Back to Long Tests report for BioC 3.22

This page was generated on 2025-12-13 23:55 -0500 (Sat, 13 Dec 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 4882
merida1macOS 12.7.6 Montereyx86_644.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 4673
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: 2025-12-13 09:55 -0500 (Sat, 13 Dec 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: 2025-12-13 16:02:25 -0500 (Sat, 13 Dec 2025)
EndedAt: 2025-12-13 16:03:29 -0500 (Sat, 13 Dec 2025)
EllapsedTime: 64.1 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 [2025-12-13 16:03:26.269][biodb::testContext]
biodb.INFO [2025-12-13 16:03:26.271][biodb::testContext] ********************************************************************************
biodb.INFO [2025-12-13 16:03:26.272][biodb::testContext] Test context - Generic long tests
biodb.INFO [2025-12-13 16:03:26.273][biodb::testContext] ********************************************************************************
biodb.INFO [2025-12-13 16:03:26.273][biodb::testContext]
biodb.INFO [2025-12-13 16:03:26.280][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.18.0.
biodb.DEBUG[2025-12-13 16:03:26.281][self$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.22-bioc/R/site-library/biodb/definitions.yml".
biodb.DEBUG[2025-12-13 16:03:26.288][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-12-13 16:03:26.289][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-12-13 16:03:26.290][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-12-13 16:03:26.291][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:03:26.292][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:03:26.293][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:03:26.294][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-12-13 16:03:26.310][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-12-13 16:03:26.311][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:03:26.312][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:03:26.313][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:03:26.314][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-12-13 16:03:26.315][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-12-13 16:03:26.316][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:03:26.325][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:03:26.326][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:03:26.327][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-12-13 16:03:26.328][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-12-13 16:03:26.329][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-12-13 16:03:26.330][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:03:26.330][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:03:26.331][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:03:26.332][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-12-13 16:03:26.333][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-12-13 16:03:26.334][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-12-13 16:03:26.335][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:03:26.336][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:03:26.337][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:03:26.337][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-12-13 16:03:26.338][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-12-13 16:03:26.339][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:03:26.340][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:03:26.341][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:03:26.342][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-12-13 16:03:26.343][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-12-13 16:03:26.344][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-12-13 16:03:26.345][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:03:26.345][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:03:26.346][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:03:26.347][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-12-13 16:03:26.348][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-12-13 16:03:26.349][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:03:26.350][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:03:26.351][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:03:26.352][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-12-13 16:03:26.353][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-12-13 16:03:26.354][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-12-13 16:03:26.354][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:03:26.355][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:03:26.356][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:03:26.357][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-12-13 16:03:26.358][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-12-13 16:03:26.359][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-12-13 16:03:26.360][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-12-13 16:03:26.361][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-12-13 16:03:26.362][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-12-13 16:03:26.363][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:03:26.363][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:03:26.364][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:03:26.365][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-12-13 16:03:26.366][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-12-13 16:03:26.367][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:03:26.368][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:03:26.369][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:03:26.369][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-12-13 16:03:26.370][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-12-13 16:03:26.371][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:03:26.372][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:03:26.373][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:03:26.374][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-12-13 16:03:26.375][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-12-13 16:03:26.376][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:03:26.376][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:03:26.377][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:03:26.378][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-12-13 16:03:26.379][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-12-13 16:03:26.380][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-12-13 16:03:26.381][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:03:26.382][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:03:26.383][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[2025-12-13 16:03:26.384][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-12-13 16:03:26.384][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-12-13 16:03:26.388][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-12-13 16:03:26.389][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:03:26.390][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:03:26.391][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:03:26.392][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-12-13 16:03:26.393][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-12-13 16:03:26.394][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-12-13 16:03:26.394][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:03:26.395][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:03:26.396][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:03:26.399][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-12-13 16:03:26.430][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-12-13 16:03:26.445][self$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[2025-12-13 16:03:26.446][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-12-13 16:03:26.447][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-12-13 16:03:26.448][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-12-13 16:03:26.449][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-12-13 16:03:26.450][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-12-13 16:03:26.450][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-12-13 16:03:26.451][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-12-13 16:03:26.452][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-12-13 16:03:26.453][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-12-13 16:03:26.454][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-12-13 16:03:26.455][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-12-13 16:03:26.456][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-12-13 16:03:26.457][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-12-13 16:03:26.458][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-12-13 16:03:26.458][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-12-13 16:03:26.458][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-12-13 16:03:26.458][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-12-13 16:03:26.458][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-12-13 16:03:26.459][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-12-13 16:03:26.460][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-12-13 16:03:26.461][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-12-13 16:03:26.461][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-12-13 16:03:26.462][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-12-13 16:03:26.463][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-12-13 16:03:26.464][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-12-13 16:03:26.465][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-12-13 16:03:26.466][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-12-13 16:03:26.467][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-12-13 16:03:26.468][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-12-13 16:03:26.469][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-12-13 16:03:26.470][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-12-13 16:03:26.471][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-12-13 16:03:26.472][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-12-13 16:03:26.473][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-12-13 16:03:26.474][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-12-13 16:03:26.475][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-12-13 16:03:26.476][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-12-13 16:03:26.477][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-12-13 16:03:26.478][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-12-13 16:03:26.483][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-12-13 16:03:26.484][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-12-13 16:03:26.485][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-12-13 16:03:26.486][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-12-13 16:03:26.487][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-12-13 16:03:26.488][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-12-13 16:03:26.489][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-12-13 16:03:26.489][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-12-13 16:03:26.489][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-12-13 16:03:26.489][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-12-13 16:03:26.489][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-12-13 16:03:26.489][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-12-13 16:03:26.490][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-12-13 16:03:26.491][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-12-13 16:03:26.492][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-12-13 16:03:26.493][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-12-13 16:03:26.494][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-12-13 16:03:26.495][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-12-13 16:03:26.496][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-12-13 16:03:26.497][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-12-13 16:03:26.497][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-12-13 16:03:26.498][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-12-13 16:03:26.499][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-12-13 16:03:26.500][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-12-13 16:03:26.501][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-12-13 16:03:26.503][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-12-13 16:03:26.504][self$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[2025-12-13 16:03:26.505][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-12-13 16:03:26.506][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-12-13 16:03:26.507][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-12-13 16:03:26.508][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-12-13 16:03:26.509][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-12-13 16:03:26.509][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-12-13 16:03:26.510][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-12-13 16:03:26.511][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-12-13 16:03:26.512][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-12-13 16:03:26.513][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-12-13 16:03:26.514][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-12-13 16:03:26.515][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-12-13 16:03:26.516][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-12-13 16:03:26.517][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-12-13 16:03:26.518][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-12-13 16:03:26.519][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-12-13 16:03:26.520][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-12-13 16:03:26.520][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-12-13 16:03:26.521][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-12-13 16:03:26.522][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-12-13 16:03:26.523][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-12-13 16:03:26.524][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-12-13 16:03:26.525][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-12-13 16:03:26.526][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-12-13 16:03:26.527][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-12-13 16:03:26.528][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-12-13 16:03:26.529][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-12-13 16:03:26.530][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-12-13 16:03:26.531][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-12-13 16:03:26.532][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-12-13 16:03:26.533][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-12-13 16:03:26.534][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-12-13 16:03:26.535][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-12-13 16:03:26.536][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-12-13 16:03:26.537][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-12-13 16:03:26.538][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-12-13 16:03:26.539][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-12-13 16:03:26.540][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-12-13 16:03:26.541][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-12-13 16:03:26.542][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-12-13 16:03:26.543][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-12-13 16:03:26.543][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-12-13 16:03:26.544][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-12-13 16:03:26.545][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-12-13 16:03:26.546][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-12-13 16:03:26.547][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-12-13 16:03:26.548][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-12-13 16:03:26.549][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-12-13 16:03:26.550][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-12-13 16:03:26.551][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-12-13 16:03:26.552][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-12-13 16:03:26.552][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-12-13 16:03:26.553][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-12-13 16:03:26.554][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-12-13 16:03:26.555][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-12-13 16:03:26.559][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-12-13 16:03:26.559][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:03:26.560][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:03:26.561][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:03:26.562][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-13 16:03:26.563][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-13 16:03:26.564][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:03:26.564][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:03:26.565][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:03:26.566][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-13 16:03:26.567][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-13 16:03:26.568][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:03:26.569][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:03:26.569][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:03:26.570][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-13 16:03:26.571][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-13 16:03:26.572][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:03:26.573][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:03:26.574][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:03:26.574][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-13 16:03:26.575][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-13 16:03:26.576][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:03:26.577][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:03:26.578][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:03:26.578][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-13 