Back to Long Tests report for BioC 3.21

This page was generated on 2025-10-11 23:55 -0400 (Sat, 11 Oct 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4833
merida1macOS 12.7.5 Montereyx86_644.5.1 RC (2025-06-05 r88288) -- "Great Square Root" 4614
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 9/30HostnameOS / ArchCHECK
biodbNci 1.12.0  (landing page)
Pierrick Roger
Snapshot Date: 2025-10-11 09:55 -0400 (Sat, 11 Oct 2025)
git_url: https://git.bioconductor.org/packages/biodbNci
git_branch: RELEASE_3_21
git_last_commit: a398ae4
git_last_commit_date: 2025-04-15 12:47:37 -0400 (Tue, 15 Apr 2025)
nebbiolo1Linux (Ubuntu 24.04.3 LTS) / x86_64  ERROR  
merida1macOS 12.7.5 Monterey / x86_64  ERROR  

CHECK results for biodbNci on nebbiolo1

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: 1.12.0
Command: /home/biocbuild/bbs-3.21-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_1.12.0.tar.gz
StartedAt: 2025-10-11 16:02:30 -0400 (Sat, 11 Oct 2025)
EndedAt: 2025-10-11 16:03:32 -0400 (Sat, 11 Oct 2025)
EllapsedTime: 62.1 seconds
RetCode: 1
Status:   ERROR  
CheckDir: biodbNci.Rcheck
Warnings: NA

Tests output

biodbNci.Rcheck/tests/testthat.Rout.fail


R version 4.5.1 (2025-06-13) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

