.607][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-11-22 16:03:18.608][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:18.609][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:18.611][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-11-22 16:03:18.612][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-11-22 16:03:18.612][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:18.613][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:18.614][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-11-22 16:03:18.615][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-11-22 16:03:18.616][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:18.617][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:18.619][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-11-22 16:03:18.620][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-11-22 16:03:18.621][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:18.621][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:18.622][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-11-22 16:03:18.623][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-11-22 16:03:18.624][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:18.625][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:18.626][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-22 16:03:18.627][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-22 16:03:18.628][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:18.629][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:18.630][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-11-22 16:03:18.631][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-11-22 16:03:18.632][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:18.633][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:18.634][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-22 16:03:18.635][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-22 16:03:18.641][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:18.642][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:18.643][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-22 16:03:18.644][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-22 16:03:18.645][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:18.646][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:18.647][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-22 16:03:18.648][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-22 16:03:18.649][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:18.650][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:18.681][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-22 16:03:18.682][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-22 16:03:18.683][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:18.684][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:18.685][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-22 16:03:18.686][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-22 16:03:18.687][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:18.688][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:18.688][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-22 16:03:18.689][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-22 16:03:18.690][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:18.691][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-11-22 16:03:18.692][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 749674.
biodb.TRACE[2025-11-22 16:03:18.694][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-11-22 16:03:18.696][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-11-22 16:03:18.696][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:18.697][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:18.698][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-11-22 16:03:18.699][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-11-22 16:03:18.700][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:18.701][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:18.702][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-11-22 16:03:18.703][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-11-22 16:03:18.704][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:18.705][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:18.706][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-11-22 16:03:18.707][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-11-22 16:03:18.708][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:18.708][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:18.711][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-22 16:03:18.712][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-22 16:03:18.713][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:18.713][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:18.726][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-11-22 16:03:18.727][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-11-22 16:03:18.728][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:18.729][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:18.733][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-22 16:03:18.734][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-22 16:03:18.735][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:18.736][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:18.737][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-22 16:03:18.738][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-22 16:03:18.739][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:18.740][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:18.741][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-22 16:03:18.742][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-22 16:03:18.742][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:18.743][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:18.746][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-22 16:03:18.747][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-22 16:03:18.748][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:18.749][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:18.750][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-22 16:03:18.793][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-22 16:03:18.794][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:18.795][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:18.795][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-22 16:03:18.796][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-22 16:03:18.797][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:18.798][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:18.799][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-11-22 16:03:18.800][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-11-22 16:03:18.801][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:18.802][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:18.803][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-11-22 16:03:18.804][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-11-22 16:03:18.805][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:18.806][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:18.807][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-11-22 16:03:18.808][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-11-22 16:03:18.809][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:18.810][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:18.817][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-22 16:03:18.818][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-22 16:03:18.819][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:18.820][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:18.821][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-22 16:03:18.822][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-22 16:03:18.823][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:18.823][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:18.824][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-22 16:03:18.825][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-22 16:03:18.826][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:18.827][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:18.828][ef$get] Asked field names are: accession.
biodb.TRACE[2025-11-22 16:03:18.829][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-22 16:03:18.830][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:18.831][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:18.832][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-22 16:03:18.833][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-22 16:03:18.834][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:18.835][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:18.843][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-11-22 16:03:18.844][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-11-22 16:03:18.845][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:18.846][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:18.846][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-11-22 16:03:18.847][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-11-22 16:03:18.848][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:18.849][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:18.850][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-11-22 16:03:18.851][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-11-22 16:03:18.852][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:18.853][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:18.854][ef$get] Asked field names are: formula.
biodb.TRACE[2025-11-22 16:03:18.855][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-11-22 16:03:18.856][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:18.857][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:18.858][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-11-22 16:03:18.859][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-11-22 16:03:18.860][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:18.860][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:18.868][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-11-22 16:03:18.869][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-11-22 16:03:18.870][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:18.871][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:18.872][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-11-22 16:03:18.873][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-11-22 16:03:18.873][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:18.874][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:18.875][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-11-22 16:03:18.876][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-11-22 16:03:18.877][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:18.878][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:18.879][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-11-22 16:03:18.880][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-11-22 16:03:18.881][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:18.882][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:18.883][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-11-22 16:03:18.884][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-11-22 16:03:18.884][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:18.885][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:18.893][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-11-22 16:03:18.894][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-11-22 16:03:18.894][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:18.895][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:18.896][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-11-22 16:03:18.897][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-11-22 16:03:18.898][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:18.899][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:18.900][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-11-22 16:03:18.901][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-11-22 16:03:18.902][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:18.903][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:18.904][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-11-22 16:03:18.905][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-11-22 16:03:18.906][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:18.906][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:18.907][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-11-22 16:03:18.908][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-11-22 16:03:18.909][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:18.910][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:18.921][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-11-22 16:03:18.922][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-11-22 16:03:18.923][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:18.924][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:18.925][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-11-22 16:03:18.926][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-11-22 16:03:18.927][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:18.928][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:18.929][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-11-22 16:03:18.930][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-11-22 16:03:18.931][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:18.932][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:18.933][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-11-22 16:03:18.934][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-11-22 16:03:18.934][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:18.935][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:18.936][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-11-22 16:03:18.937][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-11-22 16:03:18.938][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:18.939][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:18.946][ef$get] Asked field names are: accession.