16:03:26.579][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-13 16:03:26.580][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:03:26.581][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:03:26.582][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:03:26.583][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-13 16:03:26.583][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-13 16:03:26.584][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:03:26.585][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:03:26.586][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:03:26.587][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-13 16:03:26.587][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-13 16:03:26.588][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:03:26.589][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:03:26.590][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:03:26.591][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-13 16:03:26.592][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-13 16:03:26.592][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:03:26.593][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:03:26.594][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:03:26.595][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-13 16:03:26.596][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-13 16:03:26.597][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:03:26.597][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:03:26.598][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:03:26.599][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-13 16:03:26.600][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-13 16:03:26.601][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:03:26.601][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:03:26.602][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:03:26.603][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-13 16:03:26.604][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-13 16:03:26.605][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:03:26.606][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:03:26.606][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:03:26.607][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-13 16:03:26.608][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-13 16:03:26.609][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:03:26.610][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:03:26.611][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:03:26.611][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-13 16:03:26.612][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-13 16:03:26.613][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:03:26.614][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:03:26.615][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:03:26.615][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-13 16:03:26.616][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-13 16:03:26.617][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:03:26.618][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:03:26.619][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:03:26.619][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-13 16:03:26.620][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-13 16:03:26.621][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:03:26.622][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:03:26.623][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:03:26.624][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-13 16:03:26.624][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-13 16:03:26.625][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:03:26.626][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:03:26.627][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-12-13 16:03:26.631][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-12-13 16:03:26.632][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-12-13 16:03:26.634][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-12-13 16:03:26.635][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-12-13 16:03:26.640][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-12-13 16:03:26.641][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-12-13 16:03:26.643][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-12-13 16:03:26.644][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-12-13 16:03:26.645][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-12-13 16:03:26.646][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-12-13 16:03:26.648][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-12-13 16:03:26.649][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-12-13 16:03:26.650][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-12-13 16:03:26.652][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-12-13 16:03:26.653][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-12-13 16:03:26.654][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-12-13 16:03:26.655][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-12-13 16:03:26.657][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-12-13 16:03:26.658][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-12-13 16:03:26.659][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-12-13 16:03:26.661][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-12-13 16:03:26.662][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-12-13 16:03:26.663][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-12-13 16:03:26.664][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-12-13 16:03:26.673][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-12-13 16:03:26.675][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-12-13 16:03:26.676][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-12-13 16:03:26.678][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-12-13 16:03:26.679][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-12-13 16:03:26.681][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-12-13 16:03:26.682][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-12-13 16:03:26.684][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-12-13 16:03:26.685][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-12-13 16:03:26.687][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-12-13 16:03:26.688][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-12-13 16:03:26.690][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-12-13 16:03:26.691][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-12-13 16:03:26.693][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-12-13 16:03:26.694][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-12-13 16:03:26.696][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-12-13 16:03:26.697][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-12-13 16:03:26.698][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-12-13 16:03:26.700][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-12-13 16:03:26.701][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-12-13 16:03:26.703][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-12-13 16:03:26.704][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-12-13 16:03:26.706][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-12-13 16:03:26.707][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-12-13 16:03:26.709][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-12-13 16:03:26.710][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-12-13 16:03:26.712][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-12-13 16:03:26.713][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-12-13 16:03:26.714][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-12-13 16:03:26.716][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-12-13 16:03:26.717][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-12-13 16:03:26.719][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-12-13 16:03:26.720][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-12-13 16:03:26.722][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-12-13 16:03:26.723][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-12-13 16:03:26.724][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-12-13 16:03:26.726][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-12-13 16:03:26.727][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-12-13 16:03:26.729][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-12-13 16:03:26.730][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-12-13 16:03:26.732][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-12-13 16:03:26.733][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-12-13 16:03:26.734][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-12-13 16:03:26.736][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-12-13 16:03:26.737][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-12-13 16:03:26.739][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-12-13 16:03:26.740][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-12-13 16:03:26.742][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-12-13 16:03:26.743][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-12-13 16:03:26.744][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-12-13 16:03:26.746][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-12-13 16:03:26.747][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-12-13 16:03:26.749][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-12-13 16:03:26.750][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-12-13 16:03:26.752][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-12-13 16:03:26.753][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-12-13 16:03:26.755][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-12-13 16:03:26.756][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-12-13 16:03:26.763][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-12-13 16:03:26.765][initialize] This is biodb version 1.18.0.
biodb.DEBUG[2025-12-13 16:03:26.768][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-12-13 16:03:26.769][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-12-13 16:03:26.770][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-13 16:03:26.771][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:03:26.772][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:03:26.777][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:03:26.778][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-13 16:03:26.779][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-13 16:03:26.780][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-13 16:03:26.781][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-13 16:03:26.782][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:03:26.783][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:03:26.783][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:03:26.784][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-13 16:03:26.785][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-13 16:03:26.786][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-13 16:03:26.787][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-13 16:03:26.788][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:03:26.789][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:03:26.790][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:03:26.791][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-13 16:03:26.792][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-13 16:03:26.793][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-13 16:03:26.793][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-13 16:03:26.794][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:03:26.795][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:03:26.796][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:03:26.797][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-13 16:03:26.798][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-13 16:03:26.799][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-13 16:03:26.800][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-13 16:03:26.801][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:03:26.802][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:03:26.803][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:03:26.803][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-13 16:03:26.804][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-13 16:03:26.805][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-13 16:03:26.806][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-13 16:03:26.807][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:03:26.808][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:03:26.809][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:03:26.821][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-13 16:03:26.822][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-13 16:03:26.823][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-13 16:03:26.824][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-13 16:03:26.825][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:03:26.826][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:03:26.827][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:03:26.828][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-13 16:03:26.829][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-13 16:03:26.830][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-13 16:03:26.831][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-13 16:03:26.832][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:03:26.832][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:03:26.833][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:03:26.834][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-13 16:03:26.835][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-13 16:03:26.836][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-13 16:03:26.837][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-13 16:03:26.838][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:03:26.839][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:03:26.840][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:03:26.841][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-13 16:03:26.842][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-13 16:03:26.842][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-13 16:03:26.843][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-13 16:03:26.844][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:03:26.845][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:03:26.846][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:03:26.847][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-13 16:03:26.848][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-13 16:03:26.849][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-13 16:03:26.850][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-13 16:03:26.850][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:03:26.851][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:03:26.852][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:03:26.853][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-13 16:03:26.854][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-13 16:03:26.855][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-13 16:03:26.855][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-13 16:03:26.856][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:03:26.857][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[2025-12-13 16:03:26.858][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:03:26.859][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-13 16:03:26.860][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-13 16:03:26.860][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-13 16:03:26.861][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-13 16:03:26.862][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:03:26.863][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:03:26.864][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:03:26.864][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-13 16:03:26.865][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-13 16:03:26.866][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-13 16:03:26.867][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-13 16:03:26.868][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:03:26.869][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:03:26.870][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:03:26.870][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-13 16:03:26.871][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-13 16:03:26.872][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-13 16:03:26.873][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-13 16:03:26.874][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:03:26.874][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:03:26.875][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:03:26.876][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-13 16:03:26.877][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-13 16:03:26.878][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-13 16:03:26.879][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-13 16:03:26.879][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:03:26.880][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:03:26.881][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:03:26.882][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-13 16:03:26.883][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-13 16:03:26.884][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-13 16:03:26.884][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-13 16:03:26.885][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:03:26.886][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:03:26.888][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNci.Rcheck/biodbNci/definitions.yml".