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> # Script needed to run testthat automatically from ‘R CMD check’. See
> # testthat::test_dir documentation.
> library(testthat)
> library(biodbNci)
> Sys.setenv(TESTTHAT_REPORTER="summary")
> Sys.setenv(BIODB_LOG_DST="console")
> test_check("biodbNci")
biodb.INFO [2025-10-11 16:03:28.222][biodb::testContext]
biodb.INFO [2025-10-11 16:03:28.224][biodb::testContext] ********************************************************************************
biodb.INFO [2025-10-11 16:03:28.225][biodb::testContext] Test context - Generic long tests
biodb.INFO [2025-10-11 16:03:28.226][biodb::testContext] ********************************************************************************
biodb.INFO [2025-10-11 16:03:28.227][biodb::testContext]
biodb.INFO [2025-10-11 16:03:28.233][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.16.1.
biodb.DEBUG[2025-10-11 16:03:28.235][self$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.21-bioc/R/site-library/biodb/definitions.yml".
biodb.DEBUG[2025-10-11 16:03:28.242][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-10-11 16:03:28.243][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-10-11 16:03:28.244][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-10-11 16:03:28.245][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:03:28.246][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:03:28.247][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-11 16:03:28.248][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-10-11 16:03:28.265][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-10-11 16:03:28.266][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:03:28.267][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:03:28.268][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-11 16:03:28.269][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-10-11 16:03:28.270][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-10-11 16:03:28.270][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:03:28.271][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:03:28.272][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-11 16:03:28.281][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-10-11 16:03:28.282][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-10-11 16:03:28.283][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-10-11 16:03:28.284][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:03:28.285][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:03:28.286][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-11 16:03:28.287][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-10-11 16:03:28.288][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-10-11 16:03:28.289][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-10-11 16:03:28.289][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:03:28.290][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:03:28.291][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-11 16:03:28.292][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-10-11 16:03:28.293][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-10-11 16:03:28.294][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:03:28.295][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:03:28.295][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-11 16:03:28.296][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-10-11 16:03:28.297][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-10-11 16:03:28.298][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-10-11 16:03:28.299][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:03:28.300][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:03:28.301][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-11 16:03:28.302][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-10-11 16:03:28.303][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-10-11 16:03:28.304][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:03:28.304][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:03:28.305][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-11 16:03:28.306][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-10-11 16:03:28.307][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-10-11 16:03:28.308][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-10-11 16:03:28.309][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:03:28.310][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:03:28.311][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-11 16:03:28.311][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-10-11 16:03:28.312][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-10-11 16:03:28.313][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-10-11 16:03:28.314][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-10-11 16:03:28.315][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-10-11 16:03:28.316][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-10-11 16:03:28.317][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:03:28.318][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:03:28.319][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-11 16:03:28.320][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-10-11 16:03:28.321][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-10-11 16:03:28.321][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:03:28.322][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:03:28.323][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-11 16:03:28.324][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-10-11 16:03:28.325][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-10-11 16:03:28.326][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:03:28.327][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:03:28.327][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-11 16:03:28.328][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-10-11 16:03:28.329][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-10-11 16:03:28.330][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:03:28.331][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:03:28.332][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-11 16:03:28.333][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-10-11 16:03:28.334][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-10-11 16:03:28.335][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-10-11 16:03:28.335][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:03:28.336][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:03:28.337][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-11 16:03:28.338][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-10-11 16:03:28.339][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-10-11 16:03:28.343][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-10-11 16:03:28.344][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:03:28.345][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:03:28.346][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-11 16:03:28.347][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-10-11 16:03:28.348][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-10-11 16:03:28.349][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-10-11 16:03:28.349][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:03:28.350][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:03:28.351][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-11 16:03:28.354][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-10-11 16:03:28.385][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-10-11 16:03:28.399][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2025-10-11 16:03:28.401][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-10-11 16:03:28.402][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-10-11 16:03:28.402][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-10-11 16:03:28.403][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-10-11 16:03:28.404][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-10-11 16:03:28.405][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-10-11 16:03:28.406][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-10-11 16:03:28.407][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-10-11 16:03:28.408][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-10-11 16:03:28.409][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-10-11 16:03:28.410][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-10-11 16:03:28.411][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-10-11 16:03:28.412][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-10-11 16:03:28.413][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-10-11 16:03:28.413][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-10-11 16:03:28.413][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-10-11 16:03:28.413][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-10-11 16:03:28.413][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-10-11 16:03:28.414][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-10-11 16:03:28.415][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-11 16:03:28.416][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-11 16:03:28.416][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-10-11 16:03:28.417][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-11 16:03:28.418][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-11 16:03:28.419][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-10-11 16:03:28.420][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-10-11 16:03:28.421][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-10-11 16:03:28.422][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-10-11 16:03:28.423][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-10-11 16:03:28.424][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-10-11 16:03:28.425][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-10-11 16:03:28.426][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-10-11 16:03:28.427][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-10-11 16:03:28.428][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-10-11 16:03:28.429][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-10-11 16:03:28.430][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-10-11 16:03:28.431][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-10-11 16:03:28.432][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-10-11 16:03:28.437][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-10-11 16:03:28.438][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-10-11 16:03:28.439][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-10-11 16:03:28.440][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-10-11 16:03:28.441][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-10-11 16:03:28.442][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-10-11 16:03:28.443][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-10-11 16:03:28.444][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-10-11 16:03:28.445][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-10-11 16:03:28.445][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-10-11 16:03:28.445][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-10-11 16:03:28.445][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-10-11 16:03:28.445][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-10-11 16:03:28.446][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-10-11 16:03:28.447][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-11 16:03:28.448][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-11 16:03:28.449][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-10-11 16:03:28.450][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-11 16:03:28.450][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-11 16:03:28.451][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-10-11 16:03:28.452][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-10-11 16:03:28.453][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-10-11 16:03:28.454][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-10-11 16:03:28.455][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-10-11 16:03:28.456][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-10-11 16:03:28.457][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-10-11 16:03:28.459][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-10-11 16:03:28.460][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2025-10-11 16:03:28.461][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-10-11 16:03:28.461][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-10-11 16:03:28.462][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-10-11 16:03:28.463][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-10-11 16:03:28.464][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-10-11 16:03:28.465][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-10-11 16:03:28.466][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-10-11 16:03:28.467][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-10-11 16:03:28.468][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-10-11 16:03:28.469][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-10-11 16:03:28.470][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-10-11 16:03:28.471][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-10-11 16:03:28.472][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-10-11 16:03:28.473][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-10-11 16:03:28.474][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-10-11 16:03:28.475][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-11 16:03:28.475][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-11 16:03:28.476][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-10-11 16:03:28.477][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-11 16:03:28.478][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-11 16:03:28.479][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-10-11 16:03:28.480][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-10-11 16:03:28.481][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-10-11 16:03:28.482][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-10-11 16:03:28.482][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-10-11 16:03:28.483][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-10-11 16:03:28.484][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-10-11 16:03:28.486][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-10-11 16:03:28.487][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-10-11 16:03:28.488][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-10-11 16:03:28.489][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-10-11 16:03:28.490][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-10-11 16:03:28.491][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-10-11 16:03:28.492][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-10-11 16:03:28.493][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-10-11 16:03:28.493][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-10-11 16:03:28.494][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-10-11 16:03:28.495][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-10-11 16:03:28.496][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-10-11 16:03:28.497][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-10-11 16:03:28.498][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-10-11 16:03:28.499][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-10-11 16:03:28.500][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-10-11 16:03:28.501][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-10-11 16:03:28.502][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-11 16:03:28.503][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-11 16:03:28.504][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-10-11 16:03:28.505][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-11 16:03:28.505][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-11 16:03:28.506][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-10-11 16:03:28.507][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-10-11 16:03:28.508][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-10-11 16:03:28.509][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-10-11 16:03:28.510][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-10-11 16:03:28.511][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-10-11 16:03:28.514][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-10-11 16:03:28.515][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:03:28.516][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-11 16:03:28.517][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:03:28.518][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:03:28.519][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:03:28.519][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:03:28.520][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.DEBUG[2025-10-11 16:03:28.521][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:03:28.522][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:03:28.523][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:03:28.524][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:03:28.524][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-11 16:03:28.525][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:03:28.526][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:03:28.527][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:03:28.528][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:03:28.529][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-11 16:03:28.530][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:03:28.530][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:03:28.531][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:03:28.532][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:03:28.533][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-11 16:03:28.534][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:03:28.535][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:03:28.535][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:03:28.536][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:03:28.537][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-11 16:03:28.538][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:03:28.539][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:03:28.540][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:03:28.540][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:03:28.541][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-11 16:03:28.542][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:03:28.543][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:03:28.544][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:03:28.545][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:03:28.545][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-11 16:03:28.546][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:03:28.547][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:03:28.548][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:03:28.549][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:03:28.550][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-11 16:03:28.551][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:03:28.551][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:03:28.552][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:03:28.553][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:03:28.554][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-11 16:03:28.555][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:03:28.556][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:03:28.556][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:03:28.557][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:03:28.558][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-11 16:03:28.559][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:03:28.560][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:03:28.561][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:03:28.561][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:03:28.562][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-11 16:03:28.563][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:03:28.564][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:03:28.565][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:03:28.566][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:03:28.567][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-11 16:03:28.567][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:03:28.568][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:03:28.569][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:03:28.570][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:03:28.571][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-11 16:03:28.572][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:03:28.572][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:03:28.573][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:03:28.574][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:03:28.575][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-11 