biodb.TRACE[2025-11-22 16:03:18.947][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-22 16:03:18.948][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:18.949][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:18.953][ef$get] Asked field names are: formula.
biodb.TRACE[2025-11-22 16:03:18.954][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-11-22 16:03:18.955][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:18.956][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:18.959][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-11-22 16:03:18.960][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-11-22 16:03:18.961][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:18.962][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:18.966][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-11-22 16:03:18.967][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-11-22 16:03:18.968][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:18.969][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:18.972][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-11-22 16:03:18.973][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-11-22 16:03:18.974][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:18.975][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:18.990][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNci.Rcheck/biodbNci/testref/entry-nci.cactus-750690-content.sdf".
biodb.DEBUG[2025-11-22 16:03:19.027][biodb$getFactory()$createEntryFromCo ...] Creating NCI CACTUS entries from 1 content(s).
biodb.DEBUG[2025-11-22 16:03:19.028][biodb$getFactory()$createEntryFromCo ...] Parsing 1 NCI CACTUS entries.
biodb.DEBUG[2025-11-22 16:03:19.030][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-11-22 16:03:19.030][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-22 16:03:19.031][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-22 16:03:19.035][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-11-22 16:03:19.036][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-22 16:03:19.037][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:03:19.038][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-11-22 16:03:19.047][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-22 16:03:19.048][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-22 16:03:19.049][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:19.050][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:19.051][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-22 16:03:19.052][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-22 16:03:19.053][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:19.053][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:19.070][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-11-22 16:03:19.071][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-11-22 16:03:19.072][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:19.073][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:19.074][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-11-22 16:03:19.075][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-11-22 16:03:19.076][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:19.077][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:19.078][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-11-22 16:03:19.079][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-11-22 16:03:19.080][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:19.081][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:19.082][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-11-22 16:03:19.083][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-11-22 16:03:19.084][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:19.085][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:19.086][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-11-22 16:03:19.087][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-11-22 16:03:19.088][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:19.089][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:19.090][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-11-22 16:03:19.091][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-11-22 16:03:19.092][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:19.092][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:19.094][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-11-22 16:03:19.095][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-11-22 16:03:19.096][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:19.097][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:19.097][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-11-22 16:03:19.098][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-11-22 16:03:19.099][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:19.100][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:19.101][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-11-22 16:03:19.102][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-11-22 16:03:19.103][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:19.104][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:19.105][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-11-22 16:03:19.106][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-11-22 16:03:19.107][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:19.108][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:19.109][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-11-22 16:03:19.110][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-11-22 16:03:19.111][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:19.111][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:19.112][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-11-22 16:03:19.113][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-11-22 16:03:19.114][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:19.115][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:19.116][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-11-22 16:03:19.117][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-11-22 16:03:19.118][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:19.119][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:19.121][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-11-22 16:03:19.122][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-11-22 16:03:19.122][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:19.123][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:19.124][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-11-22 16:03:19.125][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-11-22 16:03:19.126][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:19.127][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:19.128][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-11-22 16:03:19.129][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-11-22 16:03:19.130][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:19.131][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:19.132][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-11-22 16:03:19.133][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-11-22 16:03:19.134][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:19.135][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:19.136][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-11-22 16:03:19.137][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-11-22 16:03:19.142][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:19.143][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:19.144][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-11-22 16:03:19.145][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-11-22 16:03:19.146][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:19.146][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:19.147][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-22 16:03:19.148][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-22 16:03:19.149][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:19.150][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:19.151][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-11-22 16:03:19.152][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-11-22 16:03:19.153][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:19.154][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:19.155][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-22 16:03:19.156][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-22 16:03:19.157][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:19.158][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:19.158][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-22 16:03:19.159][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-22 16:03:19.160][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:19.161][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:19.162][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-22 16:03:19.163][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-22 16:03:19.164][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:19.165][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:19.166][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-22 16:03:19.167][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-22 16:03:19.168][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:19.169][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:19.170][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-22 16:03:19.171][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-22 16:03:19.171][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:19.172][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:19.173][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-22 16:03:19.174][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-22 16:03:19.175][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:19.176][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-11-22 16:03:19.177][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 750690.
