Back to Long Tests report for BioC 3.21

This page was generated on 2025-08-16 23:55 -0400 (Sat, 16 Aug 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4824
merida1macOS 12.7.5 Montereyx86_644.5.1 RC (2025-06-05 r88288) -- "Great Square Root" 4604
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 9/30HostnameOS / ArchCHECK
biodbNci 1.12.0  (landing page)
Pierrick Roger
Snapshot Date: 2025-08-16 09:55 -0400 (Sat, 16 Aug 2025)
git_url: https://git.bioconductor.org/packages/biodbNci
git_branch: RELEASE_3_21
git_last_commit: a398ae4
git_last_commit_date: 2025-04-15 12:47:37 -0400 (Tue, 15 Apr 2025)
nebbiolo1Linux (Ubuntu 24.04.3 LTS) / x86_64  OK  
merida1macOS 12.7.5 Monterey / x86_64  OK  


CHECK results for biodbNci on nebbiolo1

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

raw results


Summary

Package: biodbNci
Version: 1.12.0
Command: /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --test-dir=longtests --no-stop-on-test-error --no-codoc --no-examples --no-manual --ignore-vignettes --check-subdirs=no biodbNci_1.12.0.tar.gz
StartedAt: 2025-08-16 16:04:44 -0400 (Sat, 16 Aug 2025)
EndedAt: 2025-08-16 16:17:38 -0400 (Sat, 16 Aug 2025)
EllapsedTime: 774.4 seconds
RetCode: 0
Status:   OK  
CheckDir: biodbNci.Rcheck
Warnings: 0

Tests output

biodbNci.Rcheck/tests/testthat.Rout


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

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

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Type 'contributors()' for more information and
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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 [2025-08-16 16:05:41.388][biodb::testContext]
biodb.INFO [2025-08-16 16:05:41.390][biodb::testContext] ********************************************************************************
biodb.INFO [2025-08-16 16:05:41.391][biodb::testContext] Test context - Generic long tests
biodb.INFO [2025-08-16 16:05:41.392][biodb::testContext] ********************************************************************************
biodb.INFO [2025-08-16 16:05:41.393][biodb::testContext]
biodb.INFO [2025-08-16 16:05:41.399][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.16.0.
biodb.DEBUG[2025-08-16 16:05:41.401][self$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.21-bioc/R/site-library/biodb/definitions.yml".
biodb.DEBUG[2025-08-16 16:05:41.408][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-08-16 16:05:41.409][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-08-16 16:05:41.410][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-08-16 16:05:41.410][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:05:41.411][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:05:41.412][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-16 16:05:41.413][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-08-16 16:05:41.430][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-08-16 16:05:41.431][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:05:41.432][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:05:41.433][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[2025-08-16 16:05:41.434][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-08-16 16:05:41.435][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-08-16 16:05:41.436][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:05:41.437][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:05:41.438][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-16 16:05:41.438][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-08-16 16:05:41.439][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-08-16 16:05:41.440][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-08-16 16:05:41.441][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:05:41.442][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:05:41.443][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-16 16:05:41.444][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-08-16 16:05:41.445][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-08-16 16:05:41.446][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-08-16 16:05:41.447][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:05:41.448][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:05:41.448][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-16 16:05:41.449][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-08-16 16:05:41.450][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-08-16 16:05:41.451][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:05:41.452][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:05:41.453][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-16 16:05:41.454][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-08-16 16:05:41.455][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-08-16 16:05:41.456][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-08-16 16:05:41.457][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:05:41.458][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:05:41.459][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-16 16:05:41.459][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-08-16 16:05:41.460][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-08-16 16:05:41.461][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:05:41.462][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:05:41.463][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-16 16:05:41.464][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-08-16 16:05:41.465][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-08-16 16:05:41.466][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-08-16 16:05:41.467][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:05:41.468][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:05:41.469][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-16 16:05:41.469][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-08-16 16:05:41.470][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-08-16 16:05:41.471][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-08-16 16:05:41.472][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-08-16 16:05:41.473][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-08-16 16:05:41.474][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-08-16 16:05:41.475][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:05:41.476][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:05:41.477][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-16 16:05:41.478][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-08-16 16:05:41.479][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-08-16 16:05:41.480][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:05:41.481][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:05:41.481][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-16 16:05:41.482][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-08-16 16:05:41.483][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-08-16 16:05:41.484][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:05:41.485][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:05:41.486][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[2025-08-16 16:05:41.487][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-08-16 16:05:41.488][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-08-16 16:05:41.489][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:05:41.490][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:05:41.491][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-16 16:05:41.491][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-08-16 16:05:41.492][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2025-08-16 16:05:41.493][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:05:41.494][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:05:41.495][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-16 16:05:41.496][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-08-16 16:05:41.497][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-08-16 16:05:41.498][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:05:41.499][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:05:41.500][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-16 16:05:41.501][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-08-16 16:05:41.502][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-08-16 16:05:41.506][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-08-16 16:05:41.507][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:05:41.508][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:05:41.508][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-16 16:05:41.509][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-08-16 16:05:41.510][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-08-16 16:05:41.511][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-08-16 16:05:41.512][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:05:41.513][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:05:41.514][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-16 16:05:41.517][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-08-16 16:05:41.555][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-08-16 16:05:41.572][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2025-08-16 16:05:41.573][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-08-16 16:05:41.574][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-08-16 16:05:41.575][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-08-16 16:05:41.576][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-08-16 16:05:41.577][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-08-16 16:05:41.578][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-08-16 16:05:41.579][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-08-16 16:05:41.580][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-08-16 16:05:41.581][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-08-16 16:05:41.582][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-08-16 16:05:41.583][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-08-16 16:05:41.584][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-08-16 16:05:41.585][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-08-16 16:05:41.586][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-08-16 16:05:41.586][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-08-16 16:05:41.586][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-08-16 16:05:41.586][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-08-16 16:05:41.586][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-08-16 16:05:41.587][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-08-16 16:05:41.588][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-16 16:05:41.589][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-16 16:05:41.590][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-08-16 16:05:41.591][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-16 16:05:41.591][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-16 16:05:41.592][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-08-16 16:05:41.593][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-08-16 16:05:41.594][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-08-16 16:05:41.595][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-08-16 16:05:41.596][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-08-16 16:05:41.597][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-08-16 16:05:41.598][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-08-16 16:05:41.600][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-08-16 16:05:41.601][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-08-16 16:05:41.602][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-08-16 16:05:41.603][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-08-16 16:05:41.604][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-08-16 16:05:41.605][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-08-16 16:05:41.606][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-08-16 16:05:41.607][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-08-16 16:05:41.608][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-08-16 16:05:41.609][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-08-16 16:05:41.610][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-08-16 16:05:41.610][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-08-16 16:05:41.611][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-08-16 16:05:41.613][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-08-16 16:05:41.614][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-08-16 16:05:41.614][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-08-16 16:05:41.614][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-08-16 16:05:41.614][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-08-16 16:05:41.614][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-08-16 16:05:41.614][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-08-16 16:05:41.615][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-08-16 16:05:41.616][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-16 16:05:41.617][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-16 