16:03:28.576][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:03:28.577][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:03:28.577][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:03:28.578][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:03:28.579][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-11 16:03:28.580][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:03:28.581][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:03:28.582][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:03:28.583][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:03:28.583][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-11 16:03:28.584][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-10-11 16:03:28.589][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-10-11 16:03:28.590][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-10-11 16:03:28.595][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-10-11 16:03:28.597][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-10-11 16:03:28.598][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-10-11 16:03:28.605][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-10-11 16:03:28.609][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-10-11 16:03:28.611][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-10-11 16:03:28.612][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-10-11 16:03:28.614][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-10-11 16:03:28.616][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-10-11 16:03:28.618][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-10-11 16:03:28.619][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-10-11 16:03:28.621][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-10-11 16:03:28.623][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-10-11 16:03:28.624][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-10-11 16:03:28.626][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-10-11 16:03:28.628][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-10-11 16:03:28.629][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-10-11 16:03:28.631][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-10-11 16:03:28.632][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-10-11 16:03:28.634][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-10-11 16:03:28.635][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-10-11 16:03:28.637][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-10-11 16:03:28.638][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-10-11 16:03:28.640][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-10-11 16:03:28.641][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-10-11 16:03:28.643][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-10-11 16:03:28.644][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-10-11 16:03:28.646][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-10-11 16:03:28.647][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-10-11 16:03:28.649][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-10-11 16:03:28.650][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-10-11 16:03:28.652][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-10-11 16:03:28.653][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-10-11 16:03:28.655][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-10-11 16:03:28.656][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-10-11 16:03:28.658][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-10-11 16:03:28.659][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-10-11 16:03:28.661][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-10-11 16:03:28.662][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-10-11 16:03:28.663][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-10-11 16:03:28.665][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-10-11 16:03:28.666][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-10-11 16:03:28.668][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-10-11 16:03:28.669][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-10-11 16:03:28.671][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-10-11 16:03:28.672][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-10-11 16:03:28.674][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-10-11 16:03:28.675][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-10-11 16:03:28.677][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-10-11 16:03:28.678][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-10-11 16:03:28.679][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-10-11 16:03:28.681][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-10-11 16:03:28.682][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-10-11 16:03:28.684][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-10-11 16:03:28.685][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-10-11 16:03:28.687][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-10-11 16:03:28.688][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-10-11 16:03:28.690][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-10-11 16:03:28.691][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-10-11 16:03:28.692][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-10-11 16:03:28.694][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-10-11 16:03:28.695][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-10-11 16:03:28.697][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-10-11 16:03:28.698][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-10-11 16:03:28.700][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-10-11 16:03:28.701][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-10-11 16:03:28.703][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-10-11 16:03:28.704][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-10-11 16:03:28.705][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-10-11 16:03:28.707][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-10-11 16:03:28.708][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-10-11 16:03:28.710][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-10-11 16:03:28.711][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-10-11 16:03:28.713][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-10-11 16:03:28.714][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-10-11 16:03:28.715][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-10-11 16:03:28.717][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-10-11 16:03:28.718][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-10-11 16:03:28.720][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-10-11 16:03:28.721][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-10-11 16:03:28.728][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-10-11 16:03:28.731][initialize] This is biodb version 1.16.1.
biodb.DEBUG[2025-10-11 16:03:28.734][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-10-11 16:03:28.735][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:03:28.736][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:03:28.737][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:03:28.738][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-11 16:03:28.743][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:03:28.744][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-11 16:03:28.745][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-11 16:03:28.746][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:03:28.747][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:03:28.748][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:03:28.749][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-11 16:03:28.750][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:03:28.751][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-11 16:03:28.752][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-11 16:03:28.752][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:03:28.753][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:03:28.754][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:03:28.755][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-11 16:03:28.756][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:03:28.757][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-11 16:03:28.758][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-11 16:03:28.759][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:03:28.760][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:03:28.761][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:03:28.762][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-11 16:03:28.763][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:03:28.764][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-11 16:03:28.764][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-11 16:03:28.765][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:03:28.766][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:03:28.767][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:03:28.768][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-11 16:03:28.769][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:03:28.770][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-11 16:03:28.784][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-11 16:03:28.785][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:03:28.785][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:03:28.786][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:03:28.787][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-11 16:03:28.788][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:03:28.789][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-11 16:03:28.790][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-11 16:03:28.791][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:03:28.791][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:03:28.792][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:03:28.793][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-11 16:03:28.794][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:03:28.795][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-11 16:03:28.796][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-11 16:03:28.796][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:03:28.797][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:03:28.798][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:03:28.799][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-11 16:03:28.800][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:03:28.801][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-11 16:03:28.802][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-11 16:03:28.802][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:03:28.803][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:03:28.804][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:03:28.805][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-11 16:03:28.806][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:03:28.807][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-11 16:03:28.808][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-11 16:03:28.808][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:03:28.809][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:03:28.810][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:03:28.811][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-11 16:03:28.812][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:03:28.813][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-11 16:03:28.813][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-11 16:03:28.814][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:03:28.815][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:03:28.816][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:03:28.817][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-11 16:03:28.818][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:03:28.818][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-11 16:03:28.819][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-11 16:03:28.820][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:03:28.821][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:03:28.822][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:03:28.823][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-11 16:03:28.824][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:03:28.824][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-11 16:03:28.825][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-11 16:03:28.826][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:03:28.827][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:03:28.828][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:03:28.829][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-11 16:03:28.829][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:03:28.830][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-11 16:03:28.831][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-11 16:03:28.832][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:03:28.833][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:03:28.834][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:03:28.834][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-11 16:03:28.835][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:03:28.836][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-11 16:03:28.837][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-11 16:03:28.838][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:03:28.839][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:03:28.839][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:03:28.840][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-11 16:03:28.841][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:03:28.842][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-11 16:03:28.843][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-11 16:03:28.844][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:03:28.845][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:03:28.845][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:03:28.846][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-11 16:03:28.847][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:03:28.848][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-11 16:03:28.849][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-11 16:03:28.850][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:03:28.850][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:03:28.851][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:03:28.852][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-11 16:03:28.854][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.21-bioc-longtests/meat/biodbNci.Rcheck/biodbNci/definitions.yml".
biodb.DEBUG[2025-10-11 16:03:28.863][self$getDbsInfo()$define] Define connector nci.cactus.
biodb.DEBUG[2025-10-11 16:03:28.865][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-10-11 16:03:28.866][self$setPropertyValue] Setting property "description" to "National Cancer Institute (USA) CACTUS Database.".
biodb.DEBUG[2025-10-11 16:03:28.867][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-10-11 16:03:28.868][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-10-11 16:03:28.869][self$setPropertyValue] Setting property "downloadable" to "TRUE".
biodb.DEBUG[2025-10-11 16:03:28.869][self$setPropertyValue] Setting property "dwnld.ext" to "gz".
biodb.DEBUG[2025-10-11 16:03:28.870][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-10-11 16:03:28.871][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-10-11 16:03:28.872][self$setPropertyValue] Setting property "entry.content.type" to "sdf".
biodb.DEBUG[2025-10-11 16:03:28.873][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-10-11 16:03:28.874][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-10-11 16:03:28.875][self$setPropertyValue] Setting property "name" to "NCI CACTUS".
biodb.DEBUG[2025-10-11 16:03:28.876][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-10-11 16:03:28.877][self$setPropertyValue] Setting property "parsing.expr" to "NSC".
biodb.DEBUG[2025-10-11 16:03:28.877][self$setPropertyValue] Setting property "parsing.expr" to "DTP names".
biodb.DEBUG[2025-10-11 16:03:28.877][self$setPropertyValue] Setting property "parsing.expr" to "Standard InChI".
biodb.DEBUG[2025-10-11 16:03:28.877][self$setPropertyValue] Setting property "parsing.expr" to "c("Standard InChIKey", "^InChIKey=(.*)$")".
biodb.DEBUG[2025-10-11 16:03:28.877][self$setPropertyValue] Setting property "parsing.expr" to "Formula".
biodb.DEBUG[2025-10-11 16:03:28.877][self$setPropertyValue] Setting property "parsing.expr" to "Molecular Weight".
biodb.DEBUG[2025-10-11 16:03:28.877][self$setPropertyValue] Setting property "parsing.expr" to "CAS".
biodb.DEBUG[2025-10-11 16:03:28.878][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-10-11 16:03:28.879][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-10-11 16:03:28.880][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-10-11 16:03:28.881][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-11 16:03:28.882][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-11 16:03:28.883][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-10-11 16:03:28.884][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-11 16:03:28.884][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-11 16:03:28.885][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-10-11 16:03:28.886][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/".
biodb.DEBUG[2025-10-11 16:03:28.886][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/".
biodb.DEBUG[2025-10-11 16:03:28.886][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/download/nci/".
biodb.DEBUG[2025-10-11 16:03:28.886][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/download/nci/NCI-Open_2012-05-01.sdf.gz".
biodb.DEBUG[2025-10-11 16:03:28.887][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-10-11 16:03:28.888][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-10-11 16:03:28.889][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-10-11 16:03:28.890][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-10-11 16:03:28.895][self$getEntryFields()$define] Define field nci.cactus.id.
biodb.DEBUG[2025-10-11 16:03:28.917][super$initialize] Initialize connector nci.cactus.
biodb.DEBUG[2025-10-11 16:03:28.932][biodb$getFactory()$createConn] Creating new connector nci.cactus for database class nci.cactus .
biodb.INFO [2025-10-11 16:03:28.940][biodb::testThat]
biodb.INFO [2025-10-11 16:03:28.941][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2025-10-11 16:03:28.942][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-10-11 16:03:28.943][biodb::testThat]
biodb.TRACE[2025-10-11 16:03:28.952][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/bbs-3.21-bioc-longtests/meat/biodbNci.Rcheck/biodbNci/testref/entry-nci.cactus-749674-content.sdf".
biodb.DEBUG[2025-10-11 16:03:28.954][biodb$getFactory()$createEntryFromCo ...] Creating NCI CACTUS entries from 1 content(s).
biodb.DEBUG[2025-10-11 16:03:28.957][biodb$getFactory()$createEntryFromCo ...] Parsing 1 NCI CACTUS entries.