biodb.TRACE[2025-11-22 16:03:19.196][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-11-22 16:03:19.197][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-11-22 16:03:19.198][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:19.199][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:19.200][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-11-22 16:03:19.201][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-11-22 16:03:19.202][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:19.203][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:19.203][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-11-22 16:03:19.204][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-11-22 16:03:19.205][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:19.206][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:19.207][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-11-22 16:03:19.208][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-11-22 16:03:19.209][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:19.210][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:19.212][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-22 16:03:19.213][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-22 16:03:19.213][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:19.214][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:19.219][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-11-22 16:03:19.220][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-11-22 16:03:19.221][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:19.221][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:19.225][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-22 16:03:19.227][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-22 16:03:19.227][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:19.228][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:19.229][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-22 16:03:19.230][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-22 16:03:19.231][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:19.232][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:19.233][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-22 16:03:19.234][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-22 16:03:19.235][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:19.236][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:19.238][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-22 16:03:19.239][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-22 16:03:19.240][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:19.241][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:19.242][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-22 16:03:19.243][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-22 16:03:19.243][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:19.244][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:19.245][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-22 16:03:19.246][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-22 16:03:19.247][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:19.248][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:19.249][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-11-22 16:03:19.250][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-11-22 16:03:19.251][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:19.252][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:19.253][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-11-22 16:03:19.257][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-11-22 16:03:19.258][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:19.259][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:19.260][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-11-22 16:03:19.261][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-11-22 16:03:19.262][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:19.263][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:19.278][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-22 16:03:19.279][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-22 16:03:19.280][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:19.281][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:19.282][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-22 16:03:19.283][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-22 16:03:19.284][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:19.285][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:19.286][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-22 16:03:19.287][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-22 16:03:19.287][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:19.288][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:19.289][ef$get] Asked field names are: accession.
biodb.TRACE[2025-11-22 16:03:19.290][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-22 16:03:19.291][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:19.292][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:19.293][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-22 16:03:19.294][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-22 16:03:19.295][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:19.296][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:19.303][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-11-22 16:03:19.304][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-11-22 16:03:19.305][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:19.306][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:19.307][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-11-22 16:03:19.308][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-11-22 16:03:19.309][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:19.309][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:19.310][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-11-22 16:03:19.311][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-11-22 16:03:19.312][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:19.313][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:19.314][ef$get] Asked field names are: cas.id.
biodb.TRACE[2025-11-22 16:03:19.315][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-11-22 16:03:19.316][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:19.317][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:19.318][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-11-22 16:03:19.319][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-11-22 16:03:19.320][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:19.320][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:19.328][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-11-22 16:03:19.329][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-11-22 16:03:19.330][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:19.331][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:19.331][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-11-22 16:03:19.332][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-11-22 16:03:19.333][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:19.334][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:19.335][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-11-22 16:03:19.336][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-11-22 16:03:19.337][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:19.338][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:19.339][ef$get] Asked field names are: name.
biodb.TRACE[2025-11-22 16:03:19.340][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-11-22 16:03:19.341][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:19.342][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:19.343][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-11-22 16:03:19.344][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-11-22 16:03:19.344][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:19.345][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:19.353][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-11-22 16:03:19.354][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-11-22 16:03:19.354][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:19.355][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:19.356][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-11-22 16:03:19.357][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-11-22 16:03:19.358][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:19.359][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:19.360][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-11-22 16:03:19.361][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-11-22 16:03:19.362][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:19.363][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:19.364][ef$get] Asked field names are: formula.
biodb.TRACE[2025-11-22 16:03:19.365][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-11-22 16:03:19.366][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:19.366][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:19.367][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-11-22 16:03:19.368][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-11-22 16:03:19.369][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:19.370][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:19.381][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-11-22 16:03:19.382][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-11-22 16:03:19.383][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:19.384][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:19.385][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-11-22 16:03:19.386][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-11-22 16:03:19.387][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:19.388][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:19.389][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-11-22 16:03:19.390][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-11-22 16:03:19.391][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:19.392][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:19.393][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-11-22 16:03:19.394][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-11-22 16:03:19.395][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:19.395][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:19.396][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-11-22 16:03:19.397][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-11-22 16:03:19.398][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:19.399][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:19.406][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-11-22 16:03:19.407][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-11-22 16:03:19.408][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:19.409][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:19.410][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-11-22 16:03:19.411][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-11-22 16:03:19.412][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:19.413][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:19.414][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-11-22 16:03:19.415][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-11-22 16:03:19.416][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:19.417][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:19.418][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-11-22 16:03:19.418][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-11-22 16:03:19.419][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:19.420][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:19.421][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-11-22 16:03:19.422][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-11-22 16:03:19.423][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:19.424][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:19.431][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-11-22 16:03:19.432][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-11-22 16:03:19.433][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:19.434][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:19.435][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-11-22 16:03:19.436][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-11-22 16:03:19.437][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:19.438][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:19.439][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-11-22 16:03:19.440][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-11-22 16:03:19.441][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:19.442][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:19.443][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-11-22 16:03:19.444][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-11-22 16:03:19.445][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:19.445][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:19.446][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-11-22 16:03:19.447][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-11-22 16:03:19.448][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:19.449][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:19.457][ef$get] Asked field names are: accession.
biodb.TRACE[2025-11-22 16:03:19.458][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-22 16:03:19.459][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:19.459][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:19.463][ef$get] Asked field names are: cas.id.
biodb.TRACE[2025-11-22 16:03:19.464][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-11-22 16:03:19.465][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:19.466][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:19.470][ef$get] Asked field names are: formula.
biodb.TRACE[2025-11-22 16:03:19.471][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-11-22 16:03:19.472][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:19.473][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:19.476][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-11-22 16:03:19.477][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-11-22 16:03:19.478][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:19.479][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:19.483][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-11-22 16:03:19.484][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-11-22 16:03:19.485][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:19.486][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:19.493][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-11-22 16:03:19.494][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-11-22 16:03:19.495][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:19.496][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:19.500][ef$get] Asked field names are: name.