16:05:41.618][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-08-16 16:05:41.619][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-16 16:05:41.620][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-16 16:05:41.621][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-08-16 16:05:41.622][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-08-16 16:05:41.623][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-08-16 16:05:41.624][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-08-16 16:05:41.625][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-08-16 16:05:41.626][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-08-16 16:05:41.627][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-08-16 16:05:41.628][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-08-16 16:05:41.629][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2025-08-16 16:05:41.630][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-08-16 16:05:41.631][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-08-16 16:05:41.632][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-08-16 16:05:41.633][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-08-16 16:05:41.634][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-08-16 16:05:41.635][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-08-16 16:05:41.636][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-08-16 16:05:41.637][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-08-16 16:05:41.638][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-08-16 16:05:41.639][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-08-16 16:05:41.640][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-08-16 16:05:41.641][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-08-16 16:05:41.642][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-08-16 16:05:41.643][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-08-16 16:05:41.644][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-08-16 16:05:41.645][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-16 16:05:41.646][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-16 16:05:41.647][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-08-16 16:05:41.648][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-16 16:05:41.648][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-16 16:05:41.649][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-08-16 16:05:41.650][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-08-16 16:05:41.651][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-08-16 16:05:41.652][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-08-16 16:05:41.653][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-08-16 16:05:41.654][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-08-16 16:05:41.655][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-08-16 16:05:41.657][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-08-16 16:05:41.658][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-08-16 16:05:41.659][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-08-16 16:05:41.660][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-08-16 16:05:41.661][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-08-16 16:05:41.662][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-08-16 16:05:41.663][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-08-16 16:05:41.664][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-08-16 16:05:41.665][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-08-16 16:05:41.666][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-08-16 16:05:41.666][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-08-16 16:05:41.667][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-08-16 16:05:41.668][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-08-16 16:05:41.669][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-08-16 16:05:41.670][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-08-16 16:05:41.671][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-08-16 16:05:41.672][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-08-16 16:05:41.673][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-16 16:05:41.674][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-16 16:05:41.675][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-08-16 16:05:41.676][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-16 16:05:41.677][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-16 16:05:41.678][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-08-16 16:05:41.679][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-08-16 16:05:41.680][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-08-16 16:05:41.681][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-08-16 16:05:41.681][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-08-16 16:05:41.682][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-08-16 16:05:41.686][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-08-16 16:05:41.687][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:05:41.688][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-16 16:05:41.689][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:05:41.690][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-16 16:05:41.690][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-16 16:05:41.691][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:05:41.692][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[2025-08-16 16:05:41.693][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:05:41.694][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-16 16:05:41.695][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-16 16:05:41.696][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:05:41.696][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-16 16:05:41.697][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:05:41.698][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-16 16:05:41.699][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-16 16:05:41.700][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:05:41.701][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-16 16:05:41.702][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:05:41.703][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-16 16:05:41.704][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-16 16:05:41.704][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:05:41.705][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-16 16:05:41.706][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:05:41.707][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-16 16:05:41.708][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-16 16:05:41.709][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:05:41.710][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-16 16:05:41.710][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:05:41.711][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-16 16:05:41.712][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-16 16:05:41.713][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:05:41.714][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-16 16:05:41.715][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:05:41.716][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-16 16:05:41.717][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-16 16:05:41.717][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:05:41.718][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-16 16:05:41.719][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:05:41.720][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-16 16:05:41.721][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-16 16:05:41.722][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:05:41.723][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-16 16:05:41.724][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:05:41.724][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-16 16:05:41.729][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-16 16:05:41.730][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:05:41.731][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[2025-08-16 16:05:41.732][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:05:41.732][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-16 16:05:41.733][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-16 16:05:41.734][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:05:41.735][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-16 16:05:41.736][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:05:41.737][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-16 16:05:41.738][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-16 16:05:41.738][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:05:41.739][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-16 16:05:41.740][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:05:41.741][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-16 16:05:41.742][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-16 16:05:41.743][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:05:41.744][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-16 16:05:41.750][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:05:41.752][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-16 16:05:41.753][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-16 16:05:41.754][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:05:41.755][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-16 16:05:41.756][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:05:41.757][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-16 16:05:41.758][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-16 16:05:41.759][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:05:41.760][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[2025-08-16 16:05:41.762][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:05:41.763][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-16 16:05:41.764][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-16 16:05:41.765][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:05:41.766][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[2025-08-16 16:05:41.767][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:05:41.768][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-16 16:05:41.769][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-16 16:05:41.770][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:05:41.771][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[2025-08-16 16:05:41.772][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:05:41.773][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-16 16:05:41.774][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-16 16:05:41.775][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:05:41.776][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-16 16:05:41.777][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-08-16 16:05:41.783][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-08-16 16:05:41.785][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-08-16 16:05:41.786][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-08-16 16:05:41.788][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-08-16 16:05:41.789][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-08-16 16:05:41.791][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-08-16 16:05:41.792][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-08-16 16:05:41.794][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-08-16 16:05:41.795][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-08-16 16:05:41.797][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-08-16 16:05:41.798][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-08-16 16:05:41.800][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-08-16 16:05:41.801][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-08-16 16:05:41.802][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-08-16 16:05:41.804][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-08-16 16:05:41.806][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-08-16 16:05:41.807][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-08-16 16:05:41.809][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-08-16 16:05:41.810][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-08-16 16:05:41.812][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-08-16 16:05:41.813][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-08-16 16:05:41.815][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-08-16 16:05:41.816][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-08-16 16:05:41.818][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-08-16 16:05:41.819][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-08-16 16:05:41.821][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-08-16 16:05:41.822][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-08-16 16:05:41.824][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-08-16 16:05:41.825][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-08-16 16:05:41.827][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-08-16 16:05:41.828][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-08-16 