biodb.DEBUG[2025-10-11 16:03:28.964][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-10-11 16:03:28.965][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-11 16:03:28.966][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-11 16:03:28.978][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:03:28.978][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:03:28.979][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:03:28.980][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-10-11 16:03:28.996][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-11 16:03:28.997][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-11 16:03:28.998][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:03:28.999][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:03:29.000][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-11 16:03:29.011][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-11 16:03:29.012][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:03:29.013][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:03:29.016][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-10-11 16:03:29.017][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-10-11 16:03:29.017][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:03:29.018][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:03:29.042][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-10-11 16:03:29.043][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-10-11 16:03:29.044][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:03:29.045][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:03:29.046][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-10-11 16:03:29.047][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-10-11 16:03:29.048][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:03:29.049][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:03:29.050][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-10-11 16:03:29.051][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-10-11 16:03:29.052][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:03:29.053][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:03:29.055][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-10-11 16:03:29.055][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-10-11 16:03:29.056][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:03:29.057][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:03:29.058][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-10-11 16:03:29.059][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-10-11 16:03:29.060][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:03:29.061][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:03:29.062][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-10-11 16:03:29.063][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-10-11 16:03:29.064][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:03:29.065][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:03:29.066][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-10-11 16:03:29.067][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-10-11 16:03:29.068][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:03:29.069][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:03:29.070][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-10-11 16:03:29.071][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-10-11 16:03:29.072][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:03:29.073][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:03:29.074][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-10-11 16:03:29.075][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-10-11 16:03:29.076][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:03:29.077][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:03:29.078][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-11 16:03:29.079][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-11 16:03:29.080][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:03:29.087][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:03:29.087][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-10-11 16:03:29.088][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-10-11 16:03:29.089][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:03:29.090][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:03:29.091][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-11 16:03:29.092][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-11 16:03:29.093][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:03:29.094][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:03:29.095][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-11 16:03:29.096][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-11 16:03:29.097][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:03:29.098][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:03:29.099][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-11 16:03:29.100][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-11 16:03:29.101][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:03:29.101][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:03:29.132][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-11 16:03:29.134][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-11 16:03:29.134][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:03:29.135][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:03:29.136][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-11 16:03:29.137][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-11 16:03:29.138][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:03:29.139][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:03:29.140][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-11 16:03:29.141][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-11 16:03:29.142][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:03:29.143][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-10-11 16:03:29.144][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 749674.
biodb.TRACE[2025-10-11 16:03:29.146][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-10-11 16:03:29.147][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-10-11 16:03:29.148][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:03:29.149][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:03:29.150][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-10-11 16:03:29.151][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-10-11 16:03:29.152][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:03:29.153][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:03:29.154][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-10-11 16:03:29.155][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-10-11 16:03:29.156][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:03:29.156][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:03:29.157][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-10-11 16:03:29.158][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-10-11 16:03:29.159][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:03:29.160][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:03:29.162][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-11 16:03:29.163][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-11 16:03:29.164][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:03:29.165][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:03:29.177][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-10-11 16:03:29.178][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-10-11 16:03:29.179][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:03:29.180][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:03:29.184][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-11 16:03:29.185][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-11 16:03:29.186][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:03:29.187][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:03:29.188][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-11 16:03:29.189][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-11 16:03:29.190][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:03:29.191][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:03:29.192][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-11 16:03:29.233][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-11 16:03:29.234][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:03:29.235][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:03:29.238][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-11 16:03:29.239][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-11 16:03:29.239][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:03:29.240][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:03:29.241][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-11 16:03:29.242][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-11 16:03:29.243][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:03:29.244][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:03:29.245][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-11 16:03:29.246][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-11 16:03:29.247][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:03:29.248][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:03:29.249][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-10-11 16:03:29.250][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-10-11 16:03:29.251][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:03:29.252][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:03:29.253][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-10-11 16:03:29.254][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-10-11 16:03:29.255][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:03:29.256][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:03:29.257][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-10-11 16:03:29.258][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-10-11 16:03:29.258][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:03:29.259][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:03:29.266][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-11 16:03:29.267][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-11 16:03:29.268][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:03:29.269][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:03:29.270][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-11 16:03:29.271][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-11 16:03:29.272][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:03:29.272][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:03:29.273][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-11 16:03:29.274][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-11 16:03:29.275][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:03:29.276][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:03:29.277][ef$get] Asked field names are: accession.
biodb.TRACE[2025-10-11 16:03:29.278][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-11 16:03:29.279][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:03:29.280][ef$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:03:29.281][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-11 16:03:29.282][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-11 16:03:29.283][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:03:29.284][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:03:29.291][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-10-11 16:03:29.292][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-10-11 16:03:29.293][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:03:29.294][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:03:29.295][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-10-11 16:03:29.296][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-10-11 16:03:29.297][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:03:29.298][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:03:29.299][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-10-11 16:03:29.300][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-10-11 16:03:29.301][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:03:29.301][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:03:29.302][ef$get] Asked field names are: formula.
biodb.TRACE[2025-10-11 16:03:29.303][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-10-11 16:03:29.304][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:03:29.305][ef$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:03:29.306][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-10-11 16:03:29.307][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-10-11 16:03:29.308][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:03:29.309][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:03:29.316][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-10-11 16:03:29.317][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-10-11 16:03:29.318][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:03:29.319][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:03:29.320][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-10-11 16:03:29.321][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-10-11 16:03:29.322][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:03:29.323][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:03:29.324][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-10-11 16:03:29.325][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-10-11 16:03:29.325][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:03:29.326][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:03:29.327][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-10-11 16:03:29.328][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-10-11 16:03:29.329][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:03:29.330][ef$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:03:29.331][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-10-11 16:03:29.332][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-10-11 16:03:29.333][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:03:29.334][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:03:29.341][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-10-11 16:03:29.342][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-10-11 16:03:29.343][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:03:29.344][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:03:29.345][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-10-11 16:03:29.346][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-10-11 16:03:29.347][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:03:29.348][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:03:29.349][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-10-11 16:03:29.350][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-10-11 16:03:29.354][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:03:29.355][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:03:29.356][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-10-11 16:03:29.357][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-10-11 16:03:29.358][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:03:29.359][ef$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:03:29.360][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-10-11 16:03:29.361][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-10-11 16:03:29.362][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:03:29.362][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:03:29.370][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-10-11 16:03:29.371][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-10-11 16:03:29.372][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:03:29.373][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:03:29.373][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-10-11 16:03:29.374][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-10-11 16:03:29.375][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:03:29.376][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:03:29.377][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-10-11 16:03:29.378][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-10-11 16:03:29.379][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:03:29.380][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:03:29.381][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-10-11 16:03:29.382][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-10-11 16:03:29.383][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:03:29.384][ef$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:03:29.385][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-10-11 16:03:29.386][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-10-11 16:03:29.387][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:03:29.387][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:03:29.395][ef$get] Asked field names are: accession.
biodb.TRACE[2025-10-11 16:03:29.396][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-11 16:03:29.396][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:03:29.397][ef$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:03:29.401][ef$get] Asked field names are: formula.
biodb.TRACE[2025-10-11 16:03:29.402][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-10-11 16:03:29.403][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:03:29.404][ef$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:03:29.408][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-10-11 16:03:29.409][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-10-11 16:03:29.410][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:03:29.410][ef$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:03:29.414][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-10-11 16:03:29.415][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-10-11 16:03:29.416][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:03:29.417][ef$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:03:29.421][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-10-11 16:03:29.422][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-10-11 16:03:29.423][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:03:29.424][ef$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:03:29.439][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/bbs-3.21-bioc-longtests/meat/biodbNci.Rcheck/biodbNci/testref/entry-nci.cactus-750690-content.sdf".
biodb.DEBUG[2025-10-11 16:03:29.475][biodb$getFactory()$createEntryFromCo ...] Creating NCI CACTUS entries from 1 content(s).
biodb.DEBUG[2025-10-11 16:03:29.477][biodb$getFactory()$createEntryFromCo ...] Parsing 1 NCI CACTUS entries.
biodb.DEBUG[2025-10-11 16:03:29.478][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-10-11 16:03:29.479][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-11 16:03:29.480][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-11 16:03:29.484][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:03:29.485][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:03:29.486][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:03:29.486][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-10-11 16:03:29.495][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-11 16:03:29.496][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-11 16:03:29.497][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:03:29.498][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:03:29.499][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-11 16:03:29.500][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-11 16:03:29.501][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:03:29.502][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:03:29.519][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-10-11 16:03:29.520][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-10-11 16:03:29.521][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:03:29.522][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:03:29.523][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-10-11 16:03:29.524][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-10-11 16:03:29.525][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:03:29.526][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:03:29.527][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-10-11 16:03:29.528][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-10-11 16:03:29.529][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:03:29.530][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:03:29.531][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-10-11 16:03:29.532][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-10-11 16:03:29.533][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:03:29.534][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:03:29.535][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-10-11 16:03:29.536][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-10-11 16:03:29.537][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:03:29.538][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:03:29.539][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-10-11 16:03:29.540][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-10-11 16:03:29.541][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:03:29.541][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:03:29.543][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-10-11 16:03:29.544][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-10-11 16:03:29.545][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:03:29.546][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:03:29.546][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-10-11 16:03:29.547][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-10-11 16:03:29.548][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:03:29.549][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:03:29.550][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-10-11 16:03:29.551][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-10-11 16:03:29.552][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:03:29.553][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:03:29.554][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-10-11 16:03:29.555][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-10-11 16:03:29.556][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:03:29.557][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:03:29.558][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-10-11 16:03:29.559][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-10-11 16:03:29.560][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:03:29.561][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:03:29.562][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-10-11 16:03:29.563][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-10-11 16:03:29.564][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:03:29.565][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:03:29.566][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-10-11 16:03:29.567][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-10-11 16:03:29.567][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:03:29.568][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:03:29.570][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-10-11 