biodb.TRACE[2025-11-22 16:03:19.501][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-11-22 16:03:19.502][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:19.502][ef$get] fields variable is a list.
biodb.INFO [2025-11-22 16:03:19.509][biodb::testThat]
biodb.INFO [2025-11-22 16:03:19.510][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2025-11-22 16:03:19.511][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-11-22 16:03:19.511][biodb::testThat]
biodb.DEBUG[2025-11-22 16:03:19.513][private$loadEntries] Creating entries from ids [2]: "749674, 750690".
biodb.DEBUG[2025-11-22 16:03:19.515][conn$getEntryContent] Get NCI CACTUS entry content(s) for 2 id(s)...
biodb.DEBUG[2025-11-22 16:03:19.518][self$isDownloaded] Database nci.cactus has already been downloaded.
biodb.DEBUG[2025-11-22 16:03:19.545][self$isDownloaded] Database nci.cactus has already been downloaded.
biodb.INFO [2025-11-22 16:03:19.547][self$download] Extract whole database of nci.cactus.
biodb.INFO [2025-11-22 16:03:19.547][private$doExtractDownload] Extracting content of downloaded biodbNci, a library for connecting to the National Cancer Institute (USA) CACTUS Database....
Saving _problems/test_long_100_generic-38.R
biodb.INFO [2025-11-22 16:03:19.675][biodb::testThat]
biodb.INFO [2025-11-22 16:03:19.676][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2025-11-22 16:03:19.677][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-11-22 16:03:19.678][biodb::testThat]
biodb.INFO [2025-11-22 16:03:19.683][biodb::testThat]
biodb.INFO [2025-11-22 16:03:19.684][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2025-11-22 16:03:19.685][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-11-22 16:03:19.686][biodb::testThat]
biodb.WARN [2025-11-22 16:03:19.708][self$searchForEntries] This database is not searchable by field "name".
biodb.WARN [2025-11-22 16:03:19.726][self$searchForEntries] This database is not searchable by field "name".
biodb.INFO [2025-11-22 16:03:19.733][biodb::testThat]
biodb.INFO [2025-11-22 16:03:19.734][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2025-11-22 16:03:19.735][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-11-22 16:03:19.736][biodb::testThat]
biodb.DEBUG[2025-11-22 16:03:19.752][private$loadEntries] Creating entries from ids [1]: "749674".
biodb.DEBUG[2025-11-22 16:03:19.799][conn$getEntryContent] Get NCI CACTUS entry content(s) for 1 id(s)...
biodb.DEBUG[2025-11-22 16:03:19.800][self$isDownloaded] Database nci.cactus has already been downloaded.
biodb.DEBUG[2025-11-22 16:03:19.802][self$isDownloaded] Database nci.cactus has already been downloaded.
biodb.INFO [2025-11-22 16:03:19.803][self$download] Extract whole database of nci.cactus.
biodb.INFO [2025-11-22 16:03:19.815][private$doExtractDownload] Extracting content of downloaded biodbNci, a library for connecting to the National Cancer Institute (USA) CACTUS Database....
Saving _problems/test_long_100_generic-38.R
biodb.INFO [2025-11-22 16:03:19.865][biodb::testThat]
biodb.INFO [2025-11-22 16:03:19.866][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2025-11-22 16:03:19.867][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-11-22 16:03:19.868][biodb::testThat]
biodb.INFO [2025-11-22 16:03:19.874][biodb::testThat]
biodb.INFO [2025-11-22 16:03:19.875][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2025-11-22 16:03:19.876][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-11-22 16:03:19.877][biodb::testThat]
biodb.INFO [2025-11-22 16:03:19.888][biodb::testThat]
biodb.INFO [2025-11-22 16:03:19.888][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2025-11-22 16:03:19.889][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-11-22 16:03:19.890][biodb::testThat]
biodb.INFO [2025-11-22 16:03:19.896][biodb::testThat]
biodb.INFO [2025-11-22 16:03:19.896][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2025-11-22 16:03:19.897][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-11-22 16:03:19.898][biodb::testThat]
biodb.INFO [2025-11-22 16:03:19.903][biodb$terminate] Closing BiodbMain instance...
biodb.INFO [2025-11-22 16:03:19.905][self$deleteConn] Connector "nci.cactus" deleted.
biodb.DEBUG[2025-11-22 16:03:19.905][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-11-22 16:03:19.906][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-22 16:03:19.907][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-22 16:03:19.908][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-22 16:03:19.909][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-22 16:03:19.910][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:03:19.911][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2025-11-22 16:03:19.920][biodb::testContext]
biodb.INFO [2025-11-22 16:03:19.920][biodb::testContext] ********************************************************************************
biodb.INFO [2025-11-22 16:03:19.921][biodb::testContext] Test context - Example long tests
biodb.INFO [2025-11-22 16:03:19.922][biodb::testContext] ********************************************************************************
biodb.INFO [2025-11-22 16:03:19.923][biodb::testContext]
biodb.INFO [2025-11-22 16:03:19.925][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.18.0.
biodb.DEBUG[2025-11-22 16:03:19.927][self$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.22-bioc/R/site-library/biodb/definitions.yml".