16:05:41.830][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-08-16 16:05:41.831][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-08-16 16:05:41.833][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-08-16 16:05:41.834][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-08-16 16:05:41.836][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-08-16 16:05:41.837][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-08-16 16:05:41.839][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-08-16 16:05:41.840][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-08-16 16:05:41.842][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-08-16 16:05:41.843][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-08-16 16:05:41.845][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-08-16 16:05:41.846][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-08-16 16:05:41.848][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-08-16 16:05:41.849][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-08-16 16:05:41.851][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-08-16 16:05:41.852][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-08-16 16:05:41.854][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-08-16 16:05:41.855][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-08-16 16:05:41.857][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-08-16 16:05:41.858][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-08-16 16:05:41.860][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-08-16 16:05:41.861][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-08-16 16:05:41.863][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-08-16 16:05:41.864][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-08-16 16:05:41.866][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-08-16 16:05:41.867][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-08-16 16:05:41.869][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-08-16 16:05:41.870][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-08-16 16:05:41.872][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-08-16 16:05:41.873][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-08-16 16:05:41.875][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-08-16 16:05:41.876][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-08-16 16:05:41.878][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-08-16 16:05:41.879][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-08-16 16:05:41.881][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-08-16 16:05:41.882][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-08-16 16:05:41.884][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-08-16 16:05:41.885][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-08-16 16:05:41.887][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-08-16 16:05:41.888][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-08-16 16:05:41.890][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-08-16 16:05:41.891][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-08-16 16:05:41.893][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-08-16 16:05:41.894][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-08-16 16:05:41.896][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-08-16 16:05:41.897][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-08-16 16:05:41.899][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-08-16 16:05:41.900][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-08-16 16:05:41.902][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-08-16 16:05:41.903][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-08-16 16:05:41.905][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-08-16 16:05:41.912][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-08-16 16:05:41.913][initialize] This is biodb version 1.16.0.
biodb.DEBUG[2025-08-16 16:05:41.917][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-08-16 16:05:41.918][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-08-16 16:05:41.919][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-16 16:05:41.920][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:05:41.921][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-16 16:05:41.937][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:05:41.938][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-16 16:05:41.939][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-16 16:05:41.940][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-16 16:05:41.941][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-16 16:05:41.941][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:05:41.942][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-16 16:05:41.943][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:05:41.944][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-16 16:05:41.945][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-16 16:05:41.946][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-16 16:05:41.947][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-16 16:05:41.948][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:05:41.949][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-16 16:05:41.950][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:05:41.951][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-16 16:05:41.952][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-16 16:05:41.953][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-16 16:05:41.954][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-16 16:05:41.955][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:05:41.956][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-16 16:05:41.956][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:05:41.957][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-16 16:05:41.958][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-16 16:05:41.959][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-16 16:05:41.960][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-16 16:05:41.961][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:05:41.962][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-16 16:05:41.962][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:05:41.963][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-16 16:05:41.964][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-16 16:05:41.965][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-16 16:05:41.966][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-16 16:05:41.967][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:05:41.968][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[2025-08-16 16:05:41.968][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:05:41.969][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-16 16:05:41.970][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-16 16:05:41.971][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-16 16:05:41.972][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-16 16:05:41.973][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:05:41.974][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-16 16:05:41.975][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:05:41.976][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-16 16:05:41.976][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-16 16:05:41.977][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-16 16:05:41.978][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-16 16:05:41.979][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:05:41.980][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-16 16:05:41.981][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:05:41.982][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-16 16:05:41.982][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-16 16:05:41.983][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-16 16:05:41.984][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-16 16:05:41.985][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:05:41.986][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-16 16:05:41.987][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:05:41.988][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-16 16:05:41.988][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-16 16:05:41.989][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-16 16:05:41.990][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-16 16:05:41.991][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:05:41.992][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-16 16:05:41.993][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:05:41.994][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-16 16:05:41.995][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-16 16:05:41.995][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-16 16:05:41.996][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-16 16:05:41.997][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:05:41.998][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[2025-08-16 16:05:41.999][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:05:42.000][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-16 16:05:42.001][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-16 16:05:42.001][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-16 16:05:42.002][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-16 16:05:42.003][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:05:42.004][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-16 16:05:42.005][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:05:42.006][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-16 16:05:42.007][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-16 16:05:42.008][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-16 16:05:42.008][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-16 16:05:42.009][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:05:42.010][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-16 16:05:42.011][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:05:42.013][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-16 16:05:42.014][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-16 16:05:42.015][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-16 16:05:42.017][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-16 16:05:42.017][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:05:42.018][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-16 16:05:42.019][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:05:42.020][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-16 16:05:42.021][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-16 16:05:42.022][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-16 16:05:42.023][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-16 16:05:42.024][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:05:42.024][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-16 16:05:42.025][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:05:42.026][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-16 16:05:42.027][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-16 16:05:42.028][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-16 16:05:42.029][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-16 16:05:42.030][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:05:42.031][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[2025-08-16 16:05:42.031][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:05:42.032][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-16 16:05:42.033][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-16 16:05:42.034][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-16 16:05:42.035][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-16 16:05:42.036][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:05:42.037][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[2025-08-16 16:05:42.038][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:05:42.038][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-16 16:05:42.039][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-16 16:05:42.040][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-16 16:05:42.041][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-16 16:05:42.042][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:05:42.043][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-16 16:05:42.045][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.21-bioc-longtests/meat/biodbNci.Rcheck/biodbNci/definitions.yml".
biodb.DEBUG[2025-08-16 16:05:42.054][self$getDbsInfo()$define] Define connector nci.cactus.
biodb.DEBUG[2025-08-16 16:05:42.056][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-08-16 16:05:42.057][self$setPropertyValue] Setting property "description" to "National Cancer Institute (USA) CACTUS Database.".
biodb.DEBUG[2025-08-16 16:05:42.058][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-08-16 16:05:42.059][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-08-16 16:05:42.060][self$setPropertyValue] Setting property "downloadable" to "TRUE".
biodb.DEBUG[2025-08-16 16:05:42.061][self$setPropertyValue] Setting property "dwnld.ext" to "gz".