16:03:29.571][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-10-11 16:03:29.572][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:03:29.576][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:03:29.577][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-10-11 16:03:29.578][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-10-11 16:03:29.579][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:03:29.580][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:03:29.582][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-10-11 16:03:29.583][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-10-11 16:03:29.583][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:03:29.584][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:03:29.585][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-10-11 16:03:29.586][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-10-11 16:03:29.587][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:03:29.588][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:03:29.590][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-10-11 16:03:29.591][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-10-11 16:03:29.592][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:03:29.593][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:03:29.594][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-10-11 16:03:29.595][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-10-11 16:03:29.595][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:03:29.596][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:03:29.597][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-11 16:03:29.598][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-11 16:03:29.599][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:03:29.600][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:03:29.601][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-10-11 16:03:29.602][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-10-11 16:03:29.603][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:03:29.604][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:03:29.605][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-11 16:03:29.606][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-11 16:03:29.607][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:03:29.608][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:03:29.609][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-11 16:03:29.610][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-11 16:03:29.611][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:03:29.611][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:03:29.612][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-11 16:03:29.613][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-11 16:03:29.614][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:03:29.615][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:03:29.616][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-11 16:03:29.617][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-11 16:03:29.618][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:03:29.619][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:03:29.620][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-11 16:03:29.621][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-11 16:03:29.622][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:03:29.623][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:03:29.624][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-11 16:03:29.625][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-11 16:03:29.626][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:03:29.627][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-10-11 16:03:29.628][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 750690.
biodb.TRACE[2025-10-11 16:03:29.647][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-10-11 16:03:29.648][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-10-11 16:03:29.649][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:03:29.649][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:03:29.650][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-10-11 16:03:29.651][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-10-11 16:03:29.652][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:03:29.653][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:03:29.654][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-10-11 16:03:29.655][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-10-11 16:03:29.656][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:03:29.657][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:03:29.658][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-10-11 16:03:29.659][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-10-11 16:03:29.660][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:03:29.661][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:03:29.662][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-11 16:03:29.663][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-11 16:03:29.664][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:03:29.665][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:03:29.669][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-10-11 16:03:29.670][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-10-11 16:03:29.671][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:03:29.672][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:03:29.676][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-11 16:03:29.677][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-11 16:03:29.678][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:03:29.679][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:03:29.680][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-11 16:03:29.681][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-11 16:03:29.682][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:03:29.683][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:03:29.684][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-11 16:03:29.685][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-11 16:03:29.686][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:03:29.687][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:03:29.692][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-11 16:03:29.693][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-11 16:03:29.694][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:03:29.695][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:03:29.696][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-11 16:03:29.697][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-11 16:03:29.698][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:03:29.699][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:03:29.700][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-11 16:03:29.701][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-11 16:03:29.702][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:03:29.702][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:03:29.704][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-10-11 16:03:29.705][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-10-11 16:03:29.706][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:03:29.706][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:03:29.707][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-10-11 16:03:29.708][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-10-11 16:03:29.709][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:03:29.710][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:03:29.711][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-10-11 16:03:29.712][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-10-11 16:03:29.713][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:03:29.714][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:03:29.729][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-11 16:03:29.730][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-11 16:03:29.731][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:03:29.732][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:03:29.733][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-11 16:03:29.734][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-11 16:03:29.735][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:03:29.736][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:03:29.737][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-11 16:03:29.738][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-11 16:03:29.739][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:03:29.739][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:03:29.740][ef$get] Asked field names are: accession.
biodb.TRACE[2025-10-11 16:03:29.741][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-11 16:03:29.742][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:03:29.743][ef$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:03:29.744][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-11 16:03:29.745][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-11 16:03:29.746][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:03:29.747][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:03:29.754][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-10-11 16:03:29.755][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-10-11 16:03:29.756][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:03:29.757][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:03:29.758][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-10-11 16:03:29.759][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-10-11 16:03:29.760][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:03:29.761][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:03:29.762][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-10-11 16:03:29.763][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-10-11 16:03:29.764][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:03:29.765][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:03:29.766][ef$get] Asked field names are: cas.id.
biodb.TRACE[2025-10-11 16:03:29.767][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-10-11 16:03:29.767][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:03:29.768][ef$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:03:29.769][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-10-11 16:03:29.770][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-10-11 16:03:29.771][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:03:29.772][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:03:29.779][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-10-11 16:03:29.780][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-10-11 16:03:29.781][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:03:29.782][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:03:29.783][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-10-11 16:03:29.784][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-10-11 16:03:29.785][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:03:29.786][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:03:29.787][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-10-11 16:03:29.788][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-10-11 16:03:29.789][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:03:29.790][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:03:29.791][ef$get] Asked field names are: name.
biodb.TRACE[2025-10-11 16:03:29.792][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-10-11 16:03:29.793][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:03:29.793][ef$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:03:29.794][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-10-11 16:03:29.795][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-10-11 16:03:29.796][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:03:29.797][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:03:29.808][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-10-11 16:03:29.809][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-10-11 16:03:29.810][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:03:29.811][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:03:29.812][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-10-11 16:03:29.813][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-10-11 16:03:29.814][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:03:29.815][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:03:29.816][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-10-11 16:03:29.817][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-10-11 16:03:29.818][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:03:29.818][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:03:29.819][ef$get] Asked field names are: formula.
biodb.TRACE[2025-10-11 16:03:29.820][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-10-11 16:03:29.821][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:03:29.822][ef$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:03:29.823][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-10-11 16:03:29.824][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-10-11 16:03:29.825][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:03:29.826][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:03:29.833][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-10-11 16:03:29.834][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-10-11 16:03:29.835][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:03:29.836][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:03:29.837][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-10-11 16:03:29.838][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-10-11 16:03:29.839][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:03:29.840][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:03:29.841][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-10-11 16:03:29.842][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-10-11 16:03:29.843][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:03:29.844][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:03:29.845][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-10-11 16:03:29.846][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-10-11 16:03:29.847][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:03:29.847][ef$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:03:29.848][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-10-11 16:03:29.849][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-10-11 16:03:29.850][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:03:29.851][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:03:29.859][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-10-11 16:03:29.860][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-10-11 16:03:29.861][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:03:29.861][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:03:29.862][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-10-11 16:03:29.863][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-10-11 16:03:29.864][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:03:29.865][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:03:29.866][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-10-11 16:03:29.867][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-10-11 16:03:29.868][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:03:29.869][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:03:29.870][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-10-11 16:03:29.871][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-10-11 16:03:29.872][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:03:29.873][ef$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:03:29.874][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-10-11 16:03:29.875][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-10-11 16:03:29.876][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:03:29.876][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:03:29.884][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-10-11 16:03:29.885][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-10-11 16:03:29.886][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:03:29.886][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:03:29.887][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-10-11 16:03:29.888][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-10-11 16:03:29.889][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:03:29.890][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:03:29.891][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-10-11 16:03:29.892][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-10-11 16:03:29.893][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:03:29.894][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:03:29.895][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-10-11 16:03:29.896][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-10-11 16:03:29.897][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:03:29.898][ef$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:03:29.899][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-10-11 16:03:29.900][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-10-11 16:03:29.901][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:03:29.901][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:03:29.909][ef$get] Asked field names are: accession.
biodb.TRACE[2025-10-11 16:03:29.910][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-11 16:03:29.911][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:03:29.912][ef$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:03:29.916][ef$get] Asked field names are: cas.id.
biodb.TRACE[2025-10-11 16:03:29.917][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-10-11 16:03:29.918][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:03:29.918][ef$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:03:29.922][ef$get] Asked field names are: formula.
biodb.TRACE[2025-10-11 16:03:29.927][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-10-11 16:03:29.928][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:03:29.929][ef$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:03:29.933][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-10-11 16:03:29.934][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-10-11 16:03:29.934][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:03:29.935][ef$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:03:29.939][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-10-11 16:03:29.940][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-10-11 16:03:29.941][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:03:29.942][ef$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:03:29.946][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-10-11 16:03:29.947][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-10-11 16:03:29.948][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:03:29.949][ef$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:03:29.953][ef$get] Asked field names are: name.
biodb.TRACE[2025-10-11 16:03:29.954][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-10-11 16:03:29.954][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:03:29.955][ef$get] fields variable is a list.
biodb.INFO [2025-10-11 16:03:29.962][biodb::testThat]
biodb.INFO [2025-10-11 16:03:29.963][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2025-10-11 16:03:29.963][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-10-11 16:03:29.964][biodb::testThat]
biodb.DEBUG[2025-10-11 16:03:29.966][private$loadEntries] Creating entries from ids [2]: "749674, 750690".
biodb.DEBUG[2025-10-11 16:03:29.968][conn$getEntryContent] Get NCI CACTUS entry content(s) for 2 id(s)...
biodb.DEBUG[2025-10-11 16:03:29.971][self$isDownloaded] Database nci.cactus has already been downloaded.
biodb.DEBUG[2025-10-11 16:03:29.999][self$isDownloaded] Database nci.cactus has already been downloaded.
biodb.INFO [2025-10-11 16:03:30.000][self$download] Extract whole database of nci.cactus.
biodb.INFO [2025-10-11 16:03:30.001][private$doExtractDownload] Extracting content of downloaded biodbNci, a library for connecting to the National Cancer Institute (USA) CACTUS Database....
biodb.INFO [2025-10-11 16:03:30.043][biodb::testThat]
biodb.INFO [2025-10-11 16:03:30.044][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2025-10-11 16:03:30.045][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-10-11 16:03:30.046][biodb::testThat]
biodb.INFO [2025-10-11 16:03:30.051][biodb::testThat]
biodb.INFO [2025-10-11 16:03:30.052][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2025-10-11 16:03:30.053][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-10-11 16:03:30.054][biodb::testThat]
biodb.WARN [2025-10-11 16:03:30.072][self$searchForEntries] This database is not searchable by field "name".
biodb.WARN [2025-10-11 16:03:30.089][self$searchForEntries] This database is not searchable by field "name".
biodb.INFO [2025-10-11 16:03:30.097][biodb::testThat]
biodb.INFO [2025-10-11 16:03:30.097][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2025-10-11 16:03:30.098][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-10-11 16:03:30.099][biodb::testThat]