biodb.DEBUG[2025-12-13 16:03:26.897][self$getDbsInfo()$define] Define connector nci.cactus.
biodb.DEBUG[2025-12-13 16:03:26.898][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-12-13 16:03:26.899][self$setPropertyValue] Setting property "description" to "National Cancer Institute (USA) CACTUS Database.".
biodb.DEBUG[2025-12-13 16:03:26.900][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-12-13 16:03:26.901][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-12-13 16:03:26.902][self$setPropertyValue] Setting property "downloadable" to "TRUE".
biodb.DEBUG[2025-12-13 16:03:26.903][self$setPropertyValue] Setting property "dwnld.ext" to "gz".
biodb.DEBUG[2025-12-13 16:03:26.904][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-12-13 16:03:26.905][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-12-13 16:03:26.906][self$setPropertyValue] Setting property "entry.content.type" to "sdf".
biodb.DEBUG[2025-12-13 16:03:26.907][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-12-13 16:03:26.908][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-12-13 16:03:26.909][self$setPropertyValue] Setting property "name" to "NCI CACTUS".
biodb.DEBUG[2025-12-13 16:03:26.910][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-12-13 16:03:26.911][self$setPropertyValue] Setting property "parsing.expr" to "NSC".
biodb.DEBUG[2025-12-13 16:03:26.911][self$setPropertyValue] Setting property "parsing.expr" to "DTP names".
biodb.DEBUG[2025-12-13 16:03:26.911][self$setPropertyValue] Setting property "parsing.expr" to "Standard InChI".
biodb.DEBUG[2025-12-13 16:03:26.911][self$setPropertyValue] Setting property "parsing.expr" to "c("Standard InChIKey", "^InChIKey=(.*)$")".
biodb.DEBUG[2025-12-13 16:03:26.911][self$setPropertyValue] Setting property "parsing.expr" to "Formula".
biodb.DEBUG[2025-12-13 16:03:26.911][self$setPropertyValue] Setting property "parsing.expr" to "Molecular Weight".
biodb.DEBUG[2025-12-13 16:03:26.911][self$setPropertyValue] Setting property "parsing.expr" to "CAS".
biodb.DEBUG[2025-12-13 16:03:26.912][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-12-13 16:03:26.913][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-12-13 16:03:26.914][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-12-13 16:03:26.914][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-12-13 16:03:26.915][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-12-13 16:03:26.916][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-12-13 16:03:26.917][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-12-13 16:03:26.918][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-12-13 16:03:26.919][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-12-13 16:03:26.920][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/".
biodb.DEBUG[2025-12-13 16:03:26.920][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/".
biodb.DEBUG[2025-12-13 16:03:26.920][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/download/nci/".
biodb.DEBUG[2025-12-13 16:03:26.920][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/download/nci/NCI-Open_2012-05-01.sdf.gz".
biodb.DEBUG[2025-12-13 16:03:26.921][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-12-13 16:03:26.921][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-12-13 16:03:26.922][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-12-13 16:03:26.923][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-12-13 16:03:26.929][self$getEntryFields()$define] Define field nci.cactus.id.
biodb.DEBUG[2025-12-13 16:03:26.950][super$initialize] Initialize connector nci.cactus.
biodb.DEBUG[2025-12-13 16:03:26.965][biodb$getFactory()$createConn] Creating new connector nci.cactus for database class nci.cactus .
biodb.INFO [2025-12-13 16:03:26.972][biodb::testThat]
biodb.INFO [2025-12-13 16:03:26.973][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2025-12-13 16:03:26.974][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-12-13 16:03:26.975][biodb::testThat]
biodb.TRACE[2025-12-13 16:03:26.978][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNci.Rcheck/biodbNci/testref/entry-nci.cactus-749674-content.sdf".
biodb.DEBUG[2025-12-13 16:03:26.980][biodb$getFactory()$createEntryFromCo ...] Creating NCI CACTUS entries from 1 content(s).
biodb.DEBUG[2025-12-13 16:03:26.983][biodb$getFactory()$createEntryFromCo ...] Parsing 1 NCI CACTUS entries.
biodb.DEBUG[2025-12-13 16:03:26.997][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-12-13 16:03:26.998][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-13 16:03:26.998][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-13 16:03:27.009][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-12-13 16:03:27.010][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-13 16:03:27.011][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:03:27.012][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-12-13 16:03:27.028][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-13 16:03:27.029][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-13 16:03:27.030][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:27.031][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:27.032][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-13 16:03:27.044][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-13 16:03:27.044][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:27.045][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:27.048][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-12-13 16:03:27.049][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-12-13 16:03:27.050][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:27.050][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:27.074][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-12-13 16:03:27.075][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-12-13 16:03:27.076][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:27.077][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:27.079][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-12-13 16:03:27.080][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-12-13 16:03:27.080][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:27.081][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:27.082][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-12-13 16:03:27.083][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-12-13 16:03:27.084][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:27.085][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:27.087][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-12-13 16:03:27.088][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-12-13 16:03:27.089][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:27.090][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:27.091][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-12-13 16:03:27.092][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-12-13 16:03:27.093][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:27.093][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:27.095][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-12-13 16:03:27.096][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-12-13 16:03:27.097][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:27.097][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:27.098][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-12-13 16:03:27.099][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-12-13 16:03:27.100][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:27.101][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:27.103][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-12-13 16:03:27.104][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-12-13 16:03:27.105][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:27.106][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:27.106][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-12-13 16:03:27.107][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-12-13 16:03:27.108][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:27.109][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:27.110][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-13 16:03:27.111][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-13 16:03:27.112][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:27.113][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:27.114][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-12-13 16:03:27.115][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-12-13 16:03:27.116][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:27.117][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:27.118][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-13 16:03:27.119][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-13 16:03:27.125][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:27.126][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:27.127][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-13 16:03:27.128][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-13 16:03:27.129][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:27.130][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:27.131][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-13 16:03:27.132][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-13 16:03:27.132][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:27.133][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:27.165][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-13 16:03:27.166][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-13 16:03:27.167][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:27.167][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:27.168][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-13 16:03:27.169][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-13 16:03:27.170][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:27.171][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:27.172][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-13 16:03:27.173][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-13 16:03:27.174][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:27.175][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-12-13 16:03:27.176][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 749674.
