Back to Long Tests report for BioC 3.20

This page was generated on 2025-03-22 23:55 -0400 (Sat, 22 Mar 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.1 LTS)x86_644.4.3 (2025-02-28) -- "Trophy Case" 4763
palomino8Windows Server 2022 Datacenterx644.4.3 (2025-02-28 ucrt) -- "Trophy Case" 4494
merida1macOS 12.7.5 Montereyx86_644.4.3 (2025-02-28) -- "Trophy Case" 4521
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 11/32HostnameOS / ArchCHECK
biodbNci 1.10.0  (landing page)
Pierrick Roger
Snapshot Date: 2025-03-22 09:55 -0400 (Sat, 22 Mar 2025)
git_url: https://git.bioconductor.org/packages/biodbNci
git_branch: RELEASE_3_20
git_last_commit: d666b49
git_last_commit_date: 2024-10-29 11:09:24 -0400 (Tue, 29 Oct 2024)
nebbiolo2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK  
palomino8Windows Server 2022 Datacenter / x64  ERROR  
merida1macOS 12.7.5 Monterey / x86_64  OK  

CHECK results for biodbNci on merida1

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: 1.10.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --test-dir=longtests --no-stop-on-test-error --no-codoc --no-examples --no-manual --ignore-vignettes --check-subdirs=no biodbNci_1.10.0.tar.gz
StartedAt: 2025-03-22 16:02:27 -0400 (Sat, 22 Mar 2025)
EndedAt: 2025-03-22 16:03:41 -0400 (Sat, 22 Mar 2025)
EllapsedTime: 74.1 seconds
RetCode: 0
Status:   OK  
CheckDir: biodbNci.Rcheck
Warnings: 0

Tests output

biodbNci.Rcheck/tests/testthat.Rout


R version 4.4.3 (2025-02-28) -- "Trophy Case"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20

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Type 'license()' or 'licence()' for distribution details.

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Type 'demo()' for some demos, 'help()' for on-line help, or
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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 [2025-03-22 16:03:37.291][biodb::testContext]
biodb.INFO [2025-03-22 16:03:37.295][biodb::testContext] ********************************************************************************
biodb.INFO [2025-03-22 16:03:37.296][biodb::testContext] Test context - Generic long tests
biodb.INFO [2025-03-22 16:03:37.297][biodb::testContext] ********************************************************************************
biodb.INFO [2025-03-22 16:03:37.298][biodb::testContext]
biodb.INFO [2025-03-22 16:03:37.305][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.14.0.
biodb.DEBUG[2025-03-22 16:03:37.307][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2025-03-22 16:03:37.314][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-03-22 16:03:37.316][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-03-22 16:03:37.317][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-03-22 16:03:37.318][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:03:37.319][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:03:37.320][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:03:37.321][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-03-22 16:03:37.346][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-03-22 16:03:37.347][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:03:37.348][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:03:37.349][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[2025-03-22 16:03:37.351][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-03-22 16:03:37.352][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-03-22 16:03:37.353][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:03:37.354][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:03:37.355][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:03:37.356][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-03-22 16:03:37.358][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-03-22 16:03:37.359][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-03-22 16:03:37.360][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:03:37.361][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:03:37.362][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:03:37.363][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-03-22 16:03:37.365][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-03-22 16:03:37.366][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-03-22 16:03:37.367][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:03:37.368][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:03:37.369][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:03:37.370][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-03-22 16:03:37.372][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-03-22 16:03:37.373][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:03:37.374][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:03:37.375][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:03:37.376][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-03-22 16:03:37.377][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-03-22 16:03:37.378][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-03-22 16:03:37.379][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:03:37.381][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:03:37.382][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:03:37.383][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-03-22 16:03:37.384][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-03-22 16:03:37.385][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:03:37.386][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:03:37.387][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:03:37.388][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-03-22 16:03:37.390][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-03-22 16:03:37.391][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-03-22 16:03:37.392][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:03:37.393][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:03:37.394][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:03:37.395][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-03-22 16:03:37.397][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-03-22 16:03:37.398][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-03-22 16:03:37.399][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-03-22 16:03:37.400][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-03-22 16:03:37.402][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-03-22 16:03:37.403][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:03:37.404][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:03:37.405][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:03:37.406][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-03-22 16:03:37.407][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-03-22 16:03:37.408][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:03:37.409][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:03:37.410][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:03:37.412][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-03-22 16:03:37.413][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-03-22 16:03:37.414][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:03:37.415][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:03:37.416][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:03:37.417][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-03-22 16:03:37.419][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-03-22 16:03:37.420][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:03:37.421][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:03:37.422][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:03:37.423][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-03-22 16:03:37.424][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2025-03-22 16:03:37.426][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:03:37.427][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:03:37.428][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:03:37.429][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-03-22 16:03:37.430][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-03-22 16:03:37.431][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:03:37.432][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:03:37.433][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:03:37.435][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-03-22 16:03:37.436][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-03-22 16:03:37.447][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-03-22 16:03:37.448][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:03:37.449][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:03:37.450][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:03:37.451][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-03-22 16:03:37.452][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-03-22 16:03:37.454][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-03-22 16:03:37.455][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:03:37.456][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:03:37.457][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:03:37.461][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-03-22 16:03:37.504][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-03-22 16:03:37.532][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2025-03-22 16:03:37.533][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-22 16:03:37.534][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-22 16:03:37.536][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-22 16:03:37.537][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-22 16:03:37.538][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-22 16:03:37.539][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-22 16:03:37.540][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-03-22 16:03:37.542][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-22 16:03:37.543][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-03-22 16:03:37.544][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-03-22 16:03:37.545][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-22 16:03:37.547][self$setPropertyValue]
biodb.DEBUG[2025-03-22 16:03:37.548][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-22 16:03:37.549][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-03-22 16:03:37.549][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-03-22 16:03:37.549][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-03-22 16:03:37.549][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-03-22 16:03:37.549][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-03-22 16:03:37.550][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-22 16:03:37.552][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-22 16:03:37.553][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-22 16:03:37.554][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-22 16:03:37.555][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-22 16:03:37.556][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-22 16:03:37.557][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-22 16:03:37.558][self$setPropertyValue]
biodb.DEBUG[2025-03-22 16:03:37.560][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-22 16:03:37.561][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-22 16:03:37.562][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-22 16:03:37.563][self$setPropertyValue]
biodb.DEBUG[2025-03-22 16:03:37.564][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-03-22 16:03:37.567][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-03-22 16:03:37.568][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-03-22 16:03:37.569][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-22 16:03:37.570][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-22 16:03:37.571][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-22 16:03:37.573][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-22 16:03:37.574][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-22 16:03:37.575][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-22 16:03:37.576][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-03-22 16:03:37.578][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-22 16:03:37.579][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-03-22 16:03:37.580][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-03-22 16:03:37.581][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-22 16:03:37.582][self$setPropertyValue]
biodb.DEBUG[2025-03-22 16:03:37.584][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-22 16:03:37.585][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-03-22 16:03:37.585][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-03-22 16:03:37.585][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-03-22 16:03:37.585][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-03-22 16:03:37.585][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-03-22 16:03:37.586][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-22 16:03:37.587][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-22 16:03:37.588][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-22 16:03:37.590][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-22 16:03:37.591][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-22 16:03:37.592][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-22 16:03:37.593][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-22 16:03:37.594][self$setPropertyValue]
biodb.DEBUG[2025-03-22 16:03:37.595][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-22 16:03:37.596][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-22 16:03:37.598][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-22 16:03:37.599][self$setPropertyValue]
biodb.DEBUG[2025-03-22 16:03:37.600][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-03-22 16:03:37.602][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-03-22 16:03:37.604][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2025-03-22 16:03:37.605][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-22 16:03:37.606][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-22 16:03:37.607][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-22 16:03:37.608][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-22 16:03:37.610][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-22 16:03:37.611][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-22 16:03:37.612][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-03-22 16:03:37.613][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-22 16:03:37.614][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-03-22 16:03:37.616][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-03-22 16:03:37.617][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-22 16:03:37.618][self$setPropertyValue]
biodb.DEBUG[2025-03-22 16:03:37.619][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-22 16:03:37.620][self$setPropertyValue]
biodb.DEBUG[2025-03-22 16:03:37.622][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-22 16:03:37.623][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-22 16:03:37.624][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-22 16:03:37.625][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-22 16:03:37.626][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-22 16:03:37.627][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-22 16:03:37.628][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-22 16:03:37.630][self$setPropertyValue]
biodb.DEBUG[2025-03-22 16:03:37.631][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-22 16:03:37.632][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-22 16:03:37.633][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-22 16:03:37.634][self$setPropertyValue]
biodb.DEBUG[2025-03-22 16:03:37.636][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-03-22 16:03:37.638][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-03-22 16:03:37.639][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-03-22 16:03:37.640][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-22 16:03:37.642][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-22 16:03:37.643][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-22 16:03:37.644][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-22 16:03:37.645][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-22 16:03:37.646][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-22 16:03:37.648][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-03-22 16:03:37.649][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-22 16:03:37.650][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-03-22 16:03:37.651][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-03-22 16:03:37.652][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-22 16:03:37.654][self$setPropertyValue]
biodb.DEBUG[2025-03-22 16:03:37.655][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-22 16:03:37.656][self$setPropertyValue]
biodb.DEBUG[2025-03-22 16:03:37.657][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-22 16:03:37.659][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-22 16:03:37.660][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-22 16:03:37.661][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-22 16:03:37.662][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-22 16:03:37.663][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-22 16:03:37.664][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-22 16:03:37.665][self$setPropertyValue]
biodb.DEBUG[2025-03-22 16:03:37.667][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-22 16:03:37.668][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-22 16:03:37.669][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-22 16:03:37.670][self$setPropertyValue]