biodb.DEBUG[2025-08-16 16:05:42.062][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-08-16 16:05:42.063][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-08-16 16:05:42.064][self$setPropertyValue] Setting property "entry.content.type" to "sdf".
biodb.DEBUG[2025-08-16 16:05:42.065][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-08-16 16:05:42.066][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-08-16 16:05:42.067][self$setPropertyValue] Setting property "name" to "NCI CACTUS".
biodb.DEBUG[2025-08-16 16:05:42.068][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-08-16 16:05:42.069][self$setPropertyValue] Setting property "parsing.expr" to "NSC".
biodb.DEBUG[2025-08-16 16:05:42.069][self$setPropertyValue] Setting property "parsing.expr" to "DTP names".
biodb.DEBUG[2025-08-16 16:05:42.069][self$setPropertyValue] Setting property "parsing.expr" to "Standard InChI".
biodb.DEBUG[2025-08-16 16:05:42.069][self$setPropertyValue] Setting property "parsing.expr" to "c("Standard InChIKey", "^InChIKey=(.*)$")".
biodb.DEBUG[2025-08-16 16:05:42.069][self$setPropertyValue] Setting property "parsing.expr" to "Formula".
biodb.DEBUG[2025-08-16 16:05:42.069][self$setPropertyValue] Setting property "parsing.expr" to "Molecular Weight".
biodb.DEBUG[2025-08-16 16:05:42.069][self$setPropertyValue] Setting property "parsing.expr" to "CAS".
biodb.DEBUG[2025-08-16 16:05:42.070][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-08-16 16:05:42.071][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-08-16 16:05:42.072][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-08-16 16:05:42.073][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-16 16:05:42.074][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-16 16:05:42.075][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-08-16 16:05:42.076][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-16 16:05:42.077][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-16 16:05:42.077][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-08-16 16:05:42.078][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/".
biodb.DEBUG[2025-08-16 16:05:42.078][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/".
biodb.DEBUG[2025-08-16 16:05:42.078][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/download/nci/".
biodb.DEBUG[2025-08-16 16:05:42.078][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/download/nci/NCI-Open_2012-05-01.sdf.gz".
biodb.DEBUG[2025-08-16 16:05:42.080][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-08-16 16:05:42.080][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-08-16 16:05:42.081][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-08-16 16:05:42.082][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-08-16 16:05:42.088][self$getEntryFields()$define] Define field nci.cactus.id.
biodb.DEBUG[2025-08-16 16:05:42.110][super$initialize] Initialize connector nci.cactus.
biodb.DEBUG[2025-08-16 16:05:42.111][super$initialize] Register connector nci.cactus with the request scheduler
biodb.DEBUG[2025-08-16 16:05:42.115][private$bdb$getRequestScheduler()$re ...] Register connector nci.cactus.
biodb.DEBUG[2025-08-16 16:05:42.146][private$addConnectorRules] Create new rule for URL "cactus.nci.nih.gov" of connector "nci.cactus".
biodb.DEBUG[2025-08-16 16:05:42.150][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-08-16 16:05:42.151][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-08-16 16:05:42.152][rule$addConnector] Connector "nci.cactus" is already listed in rule "cactus.nci.nih.gov".
biodb.DEBUG[2025-08-16 16:05:42.153][rule$addConnector] Connector "nci.cactus" is already listed in rule "cactus.nci.nih.gov".
biodb.DEBUG[2025-08-16 16:05:42.155][rule$addConnector] Connector "nci.cactus" is already listed in rule "cactus.nci.nih.gov".
biodb.DEBUG[2025-08-16 16:05:42.156][biodb$getFactory()$createConn] Creating new connector nci.cactus for database class nci.cactus .
biodb.INFO [2025-08-16 16:05:42.164][biodb::testThat]
biodb.INFO [2025-08-16 16:05:42.165][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2025-08-16 16:05:42.166][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-08-16 16:05:42.167][biodb::testThat]
biodb.TRACE[2025-08-16 16:05:42.170][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/bbs-3.21-bioc-longtests/meat/biodbNci.Rcheck/biodbNci/testref/entry-nci.cactus-749674-content.sdf".
biodb.DEBUG[2025-08-16 16:05:42.171][biodb$getFactory()$createEntryFromCo ...] Creating NCI CACTUS entries from 1 content(s).
biodb.DEBUG[2025-08-16 16:05:42.174][biodb$getFactory()$createEntryFromCo ...] Parsing 1 NCI CACTUS entries.
biodb.DEBUG[2025-08-16 16:05:42.182][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-16 16:05:42.183][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-16 16:05:42.183][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-16 16:05:42.195][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-16 16:05:42.196][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-16 16:05:42.197][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:05:42.197][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-16 16:05:42.214][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-16 16:05:42.215][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-16 16:05:42.216][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:05:42.217][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:05:42.218][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-16 16:05:42.230][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-16 16:05:42.231][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:05:42.232][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:05:42.234][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-08-16 16:05:42.235][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-16 16:05:42.236][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:05:42.237][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:05:42.261][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-08-16 16:05:42.262][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-16 16:05:42.263][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:05:42.264][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:05:42.266][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-16 16:05:42.267][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-16 16:05:42.268][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:05:42.268][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:05:42.269][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-16 16:05:42.270][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-16 16:05:42.271][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:05:42.272][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:05:42.274][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-08-16 16:05:42.275][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-16 16:05:42.276][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:05:42.277][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:05:42.278][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-08-16 16:05:42.279][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-16 16:05:42.280][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:05:42.281][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:05:42.282][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-16 16:05:42.283][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-16 16:05:42.284][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:05:42.285][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:05:42.286][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-16 16:05:42.287][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-16 16:05:42.288][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:05:42.289][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:05:42.291][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-08-16 16:05:42.292][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-08-16 16:05:42.292][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:05:42.293][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:05:42.294][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-08-16 16:05:42.295][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-08-16 16:05:42.296][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:05:42.297][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:05:42.298][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-16 16:05:42.299][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-16 16:05:42.300][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:05:42.301][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:05:42.302][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-08-16 16:05:42.303][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-08-16 16:05:42.304][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:05:42.305][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:05:42.306][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-16 16:05:42.307][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-16 16:05:42.315][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:05:42.316][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:05:42.317][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-16 16:05:42.318][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-16 16:05:42.319][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:05:42.320][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:05:42.321][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-16 16:05:42.322][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-16 16:05:42.323][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:05:42.323][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:05:42.355][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-16 16:05:42.356][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-16 16:05:42.357][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:05:42.358][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:05:42.359][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-16 16:05:42.360][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-16 16:05:42.361][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:05:42.362][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:05:42.363][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-16 16:05:42.364][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-16 16:05:42.365][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:05:42.366][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-16 16:05:42.367][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 749674.