biodb.TRACE[2025-12-13 16:03:27.178][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-12-13 16:03:27.179][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-12-13 16:03:27.180][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:27.181][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:27.182][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-12-13 16:03:27.183][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-12-13 16:03:27.184][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:27.184][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:27.185][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-12-13 16:03:27.186][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-12-13 16:03:27.187][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:27.188][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:27.189][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-12-13 16:03:27.190][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-12-13 16:03:27.191][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:27.192][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:27.194][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-13 16:03:27.195][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-13 16:03:27.196][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:27.197][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:27.209][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-12-13 16:03:27.210][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-12-13 16:03:27.211][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:27.212][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:27.216][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-13 16:03:27.217][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-13 16:03:27.218][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:27.219][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:27.220][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-13 16:03:27.221][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-13 16:03:27.222][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:27.223][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:27.223][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-13 16:03:27.224][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-13 16:03:27.225][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:27.226][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:27.229][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-13 16:03:27.230][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-13 16:03:27.231][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:27.232][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:27.232][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-13 16:03:27.274][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-13 16:03:27.275][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:27.276][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:27.277][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-13 16:03:27.278][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-13 16:03:27.279][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:27.279][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:27.281][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-12-13 16:03:27.282][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-12-13 16:03:27.282][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:27.283][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:27.284][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-12-13 16:03:27.285][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-12-13 16:03:27.286][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:27.287][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:27.288][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-12-13 16:03:27.289][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-12-13 16:03:27.290][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:27.291][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:27.298][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-13 16:03:27.299][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-13 16:03:27.299][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:27.300][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:27.301][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-13 16:03:27.302][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-13 16:03:27.303][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:27.304][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:27.305][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-13 16:03:27.306][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-13 16:03:27.307][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:27.308][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:27.309][ef$get] Asked field names are: accession.
biodb.TRACE[2025-12-13 16:03:27.310][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-13 16:03:27.311][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:27.311][ef$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:27.312][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-13 16:03:27.313][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-13 16:03:27.314][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:27.315][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:27.323][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-12-13 16:03:27.324][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-12-13 16:03:27.325][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:27.326][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:27.327][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-12-13 16:03:27.328][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-12-13 16:03:27.329][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:27.329][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:27.330][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-12-13 16:03:27.331][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-12-13 16:03:27.332][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:27.333][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:27.334][ef$get] Asked field names are: formula.
biodb.TRACE[2025-12-13 16:03:27.335][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-12-13 16:03:27.336][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:27.337][ef$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:27.338][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-12-13 16:03:27.339][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-12-13 16:03:27.340][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:27.341][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:27.348][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-12-13 16:03:27.349][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-12-13 16:03:27.350][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:27.351][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:27.352][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-12-13 16:03:27.353][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-12-13 16:03:27.354][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:27.355][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:27.355][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-12-13 16:03:27.356][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-12-13 16:03:27.357][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:27.358][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:27.359][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-12-13 16:03:27.360][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-12-13 16:03:27.361][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:27.362][ef$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:27.363][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-12-13 16:03:27.364][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-12-13 16:03:27.365][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:27.366][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:27.373][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-12-13 16:03:27.374][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-12-13 16:03:27.375][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:27.376][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:27.377][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-12-13 16:03:27.378][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-12-13 16:03:27.379][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:27.379][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:27.380][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-12-13 16:03:27.381][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-12-13 16:03:27.382][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:27.383][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:27.384][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-12-13 16:03:27.385][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-12-13 16:03:27.386][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:27.387][ef$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:27.388][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-12-13 16:03:27.389][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-12-13 16:03:27.390][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:27.390][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:27.402][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-12-13 16:03:27.403][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-12-13 16:03:27.404][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:27.405][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:27.406][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-12-13 16:03:27.407][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-12-13 16:03:27.408][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:27.408][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:27.409][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-12-13 16:03:27.410][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-12-13 16:03:27.411][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:27.412][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:27.413][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-12-13 16:03:27.414][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-12-13 16:03:27.415][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:27.416][ef$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:27.417][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-12-13 16:03:27.418][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-12-13 16:03:27.419][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:27.420][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:27.427][ef$get] Asked field names are: accession.
biodb.TRACE[2025-12-13 16:03:27.428][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-13 16:03:27.429][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:27.430][ef$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:27.434][ef$get] Asked field names are: formula.
biodb.TRACE[2025-12-13 16:03:27.435][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-12-13 16:03:27.436][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:27.436][ef$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:27.440][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-12-13 16:03:27.441][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-12-13 16:03:27.442][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:27.443][ef$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:27.447][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-12-13 16:03:27.448][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-12-13 16:03:27.449][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:27.450][ef$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:27.454][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-12-13 16:03:27.455][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-12-13 16:03:27.455][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:27.456][ef$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:27.472][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNci.Rcheck/biodbNci/testref/entry-nci.cactus-750690-content.sdf".
biodb.DEBUG[2025-12-13 16:03:27.509][biodb$getFactory()$createEntryFromCo ...] Creating NCI CACTUS entries from 1 content(s).
biodb.DEBUG[2025-12-13 16:03:27.510][biodb$getFactory()$createEntryFromCo ...] Parsing 1 NCI CACTUS entries.
biodb.DEBUG[2025-12-13 16:03:27.512][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-12-13 16:03:27.512][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-13 16:03:27.513][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-13 16:03:27.518][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-12-13 16:03:27.518][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-13 16:03:27.519][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:03:27.520][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-12-13 16:03:27.529][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-13 16:03:27.530][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-13 16:03:27.531][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:27.532][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:27.533][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-13 16:03:27.534][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-13 16:03:27.535][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:27.536][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:27.553][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-12-13 16:03:27.554][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-12-13 16:03:27.555][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:27.556][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:27.557][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-12-13 16:03:27.558][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-12-13 16:03:27.559][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:27.560][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:27.561][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-12-13 16:03:27.562][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-12-13 16:03:27.563][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:27.564][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:27.565][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-12-13 16:03:27.566][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-12-13 16:03:27.567][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:27.568][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:27.569][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-12-13 16:03:27.570][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-12-13 16:03:27.571][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:27.572][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:27.573][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-12-13 16:03:27.574][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-12-13 16:03:27.574][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:27.575][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:27.577][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-12-13 16:03:27.578][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-12-13 16:03:27.578][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:27.579][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:27.580][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-12-13 16:03:27.581][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-12-13 16:03:27.582][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:27.583][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:27.584][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-12-13 16:03:27.585][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-12-13 16:03:27.586][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:27.587][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:27.588][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-12-13 16:03:27.589][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-12-13 16:03:27.590][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:27.591][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:27.592][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-12-13 16:03:27.592][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-12-13 16:03:27.593][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:27.594][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:27.595][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-12-13 16:03:27.596][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-12-13 16:03:27.597][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:27.598][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:27.599][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-12-13 16:03:27.600][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-12-13 16:03:27.601][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:27.602][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:27.603][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-12-13 16:03:27.604][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-12-13 16:03:27.605][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:27.606][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:27.607][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-12-13 16:03:27.608][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-12-13 16:03:27.609][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:27.610][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:27.611][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-12-13 16:03:27.612][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-12-13 16:03:27.613][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:27.614][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:27.615][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-12-13 16:03:27.616][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-12-13 16:03:27.617][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:27.618][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:27.623][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-12-13 16:03:27.624][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-12-13 16:03:27.624][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:27.625][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:27.626][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-12-13 16:03:27.627][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-12-13 16:03:27.628][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:27.629][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:27.630][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-13 16:03:27.631][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-13 16:03:27.632][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:27.633][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:27.634][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-12-13 16:03:27.635][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-12-13 16:03:27.636][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:27.636][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:27.637][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-13 16:03:27.638][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-13 16:03:27.639][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:27.640][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:27.641][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-13 16:03:27.642][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-13 16:03:27.643][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:27.644][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:27.645][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-13 16:03:27.646][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-13 16:03:27.647][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:27.648][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:27.649][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-13 16:03:27.650][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-13 16:03:27.651][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:27.651][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:27.652][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-13 16:03:27.653][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-13 16:03:27.654][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:27.655][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:27.656][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-13 16:03:27.657][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-13 16:03:27.658][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:27.659][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-12-13 16:03:27.660][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 750690.