biodb.DEBUG[2025-03-22 16:03:37.674][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-03-22 16:03:37.675][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:03:37.676][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:03:37.677][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:03:37.678][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:03:37.679][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-22 16:03:37.680][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:03:37.682][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:03:37.683][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:03:37.684][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:03:37.685][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-22 16:03:37.686][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:03:37.687][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:03:37.688][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:03:37.689][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:03:37.690][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-22 16:03:37.691][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:03:37.692][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:03:37.693][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:03:37.694][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:03:37.695][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-22 16:03:37.697][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:03:37.698][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:03:37.699][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:03:37.700][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:03:37.701][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-22 16:03:37.702][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:03:37.703][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:03:37.704][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:03:37.705][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:03:37.707][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-22 16:03:37.708][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:03:37.709][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:03:37.711][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:03:37.712][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:03:37.713][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-22 16:03:37.714][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:03:37.715][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:03:37.716][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:03:37.717][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:03:37.718][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-22 16:03:37.720][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:03:37.721][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:03:37.722][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:03:37.723][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:03:37.724][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-22 16:03:37.725][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:03:37.726][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[2025-03-22 16:03:37.727][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:03:37.728][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:03:37.729][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-22 16:03:37.730][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:03:37.731][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:03:37.736][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:03:37.737][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:03:37.739][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-22 16:03:37.740][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:03:37.741][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:03:37.742][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:03:37.744][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:03:37.745][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-22 16:03:37.746][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:03:37.747][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:03:37.748][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:03:37.749][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:03:37.750][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-22 16:03:37.751][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:03:37.752][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:03:37.754][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:03:37.755][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:03:37.756][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-22 16:03:37.757][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:03:37.758][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:03:37.759][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:03:37.760][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:03:37.761][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-22 16:03:37.763][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:03:37.764][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:03:37.765][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:03:37.766][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:03:37.767][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-22 16:03:37.768][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:03:37.769][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:03:37.770][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:03:37.771][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:03:37.772][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-22 16:03:37.773][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:03:37.775][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:03:37.776][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-03-22 16:03:37.780][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-03-22 16:03:37.782][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-03-22 16:03:37.784][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-03-22 16:03:37.785][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-03-22 16:03:37.787][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-03-22 16:03:37.789][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-03-22 16:03:37.791][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-03-22 16:03:37.792][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-03-22 16:03:37.794][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-03-22 16:03:37.796][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-03-22 16:03:37.797][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-03-22 16:03:37.799][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-03-22 16:03:37.801][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-03-22 16:03:37.802][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-03-22 16:03:37.804][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-03-22 16:03:37.806][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-03-22 16:03:37.807][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-03-22 16:03:37.809][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-03-22 16:03:37.811][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-03-22 16:03:37.813][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-03-22 16:03:37.814][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-03-22 16:03:37.816][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-03-22 16:03:37.818][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-03-22 16:03:37.819][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-03-22 16:03:37.821][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-03-22 16:03:37.823][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-03-22 16:03:37.824][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-03-22 16:03:37.826][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-03-22 16:03:37.828][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-03-22 16:03:37.830][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-03-22 16:03:37.831][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-03-22 16:03:37.833][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-03-22 16:03:37.835][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-03-22 16:03:37.836][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-03-22 16:03:37.838][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-03-22 16:03:37.840][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-03-22 16:03:37.841][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-03-22 16:03:37.843][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-03-22 16:03:37.845][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-03-22 16:03:37.846][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-03-22 16:03:37.848][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-03-22 16:03:37.850][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-03-22 16:03:37.852][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-03-22 16:03:37.853][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-03-22 16:03:37.855][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-03-22 16:03:37.857][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-03-22 16:03:37.858][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-03-22 16:03:37.860][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-03-22 16:03:37.862][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-03-22 16:03:37.863][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-03-22 16:03:37.865][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-03-22 16:03:37.867][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-03-22 16:03:37.868][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-03-22 16:03:37.870][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-03-22 16:03:37.872][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-03-22 16:03:37.874][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-03-22 16:03:37.875][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-03-22 16:03:37.877][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-03-22 16:03:37.879][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-03-22 16:03:37.880][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-03-22 16:03:37.882][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-03-22 16:03:37.884][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-03-22 16:03:37.885][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-03-22 16:03:37.887][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-03-22 16:03:37.889][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-03-22 16:03:37.890][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-03-22 16:03:37.892][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-03-22 16:03:37.894][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-03-22 16:03:37.896][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-03-22 16:03:37.897][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-03-22 16:03:37.899][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-03-22 16:03:37.901][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-03-22 16:03:37.902][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-03-22 16:03:37.904][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-03-22 16:03:37.906][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-03-22 16:03:37.907][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-03-22 16:03:37.909][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-03-22 16:03:37.911][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-03-22 16:03:37.913][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-03-22 16:03:37.914][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-03-22 16:03:37.916][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-03-22 16:03:37.918][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-03-22 16:03:37.925][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-03-22 16:03:37.927][initialize] This is biodb version 1.14.0.
biodb.DEBUG[2025-03-22 16:03:37.930][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-03-22 16:03:37.931][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:03:37.932][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-22 16:03:37.934][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:03:37.935][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:03:37.941][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:03:37.942][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-22 16:03:37.944][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-22 16:03:37.945][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:03:37.946][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-22 16:03:37.947][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:03:37.948][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:03:37.949][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:03:37.950][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-22 16:03:37.952][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-22 16:03:37.957][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:03:37.958][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-22 16:03:37.959][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:03:37.961][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:03:37.962][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:03:37.963][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-22 16:03:37.964][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-22 16:03:37.965][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:03:37.966][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-22 16:03:37.967][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:03:37.968][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:03:37.969][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:03:37.970][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-22 16:03:37.971][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-22 16:03:37.972][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:03:37.973][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-22 16:03:37.975][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:03:37.976][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:03:37.977][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:03:37.978][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-22 16:03:37.979][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-22 16:03:37.980][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:03:37.981][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-22 16:03:37.982][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:03:37.983][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:03:37.984][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:03:37.985][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-22 16:03:37.986][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-22 16:03:37.987][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:03:37.989][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-22 16:03:37.990][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:03:37.991][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:03:37.992][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:03:37.993][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-22 16:03:37.994][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-22 16:03:37.995][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:03:37.996][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-22 16:03:37.997][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:03:37.998][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:03:37.999][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:03:38.000][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-22 16:03:38.002][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-22 16:03:38.003][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:03:38.004][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-22 16:03:38.005][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:03:38.006][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:03:38.007][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:03:38.008][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-22 16:03:38.010][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-22 16:03:38.011][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:03:38.012][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-22 16:03:38.013][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:03:38.014][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:03:38.015][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:03:38.016][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-22 16:03:38.017][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-22 16:03:38.018][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:03:38.019][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-22 16:03:38.021][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:03:38.022][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:03:38.023][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:03:38.024][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-22 16:03:38.025][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-22 16:03:38.026][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:03:38.027][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-22 16:03:38.028][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:03:38.029][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:03:38.030][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:03:38.031][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-22 16:03:38.032][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-22 16:03:38.034][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:03:38.035][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-22 16:03:38.036][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:03:38.037][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:03:38.038][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:03:38.039][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-22 16:03:38.040][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-22 16:03:38.041][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:03:38.042][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-22 16:03:38.043][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:03:38.044][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:03:38.045][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:03:38.047][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-22 16:03:38.048][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-22 16:03:38.049][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:03:38.050][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-22 16:03:38.051][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:03:38.052][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:03:38.053][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:03:38.054][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-22 16:03:38.055][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-22 16:03:38.056][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:03:38.057][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-22 16:03:38.058][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:03:38.060][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:03:38.061][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:03:38.062][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-22 16:03:38.063][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-22 16:03:38.064][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:03:38.065][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-22 16:03:38.066][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:03:38.067][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:03:38.068][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:03:38.069][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-22 16:03:38.071][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-22 16:03:38.072][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:03:38.073][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-22 16:03:38.074][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:03:38.075][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:03:38.077][biodb$loadDefinitions] Load definitions from file "/Users/biocbuild/bbs-3.20-bioc-longtests/meat/biodbNci.Rcheck/biodbNci/definitions.yml".
biodb.DEBUG[2025-03-22 16:03:38.090][self$getDbsInfo()$define] Define connector nci.cactus.