biodb.TRACE[2025-08-16 16:05:42.369][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-08-16 16:05:42.370][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-08-16 16:05:42.371][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:05:42.372][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:05:42.373][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-08-16 16:05:42.374][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-08-16 16:05:42.375][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:05:42.376][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:05:42.377][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-08-16 16:05:42.378][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-08-16 16:05:42.379][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:05:42.380][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:05:42.381][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-08-16 16:05:42.382][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-08-16 16:05:42.383][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:05:42.384][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:05:42.398][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-16 16:05:42.399][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-16 16:05:42.400][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:05:42.401][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:05:42.413][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-08-16 16:05:42.414][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-08-16 16:05:42.415][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:05:42.416][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:05:42.421][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-16 16:05:42.422][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-16 16:05:42.422][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:05:42.423][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:05:42.424][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-16 16:05:42.425][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-16 16:05:42.426][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:05:42.427][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:05:42.428][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-16 16:05:42.429][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-16 16:05:42.430][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:05:42.431][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:05:42.434][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-16 16:05:42.435][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-16 16:05:42.436][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:05:42.436][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:05:42.437][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-16 16:05:42.438][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-16 16:05:42.439][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:05:42.440][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:05:42.441][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-16 16:05:42.442][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-16 16:05:42.443][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:05:42.448][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:05:42.449][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-08-16 16:05:42.450][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-08-16 16:05:42.451][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:05:42.452][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:05:42.453][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-08-16 16:05:42.454][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-08-16 16:05:42.455][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:05:42.456][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:05:42.457][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-08-16 16:05:42.458][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-08-16 16:05:42.459][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:05:42.460][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:05:42.466][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-16 16:05:42.467][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-16 16:05:42.468][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:05:42.469][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:05:42.470][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-16 16:05:42.471][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-16 16:05:42.472][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:05:42.473][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:05:42.474][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-16 16:05:42.475][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-16 16:05:42.476][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:05:42.477][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:05:42.478][ef$get] Asked field names are: accession.
biodb.TRACE[2025-08-16 16:05:42.479][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-16 16:05:42.480][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:05:42.481][ef$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:05:42.482][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-16 16:05:42.483][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-16 16:05:42.484][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:05:42.485][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:05:42.492][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-08-16 16:05:42.494][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-16 16:05:42.494][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:05:42.495][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:05:42.496][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-08-16 16:05:42.497][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-16 16:05:42.498][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:05:42.499][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:05:42.500][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-08-16 16:05:42.501][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-16 16:05:42.502][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:05:42.503][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:05:42.504][ef$get] Asked field names are: formula.
biodb.TRACE[2025-08-16 16:05:42.505][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-16 16:05:42.506][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:05:42.507][ef$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:05:42.508][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-08-16 16:05:42.509][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-16 16:05:42.510][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:05:42.511][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:05:42.518][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-16 16:05:42.519][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-16 16:05:42.520][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:05:42.521][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:05:42.522][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-16 16:05:42.523][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-16 16:05:42.524][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:05:42.525][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:05:42.526][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-16 16:05:42.527][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-16 16:05:42.528][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:05:42.529][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:05:42.530][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-16 16:05:42.531][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-16 16:05:42.532][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:05:42.533][ef$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:05:42.534][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-16 16:05:42.535][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-16 16:05:42.536][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:05:42.536][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:05:42.544][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-08-16 16:05:42.545][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-16 16:05:42.546][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:05:42.547][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:05:42.548][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-08-16 16:05:42.549][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-16 16:05:42.550][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:05:42.550][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:05:42.551][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-08-16 16:05:42.552][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-16 16:05:42.553][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:05:42.554][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:05:42.555][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-08-16 16:05:42.556][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-16 16:05:42.557][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:05:42.558][ef$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:05:42.559][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-08-16 16:05:42.560][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-16 16:05:42.561][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:05:42.562][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:05:42.569][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-16 16:05:42.570][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-16 16:05:42.571][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:05:42.572][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:05:42.573][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-16 16:05:42.574][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-16 16:05:42.575][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:05:42.576][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:05:42.577][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-16 16:05:42.578][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-16 16:05:42.579][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:05:42.580][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:05:42.581][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-16 16:05:42.582][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-16 16:05:42.583][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:05:42.584][ef$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:05:42.588][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-16 16:05:42.589][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-16 16:05:42.590][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:05:42.591][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:05:42.598][ef$get] Asked field names are: accession.
biodb.TRACE[2025-08-16 16:05:42.599][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-16 16:05:42.600][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:05:42.601][ef$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:05:42.605][ef$get] Asked field names are: formula.
biodb.TRACE[2025-08-16 16:05:42.606][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-16 16:05:42.607][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:05:42.608][ef$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:05:42.612][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-08-16 16:05:42.613][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-16 16:05:42.614][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:05:42.615][ef$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:05:42.618][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-16 16:05:42.620][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-16 16:05:42.620][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:05:42.621][ef$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:05:42.625][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-16 16:05:42.626][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-16 16:05:42.627][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:05:42.628][ef$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:05:42.644][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/bbs-3.21-bioc-longtests/meat/biodbNci.Rcheck/biodbNci/testref/entry-nci.cactus-750690-content.sdf".
biodb.DEBUG[2025-08-16 16:05:42.677][biodb$getFactory()$createEntryFromCo ...] Creating NCI CACTUS entries from 1 content(s).
biodb.DEBUG[2025-08-16 16:05:42.679][biodb$getFactory()$createEntryFromCo ...] Parsing 1 NCI CACTUS entries.