biodb.TRACE[2025-12-13 16:03:27.679][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-12-13 16:03:27.680][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-12-13 16:03:27.681][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:27.682][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:27.683][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-12-13 16:03:27.683][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-12-13 16:03:27.684][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:27.685][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:27.686][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-12-13 16:03:27.687][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-12-13 16:03:27.688][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:27.689][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:27.690][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-12-13 16:03:27.691][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-12-13 16:03:27.692][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:27.693][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:27.694][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-13 16:03:27.695][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-13 16:03:27.696][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:27.697][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:27.701][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-12-13 16:03:27.702][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-12-13 16:03:27.703][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:27.704][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:27.708][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-13 16:03:27.709][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-13 16:03:27.710][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:27.711][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:27.712][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-13 16:03:27.713][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-13 16:03:27.714][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:27.715][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:27.715][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-13 16:03:27.716][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-13 16:03:27.717][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:27.718][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:27.720][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-13 16:03:27.721][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-13 16:03:27.722][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:27.723][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:27.724][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-13 16:03:27.725][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-13 16:03:27.726][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:27.727][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:27.728][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-13 16:03:27.729][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-13 16:03:27.730][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:27.731][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:27.732][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-12-13 16:03:27.733][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-12-13 16:03:27.734][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:27.738][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:27.739][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-12-13 16:03:27.740][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-12-13 16:03:27.741][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:27.742][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:27.743][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-12-13 16:03:27.744][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-12-13 16:03:27.744][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:27.745][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:27.761][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-13 16:03:27.762][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-13 16:03:27.763][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:27.763][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:27.764][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-13 16:03:27.765][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-13 16:03:27.766][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:27.767][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:27.768][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-13 16:03:27.769][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-13 16:03:27.770][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:27.771][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:27.772][ef$get] Asked field names are: accession.
biodb.TRACE[2025-12-13 16:03:27.773][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-13 16:03:27.774][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:27.775][ef$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:27.775][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-13 16:03:27.776][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-13 16:03:27.777][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:27.778][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:27.786][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-12-13 16:03:27.787][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-12-13 16:03:27.788][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:27.789][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:27.790][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-12-13 16:03:27.791][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-12-13 16:03:27.791][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:27.792][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:27.793][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-12-13 16:03:27.794][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-12-13 16:03:27.795][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:27.796][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:27.797][ef$get] Asked field names are: cas.id.
biodb.TRACE[2025-12-13 16:03:27.798][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-12-13 16:03:27.799][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:27.800][ef$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:27.801][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-12-13 16:03:27.802][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-12-13 16:03:27.802][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:27.803][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:27.811][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-12-13 16:03:27.812][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-12-13 16:03:27.813][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:27.814][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:27.815][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-12-13 16:03:27.816][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-12-13 16:03:27.816][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:27.817][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:27.818][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-12-13 16:03:27.819][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-12-13 16:03:27.820][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:27.821][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:27.822][ef$get] Asked field names are: name.
biodb.TRACE[2025-12-13 16:03:27.823][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-12-13 16:03:27.824][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:27.825][ef$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:27.826][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-12-13 16:03:27.827][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-12-13 16:03:27.827][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:27.828][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:27.836][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-12-13 16:03:27.837][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-12-13 16:03:27.838][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:27.839][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:27.839][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-12-13 16:03:27.840][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-12-13 16:03:27.841][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:27.842][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:27.843][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-12-13 16:03:27.844][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-12-13 16:03:27.845][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:27.846][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:27.847][ef$get] Asked field names are: formula.
biodb.TRACE[2025-12-13 16:03:27.848][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-12-13 16:03:27.849][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:27.850][ef$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:27.850][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-12-13 16:03:27.855][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-12-13 16:03:27.856][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:27.857][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:27.864][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-12-13 16:03:27.865][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-12-13 16:03:27.866][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:27.867][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:27.868][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-12-13 16:03:27.869][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-12-13 16:03:27.870][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:27.871][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:27.872][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-12-13 16:03:27.873][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-12-13 16:03:27.874][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:27.875][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:27.876][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-12-13 16:03:27.877][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-12-13 16:03:27.877][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:27.878][ef$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:27.879][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-12-13 16:03:27.880][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-12-13 16:03:27.881][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:27.882][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:27.889][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-12-13 16:03:27.890][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-12-13 16:03:27.891][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:27.892][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:27.893][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-12-13 16:03:27.894][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-12-13 16:03:27.895][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:27.896][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:27.897][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-12-13 16:03:27.898][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-12-13 16:03:27.899][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:27.899][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:27.900][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-12-13 16:03:27.901][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-12-13 16:03:27.902][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:27.903][ef$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:27.904][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-12-13 16:03:27.905][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-12-13 16:03:27.906][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:27.907][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:27.914][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-12-13 16:03:27.915][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-12-13 16:03:27.916][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:27.917][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:27.918][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-12-13 16:03:27.919][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-12-13 16:03:27.920][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:27.921][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:27.922][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-12-13 16:03:27.923][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-12-13 16:03:27.924][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:27.924][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:27.925][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-12-13 16:03:27.926][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-12-13 16:03:27.927][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:27.928][ef$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:27.929][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-12-13 16:03:27.930][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-12-13 16:03:27.931][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:27.932][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:27.939][ef$get] Asked field names are: accession.
biodb.TRACE[2025-12-13 16:03:27.940][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-13 16:03:27.941][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:27.942][ef$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:27.946][ef$get] Asked field names are: cas.id.
biodb.TRACE[2025-12-13 16:03:27.947][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-12-13 16:03:27.948][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:27.948][ef$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:27.952][ef$get] Asked field names are: formula.
biodb.TRACE[2025-12-13 16:03:27.953][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-12-13 16:03:27.954][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:27.955][ef$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:27.959][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-12-13 16:03:27.960][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-12-13 16:03:27.961][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:27.961][ef$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:27.965][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-12-13 16:03:27.966][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-12-13 16:03:27.967][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:27.972][ef$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:27.976][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-12-13 16:03:27.977][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-12-13 16:03:27.977][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:27.978][ef$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:27.982][ef$get] Asked field names are: name.
biodb.TRACE[2025-12-13 16:03:27.983][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-12-13 16:03:27.984][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:27.985][ef$get] fields variable is a list.
biodb.INFO [2025-12-13 16:03:27.991][biodb::testThat]
biodb.INFO [2025-12-13 16:03:27.992][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2025-12-13 16:03:27.993][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-12-13 16:03:27.994][biodb::testThat]
biodb.DEBUG[2025-12-13 16:03:27.996][private$loadEntries] Creating entries from ids [2]: "749674, 750690".
biodb.DEBUG[2025-12-13 16:03:27.998][conn$getEntryContent] Get NCI CACTUS entry content(s) for 2 id(s)...
biodb.DEBUG[2025-12-13 16:03:28.001][self$isDownloaded] Database nci.cactus has already been downloaded.
biodb.DEBUG[2025-12-13 16:03:28.029][self$isDownloaded] Database nci.cactus has already been downloaded.
biodb.INFO [2025-12-13 16:03:28.030][self$download] Extract whole database of nci.cactus.
biodb.INFO [2025-12-13 16:03:28.031][private$doExtractDownload] Extracting content of downloaded biodbNci, a library for connecting to the National Cancer Institute (USA) CACTUS Database....