biodb.DEBUG[2025-10-11 16:03:30.115][private$loadEntries] Creating entries from ids [1]: "749674".
biodb.DEBUG[2025-10-11 16:03:30.162][conn$getEntryContent] Get NCI CACTUS entry content(s) for 1 id(s)...
biodb.DEBUG[2025-10-11 16:03:30.164][self$isDownloaded] Database nci.cactus has already been downloaded.
biodb.DEBUG[2025-10-11 16:03:30.165][self$isDownloaded] Database nci.cactus has already been downloaded.
biodb.INFO [2025-10-11 16:03:30.166][self$download] Extract whole database of nci.cactus.
biodb.INFO [2025-10-11 16:03:30.178][private$doExtractDownload] Extracting content of downloaded biodbNci, a library for connecting to the National Cancer Institute (USA) CACTUS Database....
biodb.INFO [2025-10-11 16:03:30.200][biodb::testThat]
biodb.INFO [2025-10-11 16:03:30.201][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2025-10-11 16:03:30.202][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-10-11 16:03:30.203][biodb::testThat]
biodb.INFO [2025-10-11 16:03:30.209][biodb::testThat]
biodb.INFO [2025-10-11 16:03:30.210][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2025-10-11 16:03:30.211][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-10-11 16:03:30.212][biodb::testThat]
biodb.INFO [2025-10-11 16:03:30.218][biodb::testThat]
biodb.INFO [2025-10-11 16:03:30.219][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2025-10-11 16:03:30.220][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-10-11 16:03:30.221][biodb::testThat]
biodb.INFO [2025-10-11 16:03:30.226][biodb::testThat]
biodb.INFO [2025-10-11 16:03:30.227][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2025-10-11 16:03:30.228][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-10-11 16:03:30.229][biodb::testThat]
biodb.INFO [2025-10-11 16:03:30.233][biodb$terminate] Closing BiodbMain instance...
biodb.INFO [2025-10-11 16:03:30.235][self$deleteConn] Connector "nci.cactus" deleted.
biodb.DEBUG[2025-10-11 16:03:30.235][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-10-11 16:03:30.240][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-11 16:03:30.241][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-11 16:03:30.242][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:03:30.242][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:03:30.243][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:03:30.244][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2025-10-11 16:03:30.253][biodb::testContext]
biodb.INFO [2025-10-11 16:03:30.254][biodb::testContext] ********************************************************************************
biodb.INFO [2025-10-11 16:03:30.255][biodb::testContext] Test context - Example long tests
biodb.INFO [2025-10-11 16:03:30.255][biodb::testContext] ********************************************************************************
biodb.INFO [2025-10-11 16:03:30.256][biodb::testContext]
biodb.INFO [2025-10-11 16:03:30.258][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.16.1.
biodb.DEBUG[2025-10-11 16:03:30.260][self$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.21-bioc/R/site-library/biodb/definitions.yml".
biodb.DEBUG[2025-10-11 16:03:30.263][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-10-11 16:03:30.264][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-10-11 16:03:30.265][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-10-11 16:03:30.266][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:03:30.267][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:03:30.268][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-11 16:03:30.269][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-10-11 16:03:30.270][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-10-11 16:03:30.271][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:03:30.271][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:03:30.272][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-11 16:03:30.273][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-10-11 16:03:30.274][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-10-11 16:03:30.275][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:03:30.276][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:03:30.277][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-11 16:03:30.277][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-10-11 16:03:30.278][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-10-11 16:03:30.279][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-10-11 16:03:30.280][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:03:30.281][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:03:30.282][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-11 16:03:30.283][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-10-11 16:03:30.284][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-10-11 16:03:30.285][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-10-11 16:03:30.286][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:03:30.286][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:03:30.287][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-11 16:03:30.288][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-10-11 16:03:30.289][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-10-11 16:03:30.290][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:03:30.291][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:03:30.292][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-11 16:03:30.293][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-10-11 16:03:30.294][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-10-11 16:03:30.295][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-10-11 16:03:30.295][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:03:30.296][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:03:30.297][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-11 16:03:30.298][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-10-11 16:03:30.299][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-10-11 16:03:30.300][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:03:30.301][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:03:30.302][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-11 16:03:30.302][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-10-11 16:03:30.303][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-10-11 16:03:30.304][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-10-11 16:03:30.305][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:03:30.306][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:03:30.307][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-11 16:03:30.308][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-10-11 16:03:30.309][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-10-11 16:03:30.310][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-10-11 16:03:30.311][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-10-11 16:03:30.312][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-10-11 16:03:30.313][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-10-11 16:03:30.313][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:03:30.314][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:03:30.315][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-11 16:03:30.316][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-10-11 16:03:30.317][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-10-11 16:03:30.318][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:03:30.319][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:03:30.319][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-11 16:03:30.320][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-10-11 16:03:30.321][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-10-11 16:03:30.322][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:03:30.323][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:03:30.324][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-11 16:03:30.325][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-10-11 16:03:30.326][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-10-11 16:03:30.327][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:03:30.327][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:03:30.328][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-11 16:03:30.329][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-10-11 16:03:30.330][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-10-11 16:03:30.331][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-10-11 16:03:30.332][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:03:30.333][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:03:30.334][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-11 16:03:30.335][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-10-11 16:03:30.336][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-10-11 16:03:30.341][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-10-11 16:03:30.342][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:03:30.343][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:03:30.343][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-11 16:03:30.344][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-10-11 16:03:30.345][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-10-11 16:03:30.346][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-10-11 16:03:30.347][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:03:30.348][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:03:30.349][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-11 16:03:30.350][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-10-11 16:03:30.352][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-10-11 16:03:30.356][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2025-10-11 16:03:30.357][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-10-11 16:03:30.358][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-10-11 16:03:30.359][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-10-11 16:03:30.360][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-10-11 16:03:30.361][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-10-11 16:03:30.362][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-10-11 16:03:30.363][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-10-11 16:03:30.364][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-10-11 16:03:30.365][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-10-11 16:03:30.366][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-10-11 16:03:30.367][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-10-11 16:03:30.368][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-10-11 16:03:30.369][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-10-11 16:03:30.370][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-10-11 16:03:30.370][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-10-11 16:03:30.370][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-10-11 16:03:30.370][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-10-11 16:03:30.370][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-10-11 16:03:30.371][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-10-11 16:03:30.372][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-11 16:03:30.373][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-11 16:03:30.374][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-10-11 16:03:30.375][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-11 16:03:30.375][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-11 16:03:30.376][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-10-11 16:03:30.377][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-10-11 16:03:30.378][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-10-11 16:03:30.379][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-10-11 16:03:30.380][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-10-11 16:03:30.381][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-10-11 16:03:30.382][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-10-11 16:03:30.384][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-10-11 16:03:30.385][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-10-11 16:03:30.386][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-10-11 16:03:30.387][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-10-11 16:03:30.388][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-10-11 16:03:30.388][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-10-11 16:03:30.389][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-10-11 16:03:30.390][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-10-11 16:03:30.391][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-10-11 16:03:30.392][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-10-11 16:03:30.393][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-10-11 16:03:30.394][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-10-11 16:03:30.395][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-10-11 16:03:30.396][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-10-11 16:03:30.397][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-10-11 16:03:30.398][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-10-11 16:03:30.398][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-10-11 16:03:30.398][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-10-11 16:03:30.398][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-10-11 16:03:30.398][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-10-11 16:03:30.399][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-10-11 16:03:30.400][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-11 16:03:30.401][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-11 16:03:30.402][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-10-11 16:03:30.402][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-11 16:03:30.403][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-11 16:03:30.404][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-10-11 16:03:30.405][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-10-11 16:03:30.406][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-10-11 16:03:30.407][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-10-11 16:03:30.408][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-10-11 16:03:30.409][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-10-11 16:03:30.410][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-10-11 16:03:30.411][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-10-11 16:03:30.412][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2025-10-11 16:03:30.413][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-10-11 16:03:30.414][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-10-11 16:03:30.415][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-10-11 16:03:30.416][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-10-11 16:03:30.417][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-10-11 16:03:30.418][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-10-11 16:03:30.419][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-10-11 16:03:30.420][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-10-11 16:03:30.421][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-10-11 16:03:30.422][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-10-11 16:03:30.423][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-10-11 16:03:30.424][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-10-11 16:03:30.425][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-10-11 16:03:30.426][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-10-11 16:03:30.427][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-10-11 16:03:30.427][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-11 16:03:30.428][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-11 16:03:30.429][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-10-11 16:03:30.430][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-11 16:03:30.431][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-11 16:03:30.432][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-10-11 16:03:30.433][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-10-11 16:03:30.434][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-10-11 16:03:30.435][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-10-11 16:03:30.435][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-10-11 16:03:30.436][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-10-11 16:03:30.437][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-10-11 16:03:30.439][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-10-11 16:03:30.440][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-10-11 16:03:30.441][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-10-11 16:03:30.442][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-10-11 16:03:30.443][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-10-11 16:03:30.444][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-10-11 16:03:30.445][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-10-11 16:03:30.446][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-10-11 16:03:30.447][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-10-11 16:03:30.448][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-10-11 16:03:30.449][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-10-11 16:03:30.450][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-10-11 16:03:30.450][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-10-11 16:03:30.451][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-10-11 16:03:30.452][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-10-11 16:03:30.453][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-10-11 16:03:30.454][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-10-11 16:03:30.455][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-11 16:03:30.456][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-11 16:03:30.457][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-10-11 16:03:30.458][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-11 16:03:30.459][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-11 16:03:30.460][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-10-11 16:03:30.461][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-10-11 16:03:30.461][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-10-11 16:03:30.462][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-10-11 16:03:30.463][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-10-11 16:03:30.464][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-10-11 16:03:30.469][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-10-11 16:03:30.470][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:03:30.471][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-11 16:03:30.472][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:03:30.472][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:03:30.473][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:03:30.474][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:03:30.475][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-11 16:03:30.476][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:03:30.477][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:03:30.477][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:03:30.478][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:03:30.479][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-11 16:03:30.480][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:03:30.481][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:03:30.482][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:03:30.483][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:03:30.483][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[2025-10-11 16:03:30.484][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:03:30.485][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:03:30.486][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:03:30.487][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:03:30.488][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-11 16:03:30.488][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:03:30.489][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:03:30.490][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:03:30.491][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:03:30.492][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-11 16:03:30.493][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:03:30.494][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:03:30.494][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:03:30.495][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:03:30.496][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-11 16:03:30.497][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:03:30.498][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:03:30.499][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:03:30.499][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:03:30.500][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-11 16:03:30.501][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:03:30.502][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:03:30.503][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:03:30.504][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:03:30.505][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-11 