biodb.DEBUG[2025-08-16 16:05:42.680][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-16 16:05:42.681][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-16 16:05:42.682][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-16 16:05:42.686][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-16 16:05:42.687][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-16 16:05:42.688][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:05:42.689][FUN] Functions in observer BiodbConfig: [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[2025-08-16 16:05:42.698][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-16 16:05:42.699][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-16 16:05:42.700][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:05:42.700][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:05:42.702][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-16 16:05:42.703][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-16 16:05:42.703][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:05:42.704][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:05:42.726][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-08-16 16:05:42.727][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-08-16 16:05:42.728][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:05:42.728][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:05:42.729][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-08-16 16:05:42.730][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-08-16 16:05:42.731][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:05:42.732][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:05:42.734][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-08-16 16:05:42.735][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-16 16:05:42.736][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:05:42.737][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:05:42.738][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-08-16 16:05:42.739][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-16 16:05:42.740][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:05:42.741][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:05:42.742][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-16 16:05:42.743][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-16 16:05:42.744][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:05:42.745][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:05:42.746][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-16 16:05:42.747][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-16 16:05:42.748][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:05:42.749][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:05:42.750][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-16 16:05:42.751][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-16 16:05:42.752][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:05:42.753][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:05:42.754][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-16 16:05:42.755][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-16 16:05:42.756][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:05:42.757][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:05:42.758][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-16 16:05:42.759][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-16 16:05:42.760][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:05:42.761][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:05:42.762][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-16 16:05:42.763][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-16 16:05:42.764][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:05:42.765][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:05:42.766][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-16 16:05:42.767][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-16 16:05:42.768][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:05:42.769][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:05:42.769][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-16 16:05:42.771][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-16 16:05:42.771][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:05:42.772][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:05:42.773][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-16 16:05:42.774][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-16 16:05:42.775][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:05:42.776][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:05:42.778][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-08-16 16:05:42.779][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-16 16:05:42.780][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:05:42.781][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:05:42.782][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-08-16 16:05:42.783][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-16 16:05:42.784][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:05:42.785][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:05:42.786][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-16 16:05:42.787][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-16 16:05:42.788][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:05:42.789][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:05:42.790][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-16 16:05:42.791][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-16 16:05:42.792][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:05:42.793][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:05:42.795][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-08-16 16:05:42.796][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-08-16 16:05:42.796][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:05:42.797][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:05:42.798][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-08-16 16:05:42.799][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-08-16 16:05:42.800][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:05:42.801][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:05:42.802][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-16 16:05:42.803][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-16 16:05:42.804][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:05:42.805][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:05:42.806][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-08-16 16:05:42.807][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-08-16 16:05:42.808][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:05:42.809][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:05:42.810][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-16 16:05:42.811][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-16 16:05:42.812][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:05:42.813][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:05:42.814][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-16 16:05:42.815][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-16 16:05:42.816][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:05:42.817][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:05:42.818][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-16 16:05:42.819][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-16 16:05:42.820][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:05:42.821][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:05:42.822][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-16 16:05:42.823][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-16 16:05:42.824][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:05:42.825][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:05:42.826][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-16 16:05:42.827][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-16 16:05:42.827][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:05:42.828][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:05:42.829][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-16 16:05:42.830][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-16 16:05:42.831][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:05:42.832][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-16 16:05:42.833][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 750690.
biodb.TRACE[2025-08-16 16:05:42.856][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-08-16 16:05:42.857][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-08-16 16:05:42.858][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:05:42.859][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:05:42.860][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-08-16 16:05:42.861][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-08-16 16:05:42.862][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:05:42.862][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:05:42.863][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-08-16 16:05:42.864][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-08-16 16:05:42.865][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:05:42.866][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:05:42.867][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-08-16 16:05:42.868][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-08-16 16:05:42.869][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:05:42.870][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:05:42.872][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-16 16:05:42.873][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-16 16:05:42.874][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:05:42.875][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:05:42.879][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-08-16 16:05:42.880][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-08-16 16:05:42.881][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:05:42.882][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:05:42.886][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-16 16:05:42.887][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-16 16:05:42.888][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:05:42.889][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:05:42.890][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-16 16:05:42.891][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-16 16:05:42.892][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:05:42.893][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:05:42.894][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-16 16:05:42.895][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-16 16:05:42.896][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:05:42.897][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:05:42.899][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-16 16:05:42.900][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-16 16:05:42.901][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:05:42.902][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:05:42.903][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-16 16:05:42.904][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-16 16:05:42.905][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:05:42.906][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:05:42.907][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-16 16:05:42.908][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-16 16:05:42.909][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:05:42.910][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:05:42.911][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-08-16 16:05:42.912][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-08-16 16:05:42.913][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:05:42.914][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:05:42.915][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-08-16 16:05:42.916][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-08-16 16:05:42.917][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:05:42.918][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:05:42.919][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-08-16 16:05:42.920][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-08-16 16:05:42.921][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:05:42.922][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:05:42.937][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-16 16:05:42.938][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-16 16:05:42.939][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:05:42.940][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:05:42.941][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-16 16:05:42.942][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-16 16:05:42.943][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:05:42.944][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:05:42.945][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-16 16:05:42.946][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-16 16:05:42.947][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:05:42.948][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:05:42.949][ef$get] Asked field names are: accession.
biodb.TRACE[2025-08-16 16:05:42.950][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-16 16:05:42.951][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:05:42.952][ef$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:05:42.953][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-16 16:05:42.954][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-16 16:05:42.955][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:05:42.956][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:05:42.963][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-08-16 16:05:42.964][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-08-16 16:05:42.965][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:05:42.966][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:05:42.967][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-08-16 16:05:42.968][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-08-16 16:05:42.969][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:05:42.970][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:05:42.971][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-08-16 16:05:42.972][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-08-16 16:05:42.973][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:05:42.974][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:05:42.975][ef$get] Asked field names are: cas.id.
biodb.TRACE[2025-08-16 16:05:42.976][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-08-16 16:05:42.977][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:05:42.978][ef$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:05:42.978][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-08-16 16:05:42.979][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-08-16 16:05:42.984][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:05:42.985][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:05:42.993][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-16 16:05:42.994][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-16 16:05:42.995][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:05:42.995][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:05:42.996][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-16 16:05:42.997][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-16 16:05:42.998][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:05:42.999][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:05:43.000][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-16 16:05:43.001][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-16 16:05:43.002][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:05:43.003][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:05:43.004][ef$get] Asked field names are: name.
biodb.TRACE[2025-08-16 16:05:43.005][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-08-16 16:05:43.006][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:05:43.007][ef$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:05:43.008][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-16 16:05:43.009][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-16 16:05:43.010][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:05:43.011][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:05:43.018][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-08-16 16:05:43.019][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-16 16:05:43.020][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:05:43.021][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:05:43.022][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-08-16 16:05:43.023][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-16 16:05:43.024][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:05:43.025][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:05:43.026][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-08-16 16:05:43.027][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-16 16:05:43.028][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:05:43.029][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:05:43.030][ef$get] Asked field names are: formula.