Saving _problems/test_long_100_generic-38.R
biodb.INFO [2025-12-13 16:03:28.159][biodb::testThat]
biodb.INFO [2025-12-13 16:03:28.160][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2025-12-13 16:03:28.161][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-12-13 16:03:28.162][biodb::testThat]
biodb.INFO [2025-12-13 16:03:28.167][biodb::testThat]
biodb.INFO [2025-12-13 16:03:28.168][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2025-12-13 16:03:28.169][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-12-13 16:03:28.170][biodb::testThat]
biodb.WARN [2025-12-13 16:03:28.192][self$searchForEntries] This database is not searchable by field "name".
biodb.WARN [2025-12-13 16:03:28.210][self$searchForEntries] This database is not searchable by field "name".
biodb.INFO [2025-12-13 16:03:28.218][biodb::testThat]
biodb.INFO [2025-12-13 16:03:28.219][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2025-12-13 16:03:28.220][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-12-13 16:03:28.221][biodb::testThat]
biodb.DEBUG[2025-12-13 16:03:28.237][private$loadEntries] Creating entries from ids [1]: "749674".
biodb.DEBUG[2025-12-13 16:03:28.285][conn$getEntryContent] Get NCI CACTUS entry content(s) for 1 id(s)...
biodb.DEBUG[2025-12-13 16:03:28.286][self$isDownloaded] Database nci.cactus has already been downloaded.
biodb.DEBUG[2025-12-13 16:03:28.287][self$isDownloaded] Database nci.cactus has already been downloaded.
biodb.INFO [2025-12-13 16:03:28.289][self$download] Extract whole database of nci.cactus.
biodb.INFO [2025-12-13 16:03:28.300][private$doExtractDownload] Extracting content of downloaded biodbNci, a library for connecting to the National Cancer Institute (USA) CACTUS Database....
Saving _problems/test_long_100_generic-38.R
biodb.INFO [2025-12-13 16:03:28.351][biodb::testThat]
biodb.INFO [2025-12-13 16:03:28.352][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2025-12-13 16:03:28.353][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-12-13 16:03:28.353][biodb::testThat]
biodb.INFO [2025-12-13 16:03:28.360][biodb::testThat]
biodb.INFO [2025-12-13 16:03:28.361][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2025-12-13 16:03:28.362][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-12-13 16:03:28.363][biodb::testThat]
biodb.INFO [2025-12-13 16:03:28.373][biodb::testThat]
biodb.INFO [2025-12-13 16:03:28.374][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2025-12-13 16:03:28.375][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-12-13 16:03:28.376][biodb::testThat]
biodb.INFO [2025-12-13 16:03:28.381][biodb::testThat]
biodb.INFO [2025-12-13 16:03:28.382][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2025-12-13 16:03:28.383][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-12-13 16:03:28.384][biodb::testThat]
biodb.INFO [2025-12-13 16:03:28.389][biodb$terminate] Closing BiodbMain instance...
biodb.INFO [2025-12-13 16:03:28.390][self$deleteConn] Connector "nci.cactus" deleted.
biodb.DEBUG[2025-12-13 16:03:28.391][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-12-13 16:03:28.391][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-13 16:03:28.392][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-13 16:03:28.393][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-13 16:03:28.394][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-13 16:03:28.395][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:03:28.396][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2025-12-13 16:03:28.404][biodb::testContext]
biodb.INFO [2025-12-13 16:03:28.405][biodb::testContext] ********************************************************************************
biodb.INFO [2025-12-13 16:03:28.406][biodb::testContext] Test context - Example long tests
biodb.INFO [2025-12-13 16:03:28.407][biodb::testContext] ********************************************************************************
biodb.INFO [2025-12-13 16:03:28.408][biodb::testContext]
biodb.INFO [2025-12-13 16:03:28.410][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.18.0.
biodb.DEBUG[2025-12-13 16:03:28.411][self$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.22-bioc/R/site-library/biodb/definitions.yml".
biodb.DEBUG[2025-12-13 16:03:28.415][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-12-13 16:03:28.416][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-12-13 16:03:28.417][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-12-13 16:03:28.417][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:03:28.418][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:03:28.419][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[2025-12-13 16:03:28.420][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-12-13 16:03:28.421][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-12-13 16:03:28.422][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:03:28.422][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:03:28.423][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:03:28.424][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-12-13 16:03:28.425][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-12-13 16:03:28.426][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:03:28.427][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:03:28.428][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:03:28.429][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-12-13 16:03:28.429][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-12-13 16:03:28.430][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-12-13 16:03:28.431][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:03:28.432][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:03:28.433][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:03:28.434][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-12-13 16:03:28.435][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-12-13 16:03:28.436][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-12-13 16:03:28.437][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:03:28.437][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:03:28.438][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:03:28.439][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-12-13 16:03:28.440][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-12-13 16:03:28.441][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:03:28.442][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:03:28.443][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:03:28.443][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-12-13 16:03:28.444][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-12-13 16:03:28.445][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-12-13 16:03:28.446][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:03:28.447][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:03:28.448][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:03:28.449][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-12-13 16:03:28.450][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-12-13 16:03:28.451][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:03:28.451][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:03:28.452][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:03:28.453][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-12-13 16:03:28.454][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-12-13 16:03:28.455][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-12-13 16:03:28.456][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:03:28.457][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:03:28.457][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:03:28.458][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-12-13 16:03:28.459][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-12-13 16:03:28.460][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-12-13 16:03:28.461][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-12-13 16:03:28.462][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-12-13 16:03:28.463][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-12-13 16:03:28.464][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:03:28.465][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:03:28.466][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:03:28.466][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-12-13 16:03:28.467][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-12-13 16:03:28.468][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:03:28.469][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:03:28.470][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:03:28.471][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-12-13 16:03:28.472][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-12-13 16:03:28.477][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:03:28.477][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:03:28.478][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:03:28.479][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-12-13 16:03:28.480][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-12-13 16:03:28.481][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:03:28.482][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:03:28.483][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:03:28.483][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-12-13 16:03:28.484][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-12-13 16:03:28.485][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-12-13 16:03:28.486][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:03:28.487][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:03:28.488][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:03:28.489][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-12-13 16:03:28.490][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-12-13 16:03:28.495][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-12-13 16:03:28.495][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:03:28.496][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:03:28.497][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:03:28.498][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-12-13 16:03:28.499][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-12-13 16:03:28.500][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-12-13 16:03:28.501][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:03:28.502][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:03:28.502][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:03:28.504][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-12-13 16:03:28.505][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-12-13 16:03:28.506][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2025-12-13 16:03:28.507][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-12-13 16:03:28.508][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-12-13 16:03:28.509][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-12-13 16:03:28.510][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-12-13 16:03:28.511][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-12-13 16:03:28.512][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-12-13 16:03:28.513][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-12-13 16:03:28.514][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-12-13 16:03:28.515][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-12-13 16:03:28.515][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-12-13 16:03:28.516][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-12-13 16:03:28.517][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-12-13 16:03:28.518][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-12-13 16:03:28.519][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-12-13 16:03:28.519][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-12-13 16:03:28.519][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-12-13 16:03:28.519][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-12-13 16:03:28.519][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-12-13 16:03:28.520][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-12-13 16:03:28.521][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-12-13 16:03:28.522][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-12-13 16:03:28.523][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-12-13 16:03:28.524][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-12-13 16:03:28.525][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-12-13 16:03:28.525][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-12-13 16:03:28.526][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-12-13 16:03:28.527][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-12-13 16:03:28.528][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-12-13 16:03:28.529][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-12-13 16:03:28.530][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-12-13 16:03:28.531][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-12-13 16:03:28.533][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-12-13 16:03:28.534][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-12-13 16:03:28.535][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-12-13 16:03:28.535][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-12-13 16:03:28.536][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-12-13 16:03:28.537][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-12-13 16:03:28.538][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-12-13 16:03:28.539][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-12-13 16:03:28.540][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-12-13 16:03:28.541][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-12-13 16:03:28.542][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-12-13 16:03:28.543][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-12-13 16:03:28.544][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-12-13 16:03:28.545][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-12-13 16:03:28.546][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-12-13 16:03:28.547][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-12-13 16:03:28.547][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-12-13 16:03:28.547][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-12-13 16:03:28.547][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-12-13 16:03:28.547][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-12-13 16:03:28.548][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-12-13 16:03:28.548][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-12-13 16:03:28.549][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-12-13 16:03:28.550][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-12-13 16:03:28.551][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-12-13 16:03:28.552][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-12-13 16:03:28.553][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-12-13 16:03:28.554][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-12-13 16:03:28.555][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-12-13 16:03:28.555][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-12-13 16:03:28.556][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-12-13 16:03:28.557][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-12-13 16:03:28.558][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-12-13 16:03:28.560][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-12-13 16:03:28.561][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2025-12-13 16:03:28.562][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-12-13 