16:03:30.505][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:03:30.506][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:03:30.507][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:03:30.508][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:03:30.509][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-11 16:03:30.510][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:03:30.510][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:03:30.511][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:03:30.512][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:03:30.513][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-11 16:03:30.514][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:03:30.515][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:03:30.515][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:03:30.516][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:03:30.517][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-11 16:03:30.518][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:03:30.519][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:03:30.520][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:03:30.521][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:03:30.521][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-11 16:03:30.522][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:03:30.523][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:03:30.524][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:03:30.525][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:03:30.526][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-11 16:03:30.526][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:03:30.527][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:03:30.528][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:03:30.529][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:03:30.530][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-11 16:03:30.531][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:03:30.531][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:03:30.532][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:03:30.533][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:03:30.534][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-11 16:03:30.535][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:03:30.536][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:03:30.537][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:03:30.537][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:03:30.538][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-11 16:03:30.539][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-10-11 16:03:30.541][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-10-11 16:03:30.542][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-10-11 16:03:30.543][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-10-11 16:03:30.544][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-10-11 16:03:30.546][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-10-11 16:03:30.547][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-10-11 16:03:30.548][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-10-11 16:03:30.550][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-10-11 16:03:30.551][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-10-11 16:03:30.552][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-10-11 16:03:30.554][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-10-11 16:03:30.555][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-10-11 16:03:30.556][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-10-11 16:03:30.557][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-10-11 16:03:30.559][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-10-11 16:03:30.560][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-10-11 16:03:30.561][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-10-11 16:03:30.563][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-10-11 16:03:30.564][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-10-11 16:03:30.565][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-10-11 16:03:30.567][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-10-11 16:03:30.568][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-10-11 16:03:30.569][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-10-11 16:03:30.571][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-10-11 16:03:30.572][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-10-11 16:03:30.573][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-10-11 16:03:30.578][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-10-11 16:03:30.579][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-10-11 16:03:30.581][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-10-11 16:03:30.582][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-10-11 16:03:30.583][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-10-11 16:03:30.585][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-10-11 16:03:30.586][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-10-11 16:03:30.587][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-10-11 16:03:30.588][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-10-11 16:03:30.590][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-10-11 16:03:30.591][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-10-11 16:03:30.592][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-10-11 16:03:30.594][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-10-11 16:03:30.595][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-10-11 16:03:30.596][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-10-11 16:03:30.598][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-10-11 16:03:30.599][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-10-11 16:03:30.600][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-10-11 16:03:30.602][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-10-11 16:03:30.603][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-10-11 16:03:30.604][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-10-11 16:03:30.606][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-10-11 16:03:30.607][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-10-11 16:03:30.608][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-10-11 16:03:30.609][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-10-11 16:03:30.611][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-10-11 16:03:30.612][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-10-11 16:03:30.613][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-10-11 16:03:30.615][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-10-11 16:03:30.616][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-10-11 16:03:30.617][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-10-11 16:03:30.618][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-10-11 16:03:30.620][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-10-11 16:03:30.621][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-10-11 16:03:30.622][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-10-11 16:03:30.624][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-10-11 16:03:30.625][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-10-11 16:03:30.626][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-10-11 16:03:30.628][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-10-11 16:03:30.629][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-10-11 16:03:30.630][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-10-11 16:03:30.631][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-10-11 16:03:30.633][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-10-11 16:03:30.634][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-10-11 16:03:30.635][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-10-11 16:03:30.637][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-10-11 16:03:30.638][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-10-11 16:03:30.639][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-10-11 16:03:30.641][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-10-11 16:03:30.642][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-10-11 16:03:30.643][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-10-11 16:03:30.644][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-10-11 16:03:30.646][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-10-11 16:03:30.647][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-10-11 16:03:30.648][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-10-11 16:03:30.650][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-10-11 16:03:30.651][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-10-11 16:03:30.653][initialize] This is biodb version 1.16.1.
biodb.DEBUG[2025-10-11 16:03:30.653][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-10-11 16:03:30.654][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:03:30.655][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:03:30.656][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:03:30.657][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-11 16:03:30.658][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:03:30.659][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-11 16:03:30.659][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-11 16:03:30.660][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:03:30.661][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:03:30.662][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:03:30.663][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-11 16:03:30.664][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:03:30.664][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-11 16:03:30.665][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-11 16:03:30.666][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:03:30.667][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:03:30.668][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:03:30.669][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-11 16:03:30.670][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:03:30.670][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-11 16:03:30.671][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-11 16:03:30.672][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:03:30.673][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:03:30.674][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:03:30.675][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-11 16:03:30.675][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:03:30.676][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-11 16:03:30.677][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-11 16:03:30.678][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:03:30.679][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:03:30.680][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:03:30.681][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-11 16:03:30.681][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:03:30.686][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-11 16:03:30.687][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-11 16:03:30.688][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:03:30.689][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:03:30.690][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:03:30.690][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-11 16:03:30.691][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:03:30.692][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-11 16:03:30.693][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-11 16:03:30.694][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:03:30.695][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:03:30.695][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:03:30.696][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-11 16:03:30.697][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:03:30.698][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-11 16:03:30.699][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-11 16:03:30.700][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:03:30.701][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:03:30.701][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:03:30.702][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-11 16:03:30.703][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:03:30.704][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-11 16:03:30.705][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-11 16:03:30.706][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:03:30.706][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:03:30.707][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:03:30.708][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-11 16:03:30.709][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:03:30.710][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-11 16:03:30.711][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-11 16:03:30.711][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:03:30.712][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:03:30.713][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:03:30.714][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-11 16:03:30.715][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:03:30.716][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-11 16:03:30.717][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-11 16:03:30.717][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:03:30.718][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:03:30.719][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:03:30.720][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-11 16:03:30.721][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:03:30.722][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-11 16:03:30.722][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-11 16:03:30.723][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:03:30.724][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:03:30.725][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:03:30.726][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-11 16:03:30.727][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:03:30.727][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-11 16:03:30.728][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-11 16:03:30.729][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:03:30.730][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:03:30.731][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:03:30.732][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-11 16:03:30.732][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:03:30.733][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-11 16:03:30.734][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-11 16:03:30.735][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:03:30.736][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:03:30.737][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:03:30.737][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-11 16:03:30.738][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:03:30.739][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-11 16:03:30.740][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-11 16:03:30.741][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:03:30.742][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:03:30.743][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:03:30.743][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-11 16:03:30.744][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:03:30.745][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-11 16:03:30.746][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-11 16:03:30.747][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:03:30.748][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:03:30.748][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:03:30.749][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-11 16:03:30.750][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:03:30.751][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-11 16:03:30.752][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-11 16:03:30.753][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:03:30.753][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:03:30.754][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:03:30.755][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-11 16:03:30.757][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.21-bioc-longtests/meat/biodbNci.Rcheck/biodbNci/definitions.yml".
biodb.DEBUG[2025-10-11 16:03:30.758][self$getDbsInfo()$define] Define connector nci.cactus.
biodb.DEBUG[2025-10-11 16:03:30.760][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-10-11 16:03:30.761][self$setPropertyValue] Setting property "description" to "National Cancer Institute (USA) CACTUS Database.".
biodb.DEBUG[2025-10-11 16:03:30.762][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-10-11 16:03:30.763][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-10-11 16:03:30.764][self$setPropertyValue] Setting property "downloadable" to "TRUE".
biodb.DEBUG[2025-10-11 16:03:30.764][self$setPropertyValue] Setting property "dwnld.ext" to "gz".
biodb.DEBUG[2025-10-11 16:03:30.765][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-10-11 16:03:30.766][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-10-11 16:03:30.767][self$setPropertyValue] Setting property "entry.content.type" to "sdf".
biodb.DEBUG[2025-10-11 16:03:30.768][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-10-11 16:03:30.769][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-10-11 16:03:30.770][self$setPropertyValue] Setting property "name" to "NCI CACTUS".
biodb.DEBUG[2025-10-11 16:03:30.771][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-10-11 16:03:30.772][self$setPropertyValue] Setting property "parsing.expr" to "NSC".
biodb.DEBUG[2025-10-11 16:03:30.772][self$setPropertyValue] Setting property "parsing.expr" to "DTP names".
biodb.DEBUG[2025-10-11 16:03:30.772][self$setPropertyValue] Setting property "parsing.expr" to "Standard InChI".
biodb.DEBUG[2025-10-11 16:03:30.772][self$setPropertyValue] Setting property "parsing.expr" to "c("Standard InChIKey", "^InChIKey=(.*)$")".
biodb.DEBUG[2025-10-11 16:03:30.772][self$setPropertyValue] Setting property "parsing.expr" to "Formula".
biodb.DEBUG[2025-10-11 16:03:30.772][self$setPropertyValue] Setting property "parsing.expr" to "Molecular Weight".
biodb.DEBUG[2025-10-11 16:03:30.772][self$setPropertyValue] Setting property "parsing.expr" to "CAS".
biodb.DEBUG[2025-10-11 16:03:30.773][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-10-11 16:03:30.774][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-10-11 16:03:30.775][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-10-11 16:03:30.776][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-11 16:03:30.777][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-11 16:03:30.778][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-10-11 16:03:30.779][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-11 16:03:30.779][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-11 16:03:30.780][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-10-11 16:03:30.781][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/".
biodb.DEBUG[2025-10-11 16:03:30.781][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/".
biodb.DEBUG[2025-10-11 16:03:30.781][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/download/nci/".
biodb.DEBUG[2025-10-11 16:03:30.781][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/download/nci/NCI-Open_2012-05-01.sdf.gz".
biodb.DEBUG[2025-10-11 16:03:30.782][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-10-11 16:03:30.783][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-10-11 16:03:30.784][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-10-11 16:03:30.785][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-10-11 16:03:30.786][self$getEntryFields()$define] Define field nci.cactus.id.
biodb.DEBUG[2025-10-11 16:03:30.789][super$initialize] Initialize connector nci.cactus.
biodb.DEBUG[2025-10-11 16:03:30.796][biodb$getFactory()$createConn] Creating new connector nci.cactus for database class nci.cactus .
biodb.INFO [2025-10-11 16:03:30.797][biodb$terminate] Closing BiodbMain instance...
biodb.INFO [2025-10-11 16:03:30.798][self$deleteConn] Connector "nci.cactus" deleted.
biodb.DEBUG[2025-10-11 16:03:30.799][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-10-11 16:03:30.800][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-11 16:03:30.800][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-11 16:03:30.801][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:03:30.802][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:03:30.803][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:03:30.804][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
[ FAIL 2 | WARN 0 | SKIP 0 | PASS 85 ]