biodb.TRACE[2025-08-16 16:05:43.031][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-16 16:05:43.032][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:05:43.033][ef$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:05:43.034][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-08-16 16:05:43.035][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-16 16:05:43.036][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:05:43.037][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:05:43.044][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-16 16:05:43.045][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-16 16:05:43.046][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:05:43.047][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:05:43.048][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-16 16:05:43.049][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-16 16:05:43.050][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:05:43.051][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:05:43.052][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-16 16:05:43.053][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-16 16:05:43.054][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:05:43.054][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:05:43.055][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-16 16:05:43.056][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-16 16:05:43.057][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:05:43.058][ef$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:05:43.059][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-16 16:05:43.060][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-16 16:05:43.061][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:05:43.062][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:05:43.070][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-08-16 16:05:43.071][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-16 16:05:43.072][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:05:43.073][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:05:43.073][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-08-16 16:05:43.075][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-16 16:05:43.076][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:05:43.076][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:05:43.077][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-08-16 16:05:43.078][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-16 16:05:43.079][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:05:43.080][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:05:43.081][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-08-16 16:05:43.082][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-16 16:05:43.083][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:05:43.084][ef$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:05:43.085][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-08-16 16:05:43.086][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-16 16:05:43.087][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:05:43.088][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:05:43.095][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-16 16:05:43.096][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-16 16:05:43.097][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:05:43.098][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:05:43.099][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-16 16:05:43.100][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-16 16:05:43.101][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:05:43.102][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:05:43.103][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-16 16:05:43.104][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-16 16:05:43.105][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:05:43.106][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:05:43.107][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-16 16:05:43.108][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-16 16:05:43.109][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:05:43.110][ef$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:05:43.111][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-16 16:05:43.112][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-16 16:05:43.113][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:05:43.114][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:05:43.125][ef$get] Asked field names are: accession.
biodb.TRACE[2025-08-16 16:05:43.126][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-16 16:05:43.127][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:05:43.128][ef$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:05:43.132][ef$get] Asked field names are: cas.id.
biodb.TRACE[2025-08-16 16:05:43.133][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-08-16 16:05:43.134][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:05:43.134][ef$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:05:43.138][ef$get] Asked field names are: formula.
biodb.TRACE[2025-08-16 16:05:43.139][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-16 16:05:43.140][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:05:43.141][ef$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:05:43.145][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-08-16 16:05:43.146][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-16 16:05:43.147][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:05:43.148][ef$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:05:43.152][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-16 16:05:43.153][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-16 16:05:43.154][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:05:43.155][ef$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:05:43.159][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-16 16:05:43.160][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-16 16:05:43.161][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:05:43.162][ef$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:05:43.166][ef$get] Asked field names are: name.
biodb.TRACE[2025-08-16 16:05:43.167][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-08-16 16:05:43.168][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:05:43.168][ef$get] fields variable is a list.
biodb.INFO [2025-08-16 16:05:43.175][biodb::testThat]
biodb.INFO [2025-08-16 16:05:43.176][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2025-08-16 16:05:43.177][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-08-16 16:05:43.178][biodb::testThat]
biodb.DEBUG[2025-08-16 16:05:43.180][private$loadEntries] Creating entries from ids [2]: "749674, 750690".
biodb.DEBUG[2025-08-16 16:05:43.186][conn$getEntryContent] Get NCI CACTUS entry content(s) for 2 id(s)...
biodb.DEBUG[2025-08-16 16:05:43.190][self$isDownloaded] Database nci.cactus has not yet been downloaded.
biodb.INFO [2025-08-16 16:05:43.191][self$download] Downloading whole database of nci.cactus.
biodb.INFO [2025-08-16 16:05:43.193][private$doDownload] Downloading NCI CACTUS database at "https://cactus.nci.nih.gov/download/nci/NCI-Open_2012-05-01.sdf.gz" ...
biodb.DEBUG[2025-08-16 16:05:43.194][sched$downloadFile] Downloading file "https://cactus.nci.nih.gov/download/nci/NCI-Open_2012-05-01.sdf.gz".
trying URL 'https://cactus.nci.nih.gov/download/nci/NCI-Open_2012-05-01.sdf.gz'
Content type 'application/x-gzip' length 206737123 bytes (197.2 MB)
==================================================
downloaded 197.2 MB

biodb.TRACE[2025-08-16 16:06:15.329][cch$addFilesToCache] Moving files to cache [1]: "/home/biocbuild/.cache/R/biodb/tmp/nci.cactus14a2051b3d9aeegz".
biodb.TRACE[2025-08-16 16:06:15.331][private$doAddFilesToCache] Destination files are [1]: "/home/biocbuild/.cache/R/biodb/nci.cactus-8efc65070d01b214e760b1d4932ee427/download.gz".
biodb.DEBUG[2025-08-16 16:06:15.332][cch$addFilesToCache] Done adding files.
biodb.DEBUG[2025-08-16 16:06:15.334][self$getDownloadPath] Download path of nci.cactus is "/home/biocbuild/.cache/R/biodb/nci.cactus-8efc65070d01b214e760b1d4932ee427/download.gz".
biodb.DEBUG[2025-08-16 16:06:15.335][self$download] Downloading of nci.cactus completed.
biodb.TRACE[2025-08-16 16:06:15.337][self$addFilesToCache] Moving files to cache [1]: "/home/biocbuild/.cache/R/biodb/tmp/marker14a205396efd11marker".
biodb.TRACE[2025-08-16 16:06:15.338][private$doAddFilesToCache] Destination files are [1]: "/home/biocbuild/.cache/R/biodb/nci.cactus-8efc65070d01b214e760b1d4932ee427/downloaded.marker".
biodb.DEBUG[2025-08-16 16:06:15.339][self$addFilesToCache] Done adding files.
biodb.DEBUG[2025-08-16 16:06:15.340][self$isDownloaded] Database nci.cactus has already been downloaded.
biodb.INFO [2025-08-16 16:06:15.342][self$download] Extract whole database of nci.cactus.
biodb.INFO [2025-08-16 16:06:15.343][private$doExtractDownload] Extracting content of downloaded biodbNci, a library for connecting to the National Cancer Institute (USA) CACTUS Database....