biodb.DEBUG[2025-11-22 16:03:19.930][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-11-22 16:03:19.931][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-11-22 16:03:19.932][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-11-22 16:03:19.933][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:03:19.934][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:03:19.934][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:03:19.935][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-11-22 16:03:19.936][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-11-22 16:03:19.937][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:03:19.938][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:03:19.939][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:03:19.940][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-11-22 16:03:19.941][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-11-22 16:03:19.941][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:03:19.942][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:03:19.943][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:03:19.944][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-11-22 16:03:19.945][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-11-22 16:03:19.946][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-11-22 16:03:19.947][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:03:19.948][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:03:19.948][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:03:19.949][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-11-22 16:03:19.950][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-11-22 16:03:19.951][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-11-22 16:03:19.952][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:03:19.953][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:03:19.954][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:03:19.955][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-11-22 16:03:19.956][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-11-22 16:03:19.956][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:03:19.957][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:03:19.958][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:03:19.959][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-11-22 16:03:19.960][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-11-22 16:03:19.961][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-11-22 16:03:19.962][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:03:19.963][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:03:19.963][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:03:19.964][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-11-22 16:03:19.965][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-11-22 16:03:19.966][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:03:19.967][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:03:19.968][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:03:19.969][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-11-22 16:03:19.970][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-11-22 16:03:19.971][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-11-22 16:03:19.971][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:03:19.972][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:03:19.973][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:03:19.974][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-11-22 16:03:19.975][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-11-22 16:03:19.976][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-11-22 16:03:19.977][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-11-22 16:03:19.978][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-11-22 16:03:19.979][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-11-22 16:03:19.980][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:03:19.980][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:03:19.981][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:03:19.982][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-11-22 16:03:19.983][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-11-22 16:03:19.984][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:03:19.985][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:03:19.986][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:03:19.987][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-11-22 16:03:19.988][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-11-22 16:03:19.988][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:03:19.989][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:03:19.990][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:03:19.991][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-11-22 16:03:19.996][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-11-22 16:03:19.997][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:03:19.998][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:03:19.999][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:03:19.999][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-11-22 16:03:20.000][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-11-22 16:03:20.001][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-11-22 16:03:20.002][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:03:20.003][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:03:20.004][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:03:20.005][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-11-22 16:03:20.006][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-11-22 16:03:20.010][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-11-22 16:03:20.011][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:03:20.012][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:03:20.013][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:03:20.014][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-11-22 16:03:20.014][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-11-22 16:03:20.015][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-11-22 16:03:20.016][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:03:20.017][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:03:20.018][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:03:20.019][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-11-22 16:03:20.021][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-11-22 16:03:20.022][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2025-11-22 16:03:20.023][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-11-22 16:03:20.024][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-11-22 16:03:20.025][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-11-22 16:03:20.025][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-11-22 16:03:20.026][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-11-22 16:03:20.027][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-11-22 16:03:20.028][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-11-22 16:03:20.029][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-11-22 16:03:20.030][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-11-22 16:03:20.031][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-11-22 16:03:20.032][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-11-22 16:03:20.033][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-11-22 16:03:20.034][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-11-22 16:03:20.035][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-11-22 16:03:20.035][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-11-22 16:03:20.035][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-11-22 16:03:20.035][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-11-22 16:03:20.035][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-11-22 16:03:20.036][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-11-22 16:03:20.037][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-11-22 16:03:20.037][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-11-22 16:03:20.038][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-11-22 16:03:20.039][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-11-22 16:03:20.040][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-11-22 16:03:20.041][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-11-22 16:03:20.042][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-11-22 16:03:20.043][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-11-22 16:03:20.044][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-11-22 16:03:20.045][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-11-22 16:03:20.045][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-11-22 16:03:20.047][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-11-22 16:03:20.048][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-11-22 16:03:20.049][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-11-22 16:03:20.050][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-11-22 16:03:20.051][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-11-22 16:03:20.052][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-11-22 16:03:20.053][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-11-22 16:03:20.054][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-11-22 16:03:20.055][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-11-22 16:03:20.056][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-11-22 16:03:20.057][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-11-22 16:03:20.058][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-11-22 16:03:20.059][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-11-22 16:03:20.059][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-11-22 16:03:20.060][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-11-22 16:03:20.061][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-11-22 16:03:20.062][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-11-22 16:03:20.062][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-11-22 16:03:20.062][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-11-22 16:03:20.062][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-11-22 16:03:20.062][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-11-22 16:03:20.063][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-11-22 16:03:20.064][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-11-22 16:03:20.065][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-11-22 16:03:20.066][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-11-22 16:03:20.067][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-11-22 16:03:20.068][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-11-22 16:03:20.068][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-11-22 16:03:20.069][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-11-22 16:03:20.070][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-11-22 16:03:20.071][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-11-22 16:03:20.072][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-11-22 16:03:20.073][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-11-22 16:03:20.074][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-11-22 16:03:20.076][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-11-22 16:03:20.077][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2025-11-22 16:03:20.078][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-11-22 16:03:20.079][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-11-22 16:03:20.080][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-11-22 16:03:20.081][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-11-22 16:03:20.081][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-11-22 16:03:20.082][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-11-22 16:03:20.083][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-11-22 16:03:20.084][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-11-22 16:03:20.085][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-11-22 16:03:20.086][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-11-22 16:03:20.087][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-11-22 16:03:20.088][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-11-22 16:03:20.089][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-11-22 16:03:20.090][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-11-22 16:03:20.091][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-11-22 16:03:20.092][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-11-22 16:03:20.093][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-11-22 16:03:20.094][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-11-22 16:03:20.095][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-11-22 16:03:20.095][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-11-22 16:03:20.096][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-11-22 16:03:20.097][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-11-22 16:03:20.098][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-11-22 16:03:20.099][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-11-22 16:03:20.100][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-11-22 16:03:20.101][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-11-22 16:03:20.106][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-11-22 16:03:20.108][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-11-22 16:03:20.109][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-11-22 16:03:20.110][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-11-22 