biodb.DEBUG[2025-03-22 16:03:38.093][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-03-22 16:03:38.094][self$setPropertyValue] Setting property "description" to "National Cancer Institute (USA) CACTUS Database.".
biodb.DEBUG[2025-03-22 16:03:38.095][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-22 16:03:38.097][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-22 16:03:38.098][self$setPropertyValue] Setting property "downloadable" to "TRUE".
biodb.DEBUG[2025-03-22 16:03:38.099][self$setPropertyValue] Setting property "dwnld.ext" to "gz".
biodb.DEBUG[2025-03-22 16:03:38.100][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-03-22 16:03:38.101][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-22 16:03:38.103][self$setPropertyValue] Setting property "entry.content.type" to "sdf".
biodb.DEBUG[2025-03-22 16:03:38.104][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-22 16:03:38.105][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-03-22 16:03:38.106][self$setPropertyValue] Setting property "name" to "NCI CACTUS".
biodb.DEBUG[2025-03-22 16:03:38.108][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-22 16:03:38.109][self$setPropertyValue] Setting property "parsing.expr" to "NSC".
biodb.DEBUG[2025-03-22 16:03:38.109][self$setPropertyValue] Setting property "parsing.expr" to "DTP names".
biodb.DEBUG[2025-03-22 16:03:38.109][self$setPropertyValue] Setting property "parsing.expr" to "Standard InChI".
biodb.DEBUG[2025-03-22 16:03:38.109][self$setPropertyValue] Setting property "parsing.expr" to "c("Standard InChIKey", "^InChIKey=(.*)$")".
biodb.DEBUG[2025-03-22 16:03:38.109][self$setPropertyValue] Setting property "parsing.expr" to "Formula".
biodb.DEBUG[2025-03-22 16:03:38.109][self$setPropertyValue] Setting property "parsing.expr" to "Molecular Weight".
biodb.DEBUG[2025-03-22 16:03:38.109][self$setPropertyValue] Setting property "parsing.expr" to "CAS".
biodb.DEBUG[2025-03-22 16:03:38.110][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-03-22 16:03:38.111][self$setPropertyValue]
biodb.DEBUG[2025-03-22 16:03:38.113][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-03-22 16:03:38.114][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-22 16:03:38.115][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-22 16:03:38.116][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-22 16:03:38.117][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-22 16:03:38.118][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-22 16:03:38.120][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-22 16:03:38.121][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/".
biodb.DEBUG[2025-03-22 16:03:38.121][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/".
biodb.DEBUG[2025-03-22 16:03:38.121][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/download/nci/".
biodb.DEBUG[2025-03-22 16:03:38.121][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/download/nci/NCI-Open_2012-05-01.sdf.gz".
biodb.DEBUG[2025-03-22 16:03:38.122][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-22 16:03:38.123][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-22 16:03:38.124][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-03-22 16:03:38.126][self$setPropertyValue]
biodb.DEBUG[2025-03-22 16:03:38.134][self$getEntryFields()$define] Define field nci.cactus.id.
biodb.DEBUG[2025-03-22 16:03:38.155][super$initialize] Initialize connector nci.cactus.
biodb.DEBUG[2025-03-22 16:03:38.156][super$initialize] Register connector nci.cactus with the request scheduler
biodb.DEBUG[2025-03-22 16:03:38.160][private$bdb$getRequestScheduler()$re ...] Register connector nci.cactus.
biodb.DEBUG[2025-03-22 16:03:38.164][private$addConnectorRules] Create new rule for URL "cactus.nci.nih.gov" of connector "nci.cactus".
biodb.DEBUG[2025-03-22 16:03:38.168][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-03-22 16:03:38.170][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-03-22 16:03:38.171][rule$addConnector] Connector "nci.cactus" is already listed in rule "cactus.nci.nih.gov".
biodb.DEBUG[2025-03-22 16:03:38.173][rule$addConnector] Connector "nci.cactus" is already listed in rule "cactus.nci.nih.gov".
biodb.DEBUG[2025-03-22 16:03:38.174][rule$addConnector] Connector "nci.cactus" is already listed in rule "cactus.nci.nih.gov".
biodb.DEBUG[2025-03-22 16:03:38.203][biodb$getFactory()$createConn] Creating new connector nci.cactus for database class nci.cactus .
biodb.INFO [2025-03-22 16:03:38.213][biodb::testThat]
biodb.INFO [2025-03-22 16:03:38.214][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2025-03-22 16:03:38.215][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-22 16:03:38.216][biodb::testThat]
biodb.TRACE[2025-03-22 16:03:38.220][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/bbs-3.20-bioc-longtests/meat/biodbNci.Rcheck/biodbNci/testref/entry-nci.cactus-749674-content.sdf".
biodb.DEBUG[2025-03-22 16:03:38.222][biodb$getFactory()$createEntryFromCo ...] Creating NCI CACTUS entries from 1 content(s).
biodb.DEBUG[2025-03-22 16:03:38.225][biodb$getFactory()$createEntryFromCo ...] Parsing 1 NCI CACTUS entries.
biodb.DEBUG[2025-03-22 16:03:38.233][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-22 16:03:38.234][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-22 16:03:38.235][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-22 16:03:38.250][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:03:38.251][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-22 16:03:38.253][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:03:38.254][FUN] Functions in observer BiodbConfig: [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[2025-03-22 16:03:38.274][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-22 16:03:38.275][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-22 16:03:38.277][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:38.278][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:03:38.279][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-22 16:03:38.296][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-22 16:03:38.298][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:38.299][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:03:38.303][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-22 16:03:38.305][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-22 16:03:38.306][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:38.307][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:03:38.344][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-22 16:03:38.345][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-22 16:03:38.346][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:38.348][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:03:38.349][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-22 16:03:38.351][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-22 16:03:38.352][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:38.353][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:03:38.355][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-22 16:03:38.356][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-22 16:03:38.357][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:38.358][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:03:38.361][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-22 16:03:38.362][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-22 16:03:38.364][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:38.365][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:03:38.366][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-22 16:03:38.368][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-22 16:03:38.369][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:38.370][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:03:38.372][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-22 16:03:38.373][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-22 16:03:38.374][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:38.376][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:03:38.377][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-22 16:03:38.378][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-22 16:03:38.379][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:38.381][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:03:38.383][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-03-22 16:03:38.384][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-03-22 16:03:38.386][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:38.387][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:03:38.388][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-03-22 16:03:38.389][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-03-22 16:03:38.391][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:38.392][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:03:38.393][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-22 16:03:38.394][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-22 16:03:38.396][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:38.397][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:03:38.398][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-03-22 16:03:38.399][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-03-22 16:03:38.401][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:38.402][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:03:38.403][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-22 16:03:38.405][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-22 16:03:38.406][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:38.407][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:03:38.408][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-22 16:03:38.410][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-22 16:03:38.411][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:38.412][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:03:38.413][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-22 16:03:38.415][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-22 16:03:38.422][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:38.424][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:03:38.471][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-22 16:03:38.472][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-22 16:03:38.473][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:38.474][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:03:38.476][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-22 16:03:38.477][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-22 16:03:38.478][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:38.479][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:03:38.481][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-22 16:03:38.482][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-22 16:03:38.483][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:38.484][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-22 16:03:38.486][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 749674.