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

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

'R CMD check' output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.21-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_1.12.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.21-bioc-longtests/meat/biodbNci.Rcheck’
* using R version 4.5.1 (2025-06-13)
* 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 ‘1.12.0’
* 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 ... OK
* 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 dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  NciCactusConn.Rd: BiodbConn
  NciCactusEntry.Rd: BiodbSdfEntry
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... SKIPPED
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... OK
* checking files in ‘vignettes’ ... SKIPPED
* checking examples ... SKIPPED
* checking for unstated dependencies in ‘longtests’ ... OK
* checking tests in ‘longtests’ ...
  Running ‘testthat.R’
 ERROR
Running the tests in ‘longtests/testthat.R’ failed.
Last 13 lines of output:
  Backtrace:
      ▆
   1. ├─base::do.call(fct, params)
   2. └─biodb (local) `<fn>`(conn = `<NcCctsCn>`, opt = `<named list>`)
   3.   └─opt$refEntries$getRealEntry(id)
   4.     └─self$getRealEntries(ids = id)
   5.       └─private$bdb$getFactory()$getEntry(...)
   6.         └─private$loadEntries(conn$getId(), missing.ids, drop = FALSE)
   7.           └─conn$getEntryContent(ids)
   8.             └─self$download()
   9.               └─private$doExtractDownload()
  
  [ FAIL 2 | WARN 0 | SKIP 0 | PASS 85 ]
  Error: Test failures
  Execution halted
* DONE

Status: 1 ERROR, 1 NOTE
See
  ‘/home/biocbuild/bbs-3.21-bioc-longtests/meat/biodbNci.Rcheck/00check.log’
for details.

Installation output

biodbNci.Rcheck/00install.out

* installing *source* package ‘biodbNci’ ...
** this is package ‘biodbNci’ version ‘1.12.0’
** 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-3.21-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-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-3.21-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-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-3.21-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-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-3.21-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-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-3.21-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-3.21-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.21-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
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (biodbNci)