16:03:20.111][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-11-22 16:03:20.111][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-11-22 16:03:20.112][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-11-22 16:03:20.113][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-11-22 16:03:20.114][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-11-22 16:03:20.115][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-11-22 16:03:20.116][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-11-22 16:03:20.117][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-11-22 16:03:20.118][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-11-22 16:03:20.119][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-11-22 16:03:20.120][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-11-22 16:03:20.121][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-11-22 16:03:20.122][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-11-22 16:03:20.123][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-11-22 16:03:20.124][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-11-22 16:03:20.124][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-11-22 16:03:20.125][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-11-22 16:03:20.126][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-11-22 16:03:20.127][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-11-22 16:03:20.128][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-11-22 16:03:20.129][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-11-22 16:03:20.130][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-11-22 16:03:20.131][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-11-22 16:03:20.131][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-11-22 16:03:20.132][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-11-22 16:03:20.134][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-11-22 16:03:20.134][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:03:20.135][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:03:20.136][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:03:20.137][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-22 16:03:20.138][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-22 16:03:20.139][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:03:20.139][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:03:20.140][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:03:20.141][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-22 16:03:20.142][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-22 16:03:20.143][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:03:20.144][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:03:20.144][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:03:20.145][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-22 16:03:20.146][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-22 16:03:20.147][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:03:20.148][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:03:20.148][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:03:20.149][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-22 16:03:20.150][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-22 16:03:20.151][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:03:20.152][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:03:20.153][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:03:20.153][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-22 16:03:20.154][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-22 16:03:20.155][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:03:20.156][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:03:20.157][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:03:20.158][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-22 16:03:20.158][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-22 16:03:20.159][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:03:20.160][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:03:20.161][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:03:20.162][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-22 16:03:20.163][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-22 16:03:20.163][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:03:20.164][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:03:20.165][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:03:20.166][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-22 16:03:20.167][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-22 16:03:20.167][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:03:20.168][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:03:20.169][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:03:20.170][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-22 16:03:20.171][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-22 16:03:20.172][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:03:20.172][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:03:20.173][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:03:20.174][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-22 16:03:20.175][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-22 16:03:20.176][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:03:20.177][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:03:20.177][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:03:20.178][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-22 16:03:20.179][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-22 16:03:20.180][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:03:20.181][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:03:20.182][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:03:20.182][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-22 16:03:20.183][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-22 16:03:20.184][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:03:20.185][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:03:20.186][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:03:20.186][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-22 16:03:20.187][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-22 16:03:20.188][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:03:20.189][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:03:20.190][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:03:20.191][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-22 16:03:20.191][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-22 16:03:20.192][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:03:20.193][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:03:20.194][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:03:20.195][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-22 16:03:20.196][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-22 16:03:20.196][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:03:20.197][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:03:20.198][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:03:20.199][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-22 16:03:20.200][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-22 16:03:20.201][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:03:20.201][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:03:20.202][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-11-22 16:03:20.204][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-11-22 16:03:20.205][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-11-22 16:03:20.206][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-11-22 16:03:20.211][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-11-22 16:03:20.213][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-11-22 16:03:20.214][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-11-22 16:03:20.215][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-11-22 16:03:20.216][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-11-22 16:03:20.218][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-11-22 16:03:20.219][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-11-22 16:03:20.220][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-11-22 16:03:20.222][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-11-22 16:03:20.223][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-11-22 16:03:20.224][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-11-22 16:03:20.225][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-11-22 16:03:20.227][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-11-22 16:03:20.228][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-11-22 16:03:20.229][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-11-22 16:03:20.231][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-11-22 16:03:20.232][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-11-22 16:03:20.233][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-11-22 16:03:20.235][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-11-22 16:03:20.236][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-11-22 16:03:20.237][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-11-22 16:03:20.238][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-11-22 16:03:20.240][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-11-22 16:03:20.241][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-11-22 16:03:20.242][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-11-22 16:03:20.243][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-11-22 16:03:20.245][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-11-22 16:03:20.246][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-11-22 16:03:20.247][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-11-22 16:03:20.249][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-11-22 16:03:20.250][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-11-22 16:03:20.251][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-11-22 16:03:20.252][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-11-22 16:03:20.254][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-11-22 16:03:20.255][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-11-22 16:03:20.256][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-11-22 16:03:20.258][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-11-22 16:03:20.259][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-11-22 16:03:20.260][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-11-22 16:03:20.261][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-11-22 16:03:20.263][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-11-22 16:03:20.264][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-11-22 16:03:20.265][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-11-22 16:03:20.267][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-11-22 16:03:20.268][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-11-22 16:03:20.269][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-11-22 16:03:20.270][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-11-22 16:03:20.272][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-11-22 16:03:20.273][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-11-22 16:03:20.274][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-11-22 16:03:20.276][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-11-22 16:03:20.277][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-11-22 16:03:20.278][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-11-22 16:03:20.279][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-11-22 16:03:20.281][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-11-22 16:03:20.282][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-11-22 16:03:20.283][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-11-22 16:03:20.285][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-11-22 16:03:20.286][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-11-22 16:03:20.287][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-11-22 16:03:20.288][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-11-22 16:03:20.290][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-11-22 16:03:20.291][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-11-22 16:03:20.292][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-11-22 16:03:20.294][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-11-22 16:03:20.295][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-11-22 16:03:20.296][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-11-22 16:03:20.297][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-11-22 16:03:20.299][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-11-22 16:03:20.300][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-11-22 16:03:20.301][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-11-22 16:03:20.303][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-11-22 16:03:20.304][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-11-22 16:03:20.305][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-11-22 16:03:20.307][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-11-22 16:03:20.308][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-11-22 16:03:20.309][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-11-22 16:03:20.314][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-11-22 16:03:20.316][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-11-22 16:03:20.317][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-11-22 16:03:20.319][initialize] This is biodb version 1.18.0.