biodb.TRACE[2025-03-22 16:03:38.488][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-03-22 16:03:38.490][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-03-22 16:03:38.491][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:38.492][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:03:38.494][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-03-22 16:03:38.495][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-03-22 16:03:38.496][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:38.498][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:03:38.499][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-03-22 16:03:38.500][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-03-22 16:03:38.501][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:38.502][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:03:38.504][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-03-22 16:03:38.505][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-03-22 16:03:38.506][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:38.507][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:03:38.525][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-22 16:03:38.527][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-22 16:03:38.528][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:38.529][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:03:38.547][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-03-22 16:03:38.548][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-03-22 16:03:38.550][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:38.551][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:03:38.557][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-22 16:03:38.559][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-22 16:03:38.560][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:38.561][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:03:38.562][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-22 16:03:38.564][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-22 16:03:38.565][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:38.566][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:03:38.567][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-22 16:03:38.569][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-22 16:03:38.570][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:38.571][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:03:38.574][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-22 16:03:38.576][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-22 16:03:38.577][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:38.578][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:03:38.579][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-22 16:03:38.581][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-22 16:03:38.582][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:38.583][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:03:38.584][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-22 16:03:38.585][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-22 16:03:38.587][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:38.588][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:03:38.589][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-03-22 16:03:38.591][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-03-22 16:03:38.592][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:38.593][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:03:38.594][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-03-22 16:03:38.596][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-03-22 16:03:38.597][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:38.598][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:03:38.604][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-03-22 16:03:38.605][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-03-22 16:03:38.606][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:38.607][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:03:38.617][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-22 16:03:38.618][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-22 16:03:38.619][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:38.620][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:03:38.622][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-22 16:03:38.623][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-22 16:03:38.624][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:38.625][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:03:38.626][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-22 16:03:38.628][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-22 16:03:38.629][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:38.630][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:03:38.631][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-22 16:03:38.633][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-22 16:03:38.634][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:38.635][ef$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:03:38.636][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-22 16:03:38.637][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-22 16:03:38.639][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:38.640][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:03:38.651][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-22 16:03:38.652][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-22 16:03:38.654][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:38.655][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:03:38.656][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-22 16:03:38.657][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-22 16:03:38.659][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:38.660][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:03:38.661][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-22 16:03:38.662][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-22 16:03:38.663][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:38.665][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:03:38.666][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-22 16:03:38.667][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-22 16:03:38.668][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:38.669][ef$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:03:38.673][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-22 16:03:38.674][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-22 16:03:38.676][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:38.677][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:03:38.688][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-22 16:03:38.689][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-22 16:03:38.690][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:38.692][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:03:38.693][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-22 16:03:38.694][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-22 16:03:38.695][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:38.696][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:03:38.698][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-22 16:03:38.699][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-22 16:03:38.700][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:38.701][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:03:38.702][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-22 16:03:38.704][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-22 16:03:38.705][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:38.706][ef$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:03:38.707][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-22 16:03:38.708][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-22 16:03:38.710][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:38.711][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:03:38.722][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-22 16:03:38.723][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-22 16:03:38.724][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:38.725][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:03:38.727][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-22 16:03:38.728][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-22 16:03:38.729][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:38.730][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:03:38.732][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-22 16:03:38.733][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-22 16:03:38.734][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:38.735][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:03:38.736][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-22 16:03:38.738][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-22 16:03:38.739][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:38.740][ef$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:03:38.741][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-22 16:03:38.742][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-22 16:03:38.744][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:38.745][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:03:38.756][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-22 16:03:38.758][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-22 16:03:38.759][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:38.760][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:03:38.761][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-22 16:03:38.763][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-22 16:03:38.764][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:38.765][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:03:38.766][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-22 16:03:38.768][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-22 16:03:38.769][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:38.770][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:03:38.771][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-22 16:03:38.773][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-22 16:03:38.774][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:38.775][ef$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:03:38.776][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-22 16:03:38.778][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-22 16:03:38.779][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:38.780][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:03:38.795][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-22 16:03:38.797][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-22 16:03:38.798][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:38.799][ef$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:03:38.805][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-22 16:03:38.806][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-22 16:03:38.807][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:38.808][ef$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:03:38.814][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-22 16:03:38.816][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-22 16:03:38.817][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:38.818][ef$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:03:38.824][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-22 16:03:38.825][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-22 16:03:38.826][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:38.827][ef$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:03:38.833][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-22 16:03:38.835][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-22 16:03:38.836][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:38.837][ef$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:03:38.860][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/bbs-3.20-bioc-longtests/meat/biodbNci.Rcheck/biodbNci/testref/entry-nci.cactus-750690-content.sdf".
biodb.DEBUG[2025-03-22 16:03:38.908][biodb$getFactory()$createEntryFromCo ...] Creating NCI CACTUS entries from 1 content(s).
biodb.DEBUG[2025-03-22 16:03:38.910][biodb$getFactory()$createEntryFromCo ...] Parsing 1 NCI CACTUS entries.
biodb.DEBUG[2025-03-22 16:03:38.912][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-22 16:03:38.913][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-22 16:03:38.914][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-22 16:03:38.920][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:03:38.921][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-22 16:03:38.923][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:03:38.924][FUN] Functions in observer BiodbConfig: [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[2025-03-22 16:03:38.938][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-22 16:03:38.940][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-22 16:03:38.941][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:38.942][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:03:38.943][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-22 16:03:38.945][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-22 16:03:38.946][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:38.947][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:03:38.977][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-03-22 16:03:38.978][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-03-22 16:03:38.980][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:38.981][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:03:38.982][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-03-22 16:03:38.983][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-03-22 16:03:38.984][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:38.986][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:03:38.988][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-22 16:03:38.989][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-22 16:03:38.990][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:38.991][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:03:38.993][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-22 16:03:38.994][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-22 16:03:38.995][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:38.996][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:03:38.998][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-22 16:03:38.999][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-22 16:03:39.001][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:39.002][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:03:39.003][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-22 16:03:39.004][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-22 16:03:39.005][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:39.007][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:03:39.008][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-22 16:03:39.010][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-22 16:03:39.011][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:39.012][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:03:39.013][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-22 16:03:39.015][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-22 16:03:39.016][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:39.017][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:03:39.019][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-22 16:03:39.020][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-22 16:03:39.021][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:39.022][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:03:39.024][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-22 16:03:39.025][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-22 16:03:39.026][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:39.027][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:03:39.028][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-22 16:03:39.030][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-22 16:03:39.033][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:39.034][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:03:39.036][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-22 16:03:39.037][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-22 16:03:39.038][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:39.039][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:03:39.041][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-22 16:03:39.042][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-22 16:03:39.043][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:39.044][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:03:39.047][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-22 16:03:39.048][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-22 16:03:39.049][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:39.051][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:03:39.052][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-22 16:03:39.053][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-22 16:03:39.054][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:39.056][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:03:39.057][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-22 16:03:39.059][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-22 16:03:39.060][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:39.061][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:03:39.062][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-22 16:03:39.064][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-22 16:03:39.065][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:39.066][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:03:39.068][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-03-22 16:03:39.070][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-03-22 16:03:39.071][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:39.072][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:03:39.073][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-03-22 16:03:39.075][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-03-22 16:03:39.076][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:39.077][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:03:39.078][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-22 16:03:39.080][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-22 16:03:39.081][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:39.082][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:03:39.083][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-03-22 16:03:39.085][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-03-22 16:03:39.086][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:39.087][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:03:39.089][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-22 16:03:39.090][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-22 16:03:39.091][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:39.092][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:03:39.093][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-22 16:03:39.095][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-22 16:03:39.096][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:39.098][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:03:39.099][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-22 16:03:39.101][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-22 16:03:39.102][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:39.103][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:03:39.104][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-22 16:03:39.106][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-22 16:03:39.107][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:39.108][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:03:39.109][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-22 16:03:39.111][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-22 16:03:39.112][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:39.113][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:03:39.114][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-22 16:03:39.116][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-22 16:03:39.117][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:39.118][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-22 16:03:39.120][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 750690.
biodb.TRACE[2025-03-22 16:03:39.149][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-03-22 16:03:39.154][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-03-22 16:03:39.156][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:39.157][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:03:39.158][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-03-22 16:03:39.159][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-03-22 16:03:39.160][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:39.162][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:03:39.163][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-03-22 16:03:39.164][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-03-22 16:03:39.165][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:39.167][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:03:39.168][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-03-22 16:03:39.169][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-03-22 16:03:39.170][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:39.171][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:03:39.316][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-22 16:03:39.318][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-22 16:03:39.319][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:39.320][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:03:39.327][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-03-22 16:03:39.329][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-03-22 16:03:39.330][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:39.331][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:03:39.337][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-22 16:03:39.339][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-22 16:03:39.340][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:39.341][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:03:39.343][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-22 16:03:39.344][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-22 16:03:39.345][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:39.346][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:03:39.348][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-22 16:03:39.349][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-22 16:03:39.351][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:39.352][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:03:39.355][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-22 16:03:39.356][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-22 16:03:39.358][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:39.359][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:03:39.360][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-22 16:03:39.362][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-22 16:03:39.363][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:39.364][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:03:39.365][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-22 16:03:39.367][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-22 16:03:39.368][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:39.370][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:03:39.371][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-03-22 16:03:39.373][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-03-22 16:03:39.374][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:39.375][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:03:39.376][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-03-22 16:03:39.378][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-03-22 16:03:39.379][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:39.380][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:03:39.381][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-03-22 16:03:39.383][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-03-22 16:03:39.384][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:39.385][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:03:39.409][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-22 16:03:39.410][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-22 16:03:39.411][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:39.413][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:03:39.414][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-22 16:03:39.416][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-22 16:03:39.417][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:39.418][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:03:39.419][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-22 16:03:39.421][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-22 16:03:39.422][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:39.423][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:03:39.424][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-22 16:03:39.426][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-22 16:03:39.427][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:39.428][ef$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:03:39.429][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-22 16:03:39.431][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-22 16:03:39.432][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:39.433][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:03:39.445][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-03-22 16:03:39.446][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-03-22 16:03:39.447][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:39.449][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:03:39.450][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-03-22 16:03:39.451][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-03-22 16:03:39.452][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:39.453][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:03:39.455][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-03-22 16:03:39.456][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-03-22 16:03:39.457][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:39.458][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:03:39.460][ef$get] Asked field names are: cas.id.