16:03:28.563][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-12-13 16:03:28.564][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-12-13 16:03:28.565][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-12-13 16:03:28.566][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-12-13 16:03:28.567][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-12-13 16:03:28.567][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-12-13 16:03:28.568][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-12-13 16:03:28.569][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-12-13 16:03:28.570][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-12-13 16:03:28.571][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-12-13 16:03:28.572][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-12-13 16:03:28.573][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-12-13 16:03:28.574][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-12-13 16:03:28.575][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-12-13 16:03:28.576][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-12-13 16:03:28.577][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-12-13 16:03:28.578][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-12-13 16:03:28.579][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-12-13 16:03:28.579][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-12-13 16:03:28.580][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-12-13 16:03:28.581][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-12-13 16:03:28.582][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-12-13 16:03:28.587][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-12-13 16:03:28.588][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-12-13 16:03:28.589][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-12-13 16:03:28.590][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-12-13 16:03:28.591][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-12-13 16:03:28.592][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-12-13 16:03:28.593][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-12-13 16:03:28.594][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-12-13 16:03:28.595][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-12-13 16:03:28.596][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-12-13 16:03:28.597][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-12-13 16:03:28.598][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-12-13 16:03:28.599][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-12-13 16:03:28.600][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-12-13 16:03:28.601][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-12-13 16:03:28.602][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-12-13 16:03:28.602][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-12-13 16:03:28.603][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-12-13 16:03:28.604][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-12-13 16:03:28.605][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-12-13 16:03:28.606][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-12-13 16:03:28.607][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-12-13 16:03:28.608][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-12-13 16:03:28.609][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-12-13 16:03:28.610][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-12-13 16:03:28.611][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-12-13 16:03:28.611][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-12-13 16:03:28.612][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-12-13 16:03:28.613][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-12-13 16:03:28.614][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-12-13 16:03:28.615][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-12-13 16:03:28.616][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-12-13 16:03:28.617][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-12-13 16:03:28.618][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:03:28.619][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:03:28.620][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:03:28.621][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-13 16:03:28.621][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-13 16:03:28.622][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:03:28.623][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:03:28.624][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:03:28.625][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-13 16:03:28.626][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-13 16:03:28.626][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:03:28.627][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:03:28.628][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:03:28.629][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-13 16:03:28.630][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-13 16:03:28.631][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:03:28.631][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:03:28.632][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:03:28.633][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-13 16:03:28.634][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-13 16:03:28.635][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:03:28.636][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:03:28.636][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:03:28.637][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-13 16:03:28.638][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-13 16:03:28.639][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:03:28.640][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:03:28.641][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:03:28.641][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-13 16:03:28.642][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-13 16:03:28.643][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:03:28.644][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:03:28.645][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:03:28.646][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-13 16:03:28.646][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-13 16:03:28.647][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:03:28.648][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:03:28.649][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:03:28.650][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-13 16:03:28.651][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-13 16:03:28.651][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:03:28.652][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:03:28.653][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:03:28.654][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-13 16:03:28.655][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-13 16:03:28.655][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:03:28.656][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:03:28.657][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:03:28.658][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-13 16:03:28.659][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-13 16:03:28.660][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:03:28.660][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:03:28.661][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:03:28.662][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-13 16:03:28.663][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-13 16:03:28.664][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:03:28.665][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:03:28.665][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:03:28.666][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-13 16:03:28.667][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-13 16:03:28.668][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:03:28.669][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:03:28.670][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:03:28.670][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-13 16:03:28.671][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-13 16:03:28.672][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:03:28.673][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:03:28.674][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:03:28.675][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-13 16:03:28.675][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-13 16:03:28.676][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:03:28.677][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:03:28.678][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:03:28.679][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-13 16:03:28.680][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-13 16:03:28.681][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:03:28.681][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:03:28.682][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:03:28.683][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-13 16:03:28.684][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-13 16:03:28.685][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:03:28.686][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:03:28.687][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-12-13 16:03:28.692][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-12-13 16:03:28.693][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-12-13 16:03:28.694][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-12-13 16:03:28.696][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-12-13 16:03:28.697][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-12-13 16:03:28.698][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-12-13 16:03:28.700][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-12-13 16:03:28.701][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-12-13 16:03:28.702][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-12-13 16:03:28.703][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-12-13 16:03:28.705][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-12-13 16:03:28.706][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-12-13 16:03:28.707][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-12-13 16:03:28.709][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-12-13 16:03:28.710][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-12-13 16:03:28.711][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-12-13 16:03:28.713][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-12-13 16:03:28.714][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-12-13 16:03:28.715][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-12-13 16:03:28.717][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-12-13 16:03:28.718][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-12-13 16:03:28.719][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-12-13 16:03:28.720][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-12-13 16:03:28.722][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-12-13 16:03:28.723][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-12-13 16:03:28.724][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-12-13 16:03:28.726][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-12-13 16:03:28.727][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-12-13 16:03:28.728][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-12-13 16:03:28.730][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-12-13 16:03:28.731][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-12-13 16:03:28.732][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-12-13 16:03:28.733][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-12-13 16:03:28.735][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-12-13 16:03:28.736][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-12-13 16:03:28.737][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-12-13 16:03:28.739][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-12-13 16:03:28.740][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-12-13 16:03:28.741][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-12-13 16:03:28.743][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-12-13 16:03:28.744][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-12-13 16:03:28.745][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-12-13 16:03:28.746][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-12-13 16:03:28.748][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-12-13 16:03:28.749][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-12-13 16:03:28.750][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-12-13 16:03:28.752][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-12-13 16:03:28.753][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-12-13 16:03:28.754][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-12-13 16:03:28.756][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-12-13 16:03:28.757][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-12-13 16:03:28.758][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-12-13 16:03:28.759][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-12-13 16:03:28.761][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-12-13 16:03:28.762][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-12-13 16:03:28.763][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-12-13 16:03:28.765][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-12-13 16:03:28.766][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-12-13 16:03:28.767][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-12-13 16:03:28.769][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-12-13 16:03:28.770][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-12-13 16:03:28.771][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-12-13 16:03:28.773][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-12-13 16:03:28.774][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-12-13 16:03:28.775][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-12-13 16:03:28.776][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-12-13 16:03:28.778][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-12-13 16:03:28.779][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-12-13 16:03:28.780][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-12-13 16:03:28.782][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-12-13 16:03:28.783][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-12-13 16:03:28.784][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-12-13 16:03:28.786][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-12-13 16:03:28.787][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-12-13 16:03:28.788][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-12-13 16:03:28.790][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-12-13 16:03:28.791][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-12-13 16:03:28.797][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-12-13 16:03:28.798][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-12-13 16:03:28.799][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-12-13 16:03:28.800][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-12-13 16:03:28.802][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-12-13 16:03:28.803][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-12-13 16:03:28.805][initialize] This is biodb version 1.18.0.