biodb.DEBUG[2025-11-22 16:03:20.319][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-11-22 16:03:20.320][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-11-22 16:03:20.321][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-22 16:03:20.322][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:03:20.323][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:03:20.324][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:03:20.324][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-22 16:03:20.325][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-22 16:03:20.326][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-22 16:03:20.327][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-22 16:03:20.328][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:03:20.329][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:03:20.329][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:03:20.330][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-22 16:03:20.331][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-22 16:03:20.332][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-22 16:03:20.333][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-22 16:03:20.334][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:03:20.334][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:03:20.335][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:03:20.336][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-22 16:03:20.337][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-22 16:03:20.338][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-22 16:03:20.338][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-22 16:03:20.339][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:03:20.340][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:03:20.341][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:03:20.342][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-22 16:03:20.343][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-22 16:03:20.343][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-22 16:03:20.344][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-22 16:03:20.345][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:03:20.346][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[2025-11-22 16:03:20.347][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:03:20.348][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-22 16:03:20.348][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-22 16:03:20.349][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-22 16:03:20.350][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-22 16:03:20.351][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:03:20.352][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:03:20.352][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:03:20.353][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-22 16:03:20.354][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-22 16:03:20.355][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-22 16:03:20.356][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-22 16:03:20.357][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:03:20.357][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:03:20.358][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:03:20.359][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-22 16:03:20.360][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-22 16:03:20.361][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-22 16:03:20.362][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-22 16:03:20.362][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:03:20.363][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:03:20.364][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:03:20.365][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-22 16:03:20.366][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-22 16:03:20.366][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-22 16:03:20.367][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-22 16:03:20.368][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:03:20.369][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:03:20.370][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:03:20.371][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-22 16:03:20.371][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-22 16:03:20.372][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-22 16:03:20.373][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-22 16:03:20.374][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:03:20.375][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:03:20.376][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:03:20.376][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-22 16:03:20.377][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-22 16:03:20.378][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-22 16:03:20.379][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-22 16:03:20.380][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:03:20.380][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:03:20.381][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:03:20.382][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-22 16:03:20.383][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-22 16:03:20.384][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-22 16:03:20.385][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-22 16:03:20.385][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:03:20.386][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:03:20.387][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:03:20.388][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-22 16:03:20.389][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-22 16:03:20.390][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-22 16:03:20.390][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-22 16:03:20.391][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:03:20.392][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:03:20.393][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:03:20.394][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-22 16:03:20.395][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-22 16:03:20.395][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-22 16:03:20.396][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-22 16:03:20.397][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:03:20.398][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:03:20.399][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:03:20.400][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-22 16:03:20.400][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-22 16:03:20.401][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-22 16:03:20.402][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-22 16:03:20.403][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:03:20.404][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:03:20.405][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:03:20.405][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-22 16:03:20.406][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-22 16:03:20.407][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-22 16:03:20.408][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-22 16:03:20.409][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:03:20.409][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:03:20.410][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:03:20.411][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-22 16:03:20.412][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-22 16:03:20.417][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-22 16:03:20.417][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-22 16:03:20.418][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:03:20.419][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:03:20.421][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNci.Rcheck/biodbNci/definitions.yml".
biodb.DEBUG[2025-11-22 16:03:20.422][self$getDbsInfo()$define] Define connector nci.cactus.
biodb.DEBUG[2025-11-22 16:03:20.424][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-11-22 16:03:20.425][self$setPropertyValue] Setting property "description" to "National Cancer Institute (USA) CACTUS Database.".
biodb.DEBUG[2025-11-22 16:03:20.425][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-11-22 16:03:20.426][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-11-22 16:03:20.427][self$setPropertyValue] Setting property "downloadable" to "TRUE".
biodb.DEBUG[2025-11-22 16:03:20.428][self$setPropertyValue] Setting property "dwnld.ext" to "gz".