biodb.TRACE[2025-03-22 16:03:39.461][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-03-22 16:03:39.462][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:39.463][ef$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:03:39.464][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-03-22 16:03:39.466][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-03-22 16:03:39.467][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:39.468][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:03:39.479][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-22 16:03:39.481][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-22 16:03:39.482][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:39.487][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:03:39.488][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-22 16:03:39.489][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-22 16:03:39.491][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:39.492][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:03:39.493][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-22 16:03:39.494][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-22 16:03:39.495][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:39.497][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:03:39.498][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-22 16:03:39.500][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-22 16:03:39.501][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:39.502][ef$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:03:39.503][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-22 16:03:39.505][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-22 16:03:39.506][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:39.507][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:03:39.518][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-22 16:03:39.520][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-22 16:03:39.521][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:39.522][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:03:39.523][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-22 16:03:39.525][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-22 16:03:39.526][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:39.527][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:03:39.528][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-22 16:03:39.530][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-22 16:03:39.531][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:39.532][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:03:39.533][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-22 16:03:39.534][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-22 16:03:39.536][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:39.537][ef$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:03:39.538][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-22 16:03:39.539][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-22 16:03:39.541][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:39.542][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:03:39.553][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-22 16:03:39.554][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-22 16:03:39.555][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:39.557][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:03:39.558][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-22 16:03:39.559][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-22 16:03:39.560][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:39.562][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:03:39.563][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-22 16:03:39.564][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-22 16:03:39.565][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:39.566][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:03:39.568][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-22 16:03:39.569][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-22 16:03:39.570][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:39.571][ef$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:03:39.573][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-22 16:03:39.574][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-22 16:03:39.575][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:39.576][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:03:39.587][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-22 16:03:39.589][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-22 16:03:39.590][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:39.591][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:03:39.593][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-22 16:03:39.594][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-22 16:03:39.595][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:39.599][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:03:39.600][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-22 16:03:39.602][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-22 16:03:39.603][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:39.604][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:03:39.605][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-22 16:03:39.607][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-22 16:03:39.608][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:39.609][ef$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:03:39.610][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-22 16:03:39.612][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-22 16:03:39.613][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:39.614][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:03:39.626][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-22 16:03:39.627][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-22 16:03:39.628][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:39.630][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:03:39.631][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-22 16:03:39.632][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-22 16:03:39.633][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:39.635][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:03:39.636][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-22 16:03:39.637][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-22 16:03:39.638][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:39.640][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:03:39.641][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-22 16:03:39.642][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-22 16:03:39.643][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:39.644][ef$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:03:39.646][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-22 16:03:39.647][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-22 16:03:39.648][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:39.649][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:03:39.661][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-22 16:03:39.662][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-22 16:03:39.663][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:39.665][ef$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:03:39.671][ef$get] Asked field names are: cas.id.
biodb.TRACE[2025-03-22 16:03:39.672][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-03-22 16:03:39.674][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:39.679][ef$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:03:39.686][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-22 16:03:39.687][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-22 16:03:39.689][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:39.690][ef$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:03:39.696][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-22 16:03:39.698][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-22 16:03:39.699][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:39.700][ef$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:03:39.707][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-22 16:03:39.708][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-22 16:03:39.709][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:39.710][ef$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:03:39.717][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-22 16:03:39.719][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-22 16:03:39.720][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:39.721][ef$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:03:39.728][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-22 16:03:39.729][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-22 16:03:39.731][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:39.732][ef$get] fields variable is a list.
biodb.INFO [2025-03-22 16:03:39.743][biodb::testThat]
biodb.INFO [2025-03-22 16:03:39.744][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2025-03-22 16:03:39.745][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-22 16:03:39.747][biodb::testThat]
biodb.DEBUG[2025-03-22 16:03:39.749][private$loadEntries] Creating entries from ids [2]: "749674, 750690".
biodb.DEBUG[2025-03-22 16:03:39.756][conn$getEntryContent] Get NCI CACTUS entry content(s) for 2 id(s)...
biodb.DEBUG[2025-03-22 16:03:39.761][self$isDownloaded] Database nci.cactus has already been downloaded.
biodb.DEBUG[2025-03-22 16:03:39.763][self$isDownloaded] Database nci.cactus has already been downloaded.
biodb.TRACE[2025-03-22 16:03:39.766][cch$loadFileContent] Trying to load 2 files from cache: [2]: "749674, 750690".
biodb.TRACE[2025-03-22 16:03:39.768][cch$loadFileContent] file.exist = [2]: "TRUE, TRUE".
biodb.TRACE[2025-03-22 16:03:39.770][loadFileContents] Loaded 2 files from cache: [2]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/nci.cactus-8efc65070d01b214e760b1d4932ee427/749674.sdf, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/nci.cactus-8efc65070d01b214e760b1d4932ee427/750690.sdf".
biodb.DEBUG[2025-03-22 16:03:39.771][conn$getEntryContent] 2 NCI CACTUS entry content(s) loaded from cache.
biodb.DEBUG[2025-03-22 16:03:39.773][self$createEntryFromContent] Creating NCI CACTUS entries from 2 content(s).
biodb.DEBUG[2025-03-22 16:03:39.774][self$createEntryFromContent] Parsing 2 NCI CACTUS entries.
biodb.DEBUG[2025-03-22 16:03:39.776][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-22 16:03:39.778][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-22 16:03:39.779][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-22 16:03:39.786][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:03:39.787][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-22 16:03:39.788][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:03:39.789][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-22 16:03:39.800][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-22 16:03:39.802][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-22 16:03:39.803][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:39.804][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:03:39.805][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-22 16:03:39.807][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-22 16:03:39.808][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:39.809][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:03:39.813][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-22 16:03:39.814][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-22 16:03:39.815][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:39.816][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:03:39.818][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-22 16:03:39.819][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-22 16:03:39.820][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:39.821][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:03:39.823][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-22 16:03:39.824][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-22 16:03:39.826][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:39.827][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:03:39.828][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-22 16:03:39.829][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-22 16:03:39.830][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:39.832][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:03:39.834][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-22 16:03:39.836][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-22 16:03:39.837][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:39.838][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:03:39.839][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-22 16:03:39.841][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-22 16:03:39.842][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:39.843][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:03:39.845][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-22 16:03:39.846][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-22 16:03:39.847][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:39.849][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:03:39.850][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-22 16:03:39.852][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-22 16:03:39.853][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:39.854][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:03:39.856][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-03-22 16:03:39.858][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-03-22 16:03:39.859][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:39.860][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:03:39.862][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-03-22 16:03:39.863][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-03-22 16:03:39.864][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:39.865][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:03:39.867][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-22 16:03:39.868][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-22 16:03:39.869][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:39.870][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:03:39.871][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-03-22 16:03:39.873][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-03-22 16:03:39.874][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:39.875][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:03:39.876][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-22 16:03:39.878][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-22 16:03:39.879][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:39.885][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:03:39.886][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-22 16:03:39.888][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-22 16:03:39.889][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:39.890][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:03:39.891][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-22 16:03:39.892][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-22 16:03:39.894][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:39.895][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-22 16:03:39.896][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-22 16:03:39.897][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-22 16:03:39.898][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-22 16:03:39.904][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:03:39.905][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-22 16:03:39.906][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:03:39.907][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-22 16:03:39.922][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-22 16:03:39.923][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-22 16:03:39.924][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:39.925][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:03:39.927][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-22 16:03:39.928][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-22 16:03:39.929][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:39.930][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:03:39.933][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-03-22 16:03:39.935][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-03-22 16:03:39.936][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:39.937][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:03:39.938][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-03-22 16:03:39.940][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-03-22 16:03:39.941][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:39.942][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:03:39.944][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-22 16:03:39.945][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-22 16:03:39.947][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:39.948][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:03:39.949][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-22 16:03:39.950][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-22 16:03:39.952][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:39.953][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:03:39.954][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-22 16:03:39.956][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-22 16:03:39.957][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:39.958][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:03:39.959][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-22 16:03:39.961][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-22 16:03:39.962][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:39.963][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:03:39.965][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-22 16:03:39.967][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-22 16:03:39.968][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:39.969][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:03:39.970][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-22 16:03:39.972][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-22 16:03:39.973][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:39.974][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:03:39.976][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-22 16:03:39.977][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-22 16:03:39.978][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:39.979][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:03:39.981][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-22 16:03:39.982][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-22 16:03:39.983][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:39.984][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:03:39.986][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-22 16:03:39.987][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-22 16:03:39.988][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:39.989][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:03:39.990][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-22 16:03:39.992][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-22 16:03:39.993][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:39.994][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:03:39.995][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-22 16:03:39.997][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-22 16:03:39.998][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:39.999][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:03:40.001][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-22 16:03:40.003][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-22 16:03:40.004][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:40.005][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:03:40.006][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-22 16:03:40.008][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-22 16:03:40.009][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:40.010][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:03:40.012][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-22 16:03:40.013][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-22 16:03:40.014][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:40.015][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:03:40.017][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-22 16:03:40.018][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-22 16:03:40.019][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:40.020][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:03:40.022][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-03-22 16:03:40.024][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-03-22 16:03:40.025][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:40.027][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:03:40.028][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-03-22 16:03:40.029][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-03-22 16:03:40.030][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:40.032][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:03:40.033][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-22 16:03:40.034][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-22 16:03:40.035][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:40.037][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:03:40.038][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-03-22 16:03:40.039][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-03-22 16:03:40.040][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:40.041][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:03:40.043][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-22 16:03:40.044][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-22 16:03:40.045][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:40.046][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:03:40.048][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-22 16:03:40.049][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-22 16:03:40.050][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:40.051][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:03:40.053][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-22 16:03:40.054][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-22 16:03:40.055][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:40.056][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:03:40.058][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-22 16:03:40.059][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-22 16:03:40.060][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:40.061][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:03:40.063][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-22 16:03:40.068][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-22 16:03:40.069][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:40.070][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:03:40.071][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-22 16:03:40.073][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-22 16:03:40.074][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:40.075][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:03:40.076][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-22 16:03:40.078][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-22 16:03:40.079][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:40.080][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:03:40.081][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-22 16:03:40.083][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-22 16:03:40.084][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:40.085][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:03:40.086][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-22 16:03:40.087][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-22 16:03:40.089][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:40.090][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-22 16:03:40.091][self$createEntryFromContent] Accession numbers: 749674, 750690.