biodb.DEBUG[2025-12-13 16:03:28.806][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-12-13 16:03:28.807][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-12-13 16:03:28.807][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-13 16:03:28.808][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:03:28.809][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:03:28.810][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:03:28.811][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-13 16:03:28.812][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-13 16:03:28.812][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-13 16:03:28.813][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-13 16:03:28.814][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:03:28.815][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:03:28.816][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:03:28.817][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-13 16:03:28.818][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-13 16:03:28.818][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-13 16:03:28.819][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-13 16:03:28.820][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:03:28.821][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:03:28.822][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:03:28.823][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-13 16:03:28.824][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-13 16:03:28.824][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-13 16:03:28.825][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-13 16:03:28.826][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:03:28.827][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:03:28.828][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:03:28.829][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-13 16:03:28.829][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-13 16:03:28.830][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-13 16:03:28.831][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-13 16:03:28.832][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:03:28.833][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[2025-12-13 16:03:28.834][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:03:28.834][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-13 16:03:28.835][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-13 16:03:28.836][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-13 16:03:28.837][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-13 16:03:28.838][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:03:28.839][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:03:28.839][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:03:28.840][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-13 16:03:28.841][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-13 16:03:28.842][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-13 16:03:28.843][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-13 16:03:28.843][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:03:28.844][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:03:28.845][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:03:28.846][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-13 16:03:28.847][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-13 16:03:28.848][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-13 16:03:28.848][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-13 16:03:28.849][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:03:28.850][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:03:28.851][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:03:28.852][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-13 16:03:28.853][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-13 16:03:28.853][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-13 16:03:28.854][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-13 16:03:28.855][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:03:28.856][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:03:28.857][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:03:28.858][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-13 16:03:28.858][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-13 16:03:28.859][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-13 16:03:28.860][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-13 16:03:28.861][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:03:28.862][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[2025-12-13 16:03:28.863][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:03:28.863][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-13 16:03:28.864][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-13 16:03:28.865][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-13 16:03:28.866][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-13 16:03:28.867][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:03:28.867][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:03:28.868][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:03:28.869][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-13 16:03:28.870][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-13 16:03:28.871][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-13 16:03:28.872][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-13 16:03:28.872][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:03:28.873][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:03:28.874][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:03:28.875][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-13 16:03:28.876][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-13 16:03:28.877][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-13 16:03:28.877][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-13 16:03:28.878][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:03:28.879][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[2025-12-13 16:03:28.880][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:03:28.881][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-13 16:03:28.881][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-13 16:03:28.882][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-13 16:03:28.883][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-13 16:03:28.884][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:03:28.885][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:03:28.886][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:03:28.886][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-13 16:03:28.887][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-13 16:03:28.888][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-13 16:03:28.889][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-13 16:03:28.890][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:03:28.891][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:03:28.891][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:03:28.892][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-13 16:03:28.893][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-13 16:03:28.894][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-13 16:03:28.895][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-13 16:03:28.896][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:03:28.900][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:03:28.901][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:03:28.902][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-13 16:03:28.903][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-13 16:03:28.904][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-13 16:03:28.904][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-13 16:03:28.905][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:03:28.906][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:03:28.908][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNci.Rcheck/biodbNci/definitions.yml".
biodb.DEBUG[2025-12-13 16:03:28.909][self$getDbsInfo()$define] Define connector nci.cactus.
biodb.DEBUG[2025-12-13 16:03:28.911][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-12-13 16:03:28.912][self$setPropertyValue] Setting property "description" to "National Cancer Institute (USA) CACTUS Database.".
biodb.DEBUG[2025-12-13 16:03:28.912][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-12-13 16:03:28.913][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-12-13 16:03:28.914][self$setPropertyValue] Setting property "downloadable" to "TRUE".
biodb.DEBUG[2025-12-13 16:03:28.915][self$setPropertyValue] Setting property "dwnld.ext" to "gz".
biodb.DEBUG[2025-12-13 16:03:28.916][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-12-13 16:03:28.917][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-12-13 16:03:28.918][self$setPropertyValue] Setting property "entry.content.type" to "sdf".
biodb.DEBUG[2025-12-13 16:03:28.919][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-12-13 16:03:28.920][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-12-13 16:03:28.921][self$setPropertyValue] Setting property "name" to "NCI CACTUS".
biodb.DEBUG[2025-12-13 16:03:28.922][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-12-13 16:03:28.923][self$setPropertyValue] Setting property "parsing.expr" to "NSC".
biodb.DEBUG[2025-12-13 16:03:28.923][self$setPropertyValue] Setting property "parsing.expr" to "DTP names".
biodb.DEBUG[2025-12-13 16:03:28.923][self$setPropertyValue] Setting property "parsing.expr" to "Standard InChI".
biodb.DEBUG[2025-12-13 16:03:28.923][self$setPropertyValue] Setting property "parsing.expr" to "c("Standard InChIKey", "^InChIKey=(.*)$")".
biodb.DEBUG[2025-12-13 16:03:28.923][self$setPropertyValue] Setting property "parsing.expr" to "Formula".
biodb.DEBUG[2025-12-13 16:03:28.923][self$setPropertyValue] Setting property "parsing.expr" to "Molecular Weight".
biodb.DEBUG[2025-12-13 16:03:28.923][self$setPropertyValue] Setting property "parsing.expr" to "CAS".
biodb.DEBUG[2025-12-13 16:03:28.924][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-12-13 16:03:28.925][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-12-13 16:03:28.926][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-12-13 16:03:28.926][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-12-13 16:03:28.927][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-12-13 16:03:28.928][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-12-13 16:03:28.929][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-12-13 16:03:28.930][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-12-13 16:03:28.931][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-12-13 16:03:28.932][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/".
biodb.DEBUG[2025-12-13 16:03:28.932][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/".
biodb.DEBUG[2025-12-13 16:03:28.932][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/download/nci/".
biodb.DEBUG[2025-12-13 16:03:28.932][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/download/nci/NCI-Open_2012-05-01.sdf.gz".
biodb.DEBUG[2025-12-13 16:03:28.933][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-12-13 16:03:28.933][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-12-13 16:03:28.934][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-12-13 16:03:28.935][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-12-13 16:03:28.936][self$getEntryFields()$define] Define field nci.cactus.id.
biodb.DEBUG[2025-12-13 16:03:28.939][super$initialize] Initialize connector nci.cactus.
biodb.DEBUG[2025-12-13 16:03:28.942][biodb$getFactory()$createConn] Creating new connector nci.cactus for database class nci.cactus .
biodb.INFO [2025-12-13 16:03:28.943][biodb$terminate] Closing BiodbMain instance...
biodb.INFO [2025-12-13 16:03:28.944][self$deleteConn] Connector "nci.cactus" deleted.
biodb.DEBUG[2025-12-13 16:03:28.945][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-12-13 16:03:28.946][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-13 16:03:28.947][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-13 16:03:28.948][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-13 16:03:28.948][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-13 16:03:28.949][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:03:28.950][FUN] Functions in observer 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)