biodb.DEBUG[2025-11-22 16:03:20.429][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-11-22 16:03:20.430][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-11-22 16:03:20.431][self$setPropertyValue] Setting property "entry.content.type" to "sdf".
biodb.DEBUG[2025-11-22 16:03:20.432][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-11-22 16:03:20.433][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-11-22 16:03:20.434][self$setPropertyValue] Setting property "name" to "NCI CACTUS".
biodb.DEBUG[2025-11-22 16:03:20.435][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-11-22 16:03:20.436][self$setPropertyValue] Setting property "parsing.expr" to "NSC".
biodb.DEBUG[2025-11-22 16:03:20.436][self$setPropertyValue] Setting property "parsing.expr" to "DTP names".
biodb.DEBUG[2025-11-22 16:03:20.436][self$setPropertyValue] Setting property "parsing.expr" to "Standard InChI".
biodb.DEBUG[2025-11-22 16:03:20.436][self$setPropertyValue] Setting property "parsing.expr" to "c("Standard InChIKey", "^InChIKey=(.*)$")".
biodb.DEBUG[2025-11-22 16:03:20.436][self$setPropertyValue] Setting property "parsing.expr" to "Formula".
biodb.DEBUG[2025-11-22 16:03:20.436][self$setPropertyValue] Setting property "parsing.expr" to "Molecular Weight".
biodb.DEBUG[2025-11-22 16:03:20.436][self$setPropertyValue] Setting property "parsing.expr" to "CAS".
biodb.DEBUG[2025-11-22 16:03:20.437][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-11-22 16:03:20.438][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-11-22 16:03:20.439][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-11-22 16:03:20.439][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-11-22 16:03:20.440][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-11-22 16:03:20.441][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-11-22 16:03:20.442][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-11-22 16:03:20.443][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-11-22 16:03:20.444][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-11-22 16:03:20.445][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/".
biodb.DEBUG[2025-11-22 16:03:20.445][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/".
biodb.DEBUG[2025-11-22 16:03:20.445][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/download/nci/".
biodb.DEBUG[2025-11-22 16:03:20.445][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/download/nci/NCI-Open_2012-05-01.sdf.gz".
biodb.DEBUG[2025-11-22 16:03:20.446][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-11-22 16:03:20.446][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-11-22 16:03:20.447][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-11-22 16:03:20.448][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-11-22 16:03:20.449][self$getEntryFields()$define] Define field nci.cactus.id.
biodb.DEBUG[2025-11-22 16:03:20.452][super$initialize] Initialize connector nci.cactus.
biodb.DEBUG[2025-11-22 16:03:20.455][biodb$getFactory()$createConn] Creating new connector nci.cactus for database class nci.cactus .
biodb.INFO [2025-11-22 16:03:20.456][biodb$terminate] Closing BiodbMain instance...
biodb.INFO [2025-11-22 16:03:20.457][self$deleteConn] Connector "nci.cactus" deleted.
biodb.DEBUG[2025-11-22 16:03:20.458][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-11-22 16:03:20.459][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-22 16:03:20.460][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-22 16:03:20.460][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-22 16:03:20.461][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-22 16:03:20.462][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:03:20.463][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
[ FAIL 2 | WARN 0 | SKIP 2 | PASS 85 ]

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

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

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

'R CMD check' output

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


* using log directory ‘/home/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNci.Rcheck’
* using R version 4.5.2 (2025-10-31)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* using options ‘--no-codoc --no-examples --no-manual --ignore-vignettes --no-stop-on-test-error’
* checking for file ‘biodbNci/DESCRIPTION’ ... OK
* this is package ‘biodbNci’ version ‘1.14.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘biodbNci’ can be installed ... OK
* used C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
* checking installed package size ... INFO
  installed size is  6.1Mb
  sub-directories of 1Mb or more:
    libs   5.8Mb
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking whether startup messages can be suppressed ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  NciCactusConn.Rd: BiodbConn
  NciCactusEntry.Rd: BiodbSdfEntry
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... SKIPPED
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... OK
* checking files in ‘vignettes’ ... SKIPPED
* checking examples ... SKIPPED
* checking for unstated dependencies in ‘longtests’ ... OK
* checking tests in ‘longtests’ ...
  Running ‘testthat.R’
 ERROR
Running the tests in ‘longtests/testthat.R’ failed.
Last 13 lines of output:
      ▆
   1. ├─base::do.call(fct, params)
   2. └─biodb (local) `<fn>`(conn = `<NcCctsCn>`, opt = `<named list>`)
   3.   └─opt$refEntries$getRealEntry(id)
   4.     └─self$getRealEntries(ids = id)
   5.       └─private$bdb$getFactory()$getEntry(...)
   6.         └─private$loadEntries(conn$getId(), missing.ids, drop = FALSE)
   7.           └─conn$getEntryContent(ids)
   8.             └─self$download()
   9.               └─private$doExtractDownload()
  
  [ FAIL 2 | WARN 0 | SKIP 2 | PASS 85 ]
  Error:
  ! Test failures.
  Execution halted
* DONE

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

Installation output

biodbNci.Rcheck/00install.out

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