biodb.TRACE[2025-03-22 16:03:40.092][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2025-03-22 16:03:40.094][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2025-03-22 16:03:40.095][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:40.096][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:03:40.097][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2025-03-22 16:03:40.099][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2025-03-22 16:03:40.100][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:40.101][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:03:40.102][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2025-03-22 16:03:40.104][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2025-03-22 16:03:40.105][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:40.106][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:03:40.113][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2025-03-22 16:03:40.114][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2025-03-22 16:03:40.115][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:40.116][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:03:40.118][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2025-03-22 16:03:40.119][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2025-03-22 16:03:40.120][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:40.121][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:03:40.123][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2025-03-22 16:03:40.124][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2025-03-22 16:03:40.125][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:40.126][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2025-03-22 16:03:40.137][biodb::testThat]
biodb.INFO [2025-03-22 16:03:40.138][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2025-03-22 16:03:40.139][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-22 16:03:40.140][biodb::testThat]
biodb.INFO [2025-03-22 16:03:40.148][biodb::testThat]
biodb.INFO [2025-03-22 16:03:40.149][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2025-03-22 16:03:40.150][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-22 16:03:40.151][biodb::testThat]
biodb.WARN [2025-03-22 16:03:40.176][self$searchForEntries] This database is not searchable by field "name".
biodb.WARN [2025-03-22 16:03:40.202][self$searchForEntries] This database is not searchable by field "name".
biodb.INFO [2025-03-22 16:03:40.213][biodb::testThat]
biodb.INFO [2025-03-22 16:03:40.214][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2025-03-22 16:03:40.215][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-22 16:03:40.216][biodb::testThat]
biodb.TRACE[2025-03-22 16:03:40.252][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-03-22 16:03:40.254][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-03-22 16:03:40.255][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:40.256][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:03:40.257][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-03-22 16:03:40.259][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-03-22 16:03:40.260][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:40.261][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:03:40.262][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-03-22 16:03:40.264][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-03-22 16:03:40.265][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:40.266][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:03:40.267][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-03-22 16:03:40.269][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-03-22 16:03:40.270][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:40.271][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:03:40.317][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-03-22 16:03:40.319][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-03-22 16:03:40.320][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:40.321][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:03:40.322][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-03-22 16:03:40.323][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-03-22 16:03:40.325][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:40.326][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:03:40.327][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-03-22 16:03:40.328][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-03-22 16:03:40.330][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:40.331][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:03:40.332][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-03-22 16:03:40.333][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-03-22 16:03:40.334][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:40.336][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2025-03-22 16:03:40.365][biodb::testThat]
biodb.INFO [2025-03-22 16:03:40.367][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2025-03-22 16:03:40.368][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-22 16:03:40.369][biodb::testThat]
biodb.INFO [2025-03-22 16:03:40.379][biodb::testThat]
biodb.INFO [2025-03-22 16:03:40.380][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2025-03-22 16:03:40.381][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-22 16:03:40.382][biodb::testThat]
biodb.INFO [2025-03-22 16:03:40.392][biodb::testThat]
biodb.INFO [2025-03-22 16:03:40.393][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2025-03-22 16:03:40.394][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-22 16:03:40.396][biodb::testThat]
biodb.INFO [2025-03-22 16:03:40.404][biodb::testThat]
biodb.INFO [2025-03-22 16:03:40.405][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2025-03-22 16:03:40.406][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-22 16:03:40.407][biodb::testThat]
biodb.INFO [2025-03-22 16:03:40.415][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2025-03-22 16:03:40.416][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector nci.cactus from the request scheduler
biodb.INFO [2025-03-22 16:03:40.418][self$deleteConn] Connector "nci.cactus" deleted.
biodb.DEBUG[2025-03-22 16:03:40.419][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-03-22 16:03:40.420][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-22 16:03:40.421][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-22 16:03:40.422][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:03:40.423][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-22 16:03:40.424][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:03:40.425][FUN] Functions in observer BiodbConfig: [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 [2025-03-22 16:03:40.441][biodb::testContext]
biodb.INFO [2025-03-22 16:03:40.443][biodb::testContext] ********************************************************************************
biodb.INFO [2025-03-22 16:03:40.444][biodb::testContext] Test context - Example long tests
biodb.INFO [2025-03-22 16:03:40.445][biodb::testContext] ********************************************************************************
biodb.INFO [2025-03-22 16:03:40.446][biodb::testContext]
biodb.INFO [2025-03-22 16:03:40.449][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.14.0.
biodb.DEBUG[2025-03-22 16:03:40.451][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2025-03-22 16:03:40.455][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-03-22 16:03:40.456][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-03-22 16:03:40.457][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-03-22 16:03:40.459][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:03:40.460][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:03:40.461][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:03:40.462][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-03-22 16:03:40.463][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-03-22 16:03:40.464][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:03:40.465][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:03:40.467][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:03:40.468][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-03-22 16:03:40.469][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-03-22 16:03:40.470][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:03:40.471][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:03:40.472][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:03:40.473][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-03-22 16:03:40.475][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-03-22 16:03:40.476][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-03-22 16:03:40.477][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:03:40.478][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:03:40.479][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[2025-03-22 16:03:40.480][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-03-22 16:03:40.482][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-03-22 16:03:40.483][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-03-22 16:03:40.484][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:03:40.485][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:03:40.486][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:03:40.487][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-03-22 16:03:40.489][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-03-22 16:03:40.490][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:03:40.491][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:03:40.492][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[2025-03-22 16:03:40.493][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-03-22 16:03:40.494][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-03-22 16:03:40.496][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-03-22 16:03:40.497][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:03:40.498][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:03:40.499][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:03:40.500][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-03-22 16:03:40.502][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-03-22 16:03:40.503][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:03:40.504][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:03:40.505][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[2025-03-22 16:03:40.506][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-03-22 16:03:40.507][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-03-22 16:03:40.509][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-03-22 16:03:40.510][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:03:40.511][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:03:40.512][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:03:40.513][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-03-22 16:03:40.514][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-03-22 16:03:40.515][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-03-22 16:03:40.517][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-03-22 16:03:40.518][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-03-22 16:03:40.519][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-03-22 16:03:40.520][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:03:40.521][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:03:40.522][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:03:40.524][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-03-22 16:03:40.525][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-03-22 16:03:40.526][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:03:40.527][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:03:40.528][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:03:40.529][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-03-22 16:03:40.531][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-03-22 16:03:40.532][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:03:40.533][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:03:40.534][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[2025-03-22 16:03:40.535][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-03-22 16:03:40.537][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-03-22 16:03:40.538][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:03:40.539][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:03:40.540][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:03:40.541][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-03-22 16:03:40.542][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2025-03-22 16:03:40.544][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:03:40.545][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:03:40.546][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:03:40.547][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-03-22 16:03:40.548][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-03-22 16:03:40.549][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:03:40.550][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:03:40.551][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:03:40.553][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-03-22 16:03:40.554][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-03-22 16:03:40.565][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-03-22 16:03:40.566][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:03:40.567][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:03:40.568][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:03:40.569][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-03-22 16:03:40.571][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-03-22 16:03:40.572][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-03-22 16:03:40.573][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:03:40.574][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:03:40.576][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:03:40.577][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-03-22 16:03:40.580][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-03-22 16:03:40.581][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2025-03-22 16:03:40.582][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-22 16:03:40.583][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-22 16:03:40.585][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-22 16:03:40.586][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-22 16:03:40.587][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-22 16:03:40.588][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-22 16:03:40.590][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-03-22 16:03:40.591][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-22 16:03:40.592][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-03-22 16:03:40.593][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-03-22 16:03:40.595][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-22 16:03:40.596][self$setPropertyValue]
biodb.DEBUG[2025-03-22 16:03:40.597][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-22 16:03:40.598][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-03-22 16:03:40.598][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-03-22 16:03:40.598][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-03-22 16:03:40.598][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-03-22 16:03:40.598][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-03-22 16:03:40.600][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-22 16:03:40.601][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-22 16:03:40.602][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-22 16:03:40.603][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-22 16:03:40.604][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-22 16:03:40.606][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-22 16:03:40.607][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-22 16:03:40.608][self$setPropertyValue]
biodb.DEBUG[2025-03-22 16:03:40.609][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-22 16:03:40.610][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-22 16:03:40.612][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-22 16:03:40.618][self$setPropertyValue]
biodb.DEBUG[2025-03-22 16:03:40.619][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-03-22 16:03:40.621][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-03-22 16:03:40.623][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-03-22 16:03:40.624][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-22 16:03:40.625][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-22 16:03:40.626][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-22 16:03:40.628][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-22 16:03:40.629][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-22 16:03:40.630][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-22 16:03:40.631][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-03-22 16:03:40.632][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-22 16:03:40.634][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-03-22 16:03:40.635][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-03-22 16:03:40.636][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-22 16:03:40.637][self$setPropertyValue]
biodb.DEBUG[2025-03-22 16:03:40.639][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-22 16:03:40.640][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-03-22 16:03:40.640][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-03-22 16:03:40.640][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-03-22 16:03:40.640][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-03-22 16:03:40.640][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-03-22 16:03:40.641][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-22 16:03:40.642][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-22 16:03:40.644][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-22 16:03:40.645][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-22 16:03:40.646][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-22 16:03:40.647][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-22 16:03:40.648][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-22 16:03:40.650][self$setPropertyValue]
biodb.DEBUG[2025-03-22 16:03:40.651][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-22 16:03:40.652][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-22 16:03:40.653][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-22 16:03:40.654][self$setPropertyValue]
biodb.DEBUG[2025-03-22 16:03:40.656][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-03-22 16:03:40.658][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-03-22 16:03:40.659][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2025-03-22 16:03:40.660][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-22 16:03:40.662][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-22 16:03:40.663][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-22 16:03:40.664][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-22 16:03:40.665][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-22 16:03:40.667][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-22 16:03:40.668][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-03-22 16:03:40.669][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-22 16:03:40.670][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-03-22 16:03:40.672][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-03-22 16:03:40.673][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-22 16:03:40.674][self$setPropertyValue]
biodb.DEBUG[2025-03-22 16:03:40.675][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-22 16:03:40.677][self$setPropertyValue]
biodb.DEBUG[2025-03-22 16:03:40.678][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-22 16:03:40.679][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-22 16:03:40.680][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-22 16:03:40.681][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-22 16:03:40.682][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-22 16:03:40.684][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-22 16:03:40.685][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-22 16:03:40.686][self$setPropertyValue]
biodb.DEBUG[2025-03-22 16:03:40.687][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-22 16:03:40.688][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-22 16:03:40.689][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-22 16:03:40.691][self$setPropertyValue]
biodb.DEBUG[2025-03-22 16:03:40.692][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-03-22 16:03:40.694][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-03-22 16:03:40.696][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-03-22 16:03:40.697][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-22 16:03:40.698][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-22 16:03:40.699][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-22 16:03:40.701][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-22 16:03:40.702][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-22 16:03:40.703][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-22 16:03:40.704][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-03-22 16:03:40.706][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-22 16:03:40.707][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-03-22 16:03:40.708][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-03-22 16:03:40.710][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-22 16:03:40.711][self$setPropertyValue]
biodb.DEBUG[2025-03-22 16:03:40.712][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-22 16:03:40.713][self$setPropertyValue]
biodb.DEBUG[2025-03-22 16:03:40.715][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-22 16:03:40.716][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-22 16:03:40.717][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-22 16:03:40.718][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-22 16:03:40.719][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-22 16:03:40.721][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-22 16:03:40.722][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-22 16:03:40.723][self$setPropertyValue]
biodb.DEBUG[2025-03-22 16:03:40.724][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-22 16:03:40.725][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-22 16:03:40.727][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-22 16:03:40.728][self$setPropertyValue]
biodb.DEBUG[2025-03-22 16:03:40.730][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-03-22 16:03:40.731][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:03:40.732][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[2025-03-22 16:03:40.733][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:03:40.734][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:03:40.735][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-22 16:03:40.736][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:03:40.737][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[2025-03-22 16:03:40.739][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:03:40.740][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:03:40.741][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-22 16:03:40.742][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:03:40.743][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[2025-03-22 16:03:40.744][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:03:40.745][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:03:40.746][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-22 16:03:40.748][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:03:40.749][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[2025-03-22 16:03:40.750][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:03:40.751][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:03:40.752][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-22 16:03:40.753][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:03:40.754][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:03:40.755][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:03:40.757][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:03:40.758][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-22 16:03:40.759][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:03:40.760][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:03:40.761][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:03:40.762][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:03:40.763][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-22 16:03:40.765][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:03:40.766][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:03:40.767][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:03:40.768][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:03:40.769][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-22 16:03:40.770][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:03:40.771][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:03:40.773][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:03:40.774][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:03:40.775][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-22 16:03:40.776][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:03:40.777][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:03:40.778][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:03:40.779][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:03:40.781][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-22 16:03:40.782][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:03:40.783][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:03:40.789][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:03:40.790][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:03:40.791][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-22 16:03:40.792][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:03:40.793][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[2025-03-22 16:03:40.794][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:03:40.796][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:03:40.797][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-22 16:03:40.798][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:03:40.799][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[2025-03-22 16:03:40.800][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:03:40.801][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:03:40.802][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-22 16:03:40.803][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:03:40.804][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".
biodb.DEBUG[2025-03-22 16:03:40.806][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:03:40.807][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:03:40.808][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-22 16:03:40.809][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:03:40.810][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:03:40.811][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:03:40.812][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:03:40.813][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-22 16:03:40.814][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:03:40.816][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:03:40.817][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:03:40.818][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:03:40.819][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-22 16:03:40.820][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:03:40.821][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:03:40.822][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:03:40.823][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:03:40.825][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-22 16:03:40.826][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:03:40.827][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:03:40.828][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:03:40.829][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:03:40.830][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-22 16:03:40.831][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:03:40.832][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:03:40.834][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-03-22 16:03:40.835][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-03-22 16:03:40.837][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-03-22 16:03:40.839][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-03-22 16:03:40.841][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-03-22 16:03:40.842][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-03-22 16:03:40.844][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-03-22 16:03:40.846][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-03-22 16:03:40.848][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-03-22 16:03:40.849][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-03-22 16:03:40.851][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-03-22 16:03:40.853][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-03-22 16:03:40.854][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-03-22 16:03:40.856][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-03-22 16:03:40.858][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-03-22 16:03:40.860][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-03-22 16:03:40.861][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-03-22 16:03:40.863][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-03-22 16:03:40.865][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-03-22 16:03:40.867][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-03-22 16:03:40.868][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-03-22 16:03:40.870][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-03-22 16:03:40.872][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-03-22 16:03:40.874][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-03-22 16:03:40.875][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-03-22 16:03:40.877][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-03-22 16:03:40.879][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-03-22 16:03:40.880][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-03-22 16:03:40.882][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-03-22 16:03:40.884][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-03-22 16:03:40.886][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-03-22 16:03:40.887][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-03-22 16:03:40.889][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-03-22 16:03:40.891][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-03-22 16:03:40.893][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-03-22 16:03:40.894][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-03-22 16:03:40.896][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-03-22 16:03:40.898][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-03-22 16:03:40.899][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-03-22 16:03:40.901][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-03-22 16:03:40.903][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-03-22 16:03:40.905][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-03-22 16:03:40.907][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-03-22 16:03:40.908][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-03-22 16:03:40.910][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-03-22 16:03:40.912][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-03-22 16:03:40.914][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-03-22 16:03:40.916][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-03-22 16:03:40.917][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-03-22 16:03:40.919][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-03-22 16:03:40.921][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-03-22 16:03:40.923][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-03-22 16:03:40.924][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-03-22 16:03:40.926][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-03-22 16:03:40.928][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-03-22 16:03:40.929][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-03-22 16:03:40.931][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-03-22 16:03:40.933][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-03-22 16:03:40.935][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-03-22 16:03:40.936][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-03-22 16:03:40.938][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-03-22 16:03:40.940][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-03-22 16:03:40.941][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-03-22 16:03:40.943][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-03-22 16:03:40.945][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-03-22 16:03:40.946][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-03-22 16:03:40.948][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-03-22 16:03:40.954][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-03-22 16:03:40.956][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-03-22 16:03:40.959][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-03-22 16:03:40.960][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-03-22 16:03:40.962][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-03-22 16:03:40.964][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-03-22 16:03:40.966][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-03-22 16:03:40.967][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-03-22 16:03:40.969][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-03-22 16:03:40.971][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-03-22 16:03:40.973][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-03-22 16:03:40.974][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-03-22 16:03:40.976][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-03-22 16:03:40.978][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-03-22 16:03:40.979][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-03-22 16:03:40.981][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-03-22 16:03:40.983][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-03-22 16:03:40.985][initialize] This is biodb version 1.14.0.
biodb.DEBUG[2025-03-22 16:03:40.986][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-03-22 16:03:40.988][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:03:40.989][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-22 16:03:40.990][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:03:40.991][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:03:40.992][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:03:40.993][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-22 16:03:40.994][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-22 16:03:40.995][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:03:40.997][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-22 16:03:40.998][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:03:40.999][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:03:41.000][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:03:41.001][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-22 16:03:41.002][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-22 16:03:41.003][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:03:41.004][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-22 16:03:41.005][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:03:41.006][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:03:41.008][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:03:41.009][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-22 16:03:41.010][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-22 16:03:41.011][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:03:41.012][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-22 16:03:41.013][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:03:41.014][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:03:41.015][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:03:41.016][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-22 16:03:41.017][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-22 16:03:41.019][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:03:41.020][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-22 16:03:41.021][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:03:41.022][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:03:41.023][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:03:41.025][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-22 16:03:41.026][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-22 16:03:41.027][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:03:41.028][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-22 16:03:41.030][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:03:41.031][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:03:41.032][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:03:41.033][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-22 16:03:41.034][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-22 16:03:41.035][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:03:41.036][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-22 16:03:41.037][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:03:41.038][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:03:41.040][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:03:41.041][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-22 16:03:41.042][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-22 16:03:41.043][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:03:41.044][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-22 16:03:41.045][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:03:41.046][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:03:41.047][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:03:41.048][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-22 16:03:41.049][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-22 16:03:41.050][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:03:41.052][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-22 16:03:41.053][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:03:41.054][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:03:41.055][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:03:41.056][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-22 16:03:41.057][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-22 16:03:41.058][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:03:41.059][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-22 16:03:41.060][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:03:41.062][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:03:41.063][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:03:41.064][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-22 16:03:41.065][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-22 16:03:41.066][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:03:41.067][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-22 16:03:41.068][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:03:41.069][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:03:41.070][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:03:41.071][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-22 16:03:41.073][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-22 16:03:41.074][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:03:41.075][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-22 16:03:41.076][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:03:41.077][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:03:41.078][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:03:41.079][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-22 16:03:41.080][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-22 16:03:41.081][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:03:41.083][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-22 16:03:41.084][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:03:41.086][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:03:41.087][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:03:41.088][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-22 16:03:41.090][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-22 16:03:41.093][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:03:41.094][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-22 16:03:41.096][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:03:41.097][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:03:41.098][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:03:41.099][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-22 16:03:41.100][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-22 16:03:41.101][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:03:41.102][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-22 16:03:41.103][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:03:41.104][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:03:41.106][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:03:41.107][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-22 16:03:41.108][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-22 16:03:41.109][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:03:41.110][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-22 16:03:41.111][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:03:41.112][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:03:41.113][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:03:41.114][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-22 16:03:41.115][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-22 16:03:41.117][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:03:41.118][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-22 16:03:41.119][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:03:41.120][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:03:41.121][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:03:41.127][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-22 16:03:41.128][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-22 16:03:41.129][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:03:41.130][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-22 16:03:41.131][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:03:41.132][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:03:41.135][biodb$loadDefinitions] Load definitions from file "/Users/biocbuild/bbs-3.20-bioc-longtests/meat/biodbNci.Rcheck/biodbNci/definitions.yml".
biodb.DEBUG[2025-03-22 16:03:41.136][self$getDbsInfo()$define] Define connector nci.cactus.
biodb.DEBUG[2025-03-22 16:03:41.139][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-03-22 16:03:41.140][self$setPropertyValue] Setting property "description" to "National Cancer Institute (USA) CACTUS Database.".
biodb.DEBUG[2025-03-22 16:03:41.141][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-22 16:03:41.142][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-22 16:03:41.144][self$setPropertyValue] Setting property "downloadable" to "TRUE".
biodb.DEBUG[2025-03-22 16:03:41.145][self$setPropertyValue] Setting property "dwnld.ext" to "gz".
biodb.DEBUG[2025-03-22 16:03:41.146][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-03-22 16:03:41.147][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-22 16:03:41.149][self$setPropertyValue] Setting property "entry.content.type" to "sdf".
biodb.DEBUG[2025-03-22 16:03:41.150][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-22 16:03:41.151][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-03-22 16:03:41.152][self$setPropertyValue] Setting property "name" to "NCI CACTUS".
biodb.DEBUG[2025-03-22 16:03:41.154][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-22 16:03:41.155][self$setPropertyValue] Setting property "parsing.expr" to "NSC".
biodb.DEBUG[2025-03-22 16:03:41.155][self$setPropertyValue] Setting property "parsing.expr" to "DTP names".
biodb.DEBUG[2025-03-22 16:03:41.155][self$setPropertyValue] Setting property "parsing.expr" to "Standard InChI".
biodb.DEBUG[2025-03-22 16:03:41.155][self$setPropertyValue] Setting property "parsing.expr" to "c("Standard InChIKey", "^InChIKey=(.*)$")".
biodb.DEBUG[2025-03-22 16:03:41.155][self$setPropertyValue] Setting property "parsing.expr" to "Formula".
biodb.DEBUG[2025-03-22 16:03:41.155][self$setPropertyValue] Setting property "parsing.expr" to "Molecular Weight".
biodb.DEBUG[2025-03-22 16:03:41.155][self$setPropertyValue] Setting property "parsing.expr" to "CAS".
biodb.DEBUG[2025-03-22 16:03:41.156][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-03-22 16:03:41.158][self$setPropertyValue]
biodb.DEBUG[2025-03-22 16:03:41.159][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-03-22 16:03:41.160][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-22 16:03:41.161][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-22 16:03:41.162][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-22 16:03:41.164][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-22 16:03:41.165][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-22 16:03:41.166][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-22 16:03:41.167][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/".
biodb.DEBUG[2025-03-22 16:03:41.167][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/".
biodb.DEBUG[2025-03-22 16:03:41.167][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/download/nci/".
biodb.DEBUG[2025-03-22 16:03:41.167][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/download/nci/NCI-Open_2012-05-01.sdf.gz".
biodb.DEBUG[2025-03-22 16:03:41.168][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-22 16:03:41.170][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-22 16:03:41.171][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-03-22 16:03:41.172][self$setPropertyValue]
biodb.DEBUG[2025-03-22 16:03:41.174][self$getEntryFields()$define] Define field nci.cactus.id.
biodb.DEBUG[2025-03-22 16:03:41.177][super$initialize] Initialize connector nci.cactus.
biodb.DEBUG[2025-03-22 16:03:41.179][super$initialize] Register connector nci.cactus with the request scheduler
biodb.DEBUG[2025-03-22 16:03:41.180][private$bdb$getRequestScheduler()$re ...] Register connector nci.cactus.
biodb.DEBUG[2025-03-22 16:03:41.182][private$addConnectorRules] Create new rule for URL "cactus.nci.nih.gov" of connector "nci.cactus".
biodb.DEBUG[2025-03-22 16:03:41.183][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-03-22 16:03:41.185][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-03-22 16:03:41.186][rule$addConnector] Connector "nci.cactus" is already listed in rule "cactus.nci.nih.gov".
biodb.DEBUG[2025-03-22 16:03:41.188][rule$addConnector] Connector "nci.cactus" is already listed in rule "cactus.nci.nih.gov".
biodb.DEBUG[2025-03-22 16:03:41.189][rule$addConnector] Connector "nci.cactus" is already listed in rule "cactus.nci.nih.gov".
biodb.DEBUG[2025-03-22 16:03:41.190][biodb$getFactory()$createConn] Creating new connector nci.cactus for database class nci.cactus .
biodb.INFO [2025-03-22 16:03:41.192][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2025-03-22 16:03:41.193][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector nci.cactus from the request scheduler
biodb.INFO [2025-03-22 16:03:41.194][self$deleteConn] Connector "nci.cactus" deleted.
biodb.DEBUG[2025-03-22 16:03:41.195][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-03-22 16:03:41.197][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-22 16:03:41.198][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-22 16:03:41.199][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:03:41.200][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-22 16:03:41.201][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:03:41.202][FUN] Functions in observer 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 0 | WARN 0 | SKIP 0 | PASS 92 ]
> 
> proc.time()
   user  system elapsed 
  5.671   0.324   6.162

'R CMD check' output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --test-dir=longtests --no-stop-on-test-error --no-codoc --no-examples --no-manual --ignore-vignettes --check-subdirs=no biodbNci_1.10.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.20-bioc-longtests/meat/biodbNci.Rcheck’
* using R version 4.4.3 (2025-02-28)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.6
* 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 ‘1.10.0’
* 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: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
* used SDK: ‘MacOSX11.3.sdk’
* 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 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 ... OK
* 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’
 OK
* DONE

Status: OK

Installation output

biodbNci.Rcheck/00install.out

* installing *source* package ‘biodbNci’ ...
** using staged installation
** libs
using C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
using SDK: ‘MacOSX11.3.sdk’
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/testthat/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c RcppExports.cpp -o RcppExports.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/testthat/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c extractEntries.cpp -o extractEntries.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/testthat/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c test-100-example.cpp -o test-100-example.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/testthat/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c test-runner.cpp -o test-runner.o
clang++ -arch x86_64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/lib -o biodbNci.so RcppExports.o extractEntries.o test-100-example.o test-runner.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.20-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)