biodb.DEBUG[2025-08-16 16:06:15.344][self$getDownloadPath] Download path of nci.cactus is "/home/biocbuild/.cache/R/biodb/nci.cactus-8efc65070d01b214e760b1d4932ee427/download.gz".
biodb.DEBUG[2025-08-16 16:07:19.211][private$doExtractDownload] Delete existing entry files in cache system.
biodb.DEBUG[2025-08-16 16:07:19.215][private$doExtractDownload] Extract single entries from downloaded file "/home/biocbuild/.cache/R/biodb/tmp/cactus_rdfs", into "/home/biocbuild/.cache/R/biodb/tmp".
biodb.TRACE[2025-08-16 16:17:27.100][self$addFilesToCache] Moving files to cache [265242]: "/home/biocbuild/.cache/R/biodb/tmp/entry_1.txt, /home/biocbuild/.cache/R/biodb/tmp/entry_2.txt, /home/biocbuild/.cache/R/biodb/tmp/entry_3.txt, /home/biocbuild/.cache/R/biodb/tmp/entry_4.txt, /home/biocbuild/.cache/R/biodb/tmp/entry_5.txt, /home/biocbuild/.cache/R/biodb/tmp/entry_6.txt, /home/biocbuild/.cache/R/biodb/tmp/entry_7.txt, /home/biocbuild/.cache/R/biodb/tmp/entry_8.txt, /home/biocbuild/.cache/R/biodb/tmp/entry_9.txt, /home/biocbuild/.cache/R/biodb/tmp/entry_10.txt, ...".
biodb.TRACE[2025-08-16 16:17:27.492][private$doAddFilesToCache] Destination files are [265242]: "/home/biocbuild/.cache/R/biodb/nci.cactus-8efc65070d01b214e760b1d4932ee427/1.sdf, /home/biocbuild/.cache/R/biodb/nci.cactus-8efc65070d01b214e760b1d4932ee427/2.sdf, /home/biocbuild/.cache/R/biodb/nci.cactus-8efc65070d01b214e760b1d4932ee427/3.sdf, /home/biocbuild/.cache/R/biodb/nci.cactus-8efc65070d01b214e760b1d4932ee427/4.sdf, /home/biocbuild/.cache/R/biodb/nci.cactus-8efc65070d01b214e760b1d4932ee427/5.sdf, /home/biocbuild/.cache/R/biodb/nci.cactus-8efc65070d01b214e760b1d4932ee427/6.sdf, /home/biocbuild/.cache/R/biodb/nci.cactus-8efc65070d01b214e760b1d4932ee427/7.sdf, /home/biocbuild/.cache/R/biodb/nci.cactus-8efc65070d01b214e760b1d4932ee427/8.sdf, /home/biocbuild/.cache/R/biodb/nci.cactus-8efc65070d01b214e760b1d4932ee427/9.sdf, /home/biocbuild/.cache/R/biodb/nci.cactus-8efc65070d01b214e760b1d4932ee427/10.sdf, ...".
biodb.DEBUG[2025-08-16 16:17:36.163][self$addFilesToCache] Done adding files.
biodb.DEBUG[2025-08-16 16:17:36.165][private$doExtractDownload] Delete extracted database.
biodb.TRACE[2025-08-16 16:17:36.173][self$addFilesToCache] Moving files to cache [1]: "/home/biocbuild/.cache/R/biodb/tmp/marker14a2054a5dabb4marker".
biodb.TRACE[2025-08-16 16:17:36.175][private$doAddFilesToCache] Destination files are [1]: "/home/biocbuild/.cache/R/biodb/nci.cactus-8efc65070d01b214e760b1d4932ee427/extracted.marker".
biodb.DEBUG[2025-08-16 16:17:36.176][self$addFilesToCache] Done adding files.
biodb.TRACE[2025-08-16 16:17:36.178][cch$loadFileContent] Trying to load 2 files from cache: [2]: "749674, 750690".
biodb.TRACE[2025-08-16 16:17:36.179][cch$loadFileContent] file.exist = [2]: "TRUE, TRUE".
biodb.TRACE[2025-08-16 16:17:36.181][loadFileContents] Loaded 2 files from cache: [2]: "/home/biocbuild/.cache/R/biodb/nci.cactus-8efc65070d01b214e760b1d4932ee427/749674.sdf, /home/biocbuild/.cache/R/biodb/nci.cactus-8efc65070d01b214e760b1d4932ee427/750690.sdf".
biodb.DEBUG[2025-08-16 16:17:36.182][conn$getEntryContent] 2 NCI CACTUS entry content(s) loaded from cache.
biodb.DEBUG[2025-08-16 16:17:36.184][self$createEntryFromContent] Creating NCI CACTUS entries from 2 content(s).
biodb.DEBUG[2025-08-16 16:17:36.185][self$createEntryFromContent] Parsing 2 NCI CACTUS entries.
biodb.DEBUG[2025-08-16 16:17:36.187][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-16 16:17:36.188][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-16 16:17:36.189][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-16 16:17:36.194][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-16 16:17:36.195][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-16 16:17:36.196][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:17:36.197][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-16 16:17:36.206][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-16 16:17:36.208][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-16 16:17:36.209][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:17:36.210][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:17:36.211][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-16 16:17:36.212][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-16 16:17:36.213][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:17:36.214][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:17:36.217][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-08-16 16:17:36.218][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-16 16:17:36.219][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:17:36.220][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:17:36.221][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-08-16 16:17:36.223][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-16 16:17:36.224][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:17:36.225][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:17:36.226][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-16 16:17:36.227][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-16 16:17:36.228][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:17:36.229][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:17:36.231][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-16 16:17:36.232][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-16 16:17:36.233][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:17:36.234][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:17:36.236][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-08-16 16:17:36.237][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-16 16:17:36.238][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:17:36.239][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:17:36.240][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-08-16 16:17:36.241][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-16 16:17:36.242][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:17:36.243][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:17:36.245][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-16 16:17:36.246][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-16 16:17:36.247][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:17:36.248][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:17:36.249][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-16 16:17:36.250][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-16 16:17:36.251][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:17:36.252][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:17:36.254][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-08-16 16:17:36.255][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-08-16 16:17:36.256][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:17:36.257][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:17:36.259][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-08-16 16:17:36.260][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-08-16 16:17:36.261][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:17:36.262][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:17:36.263][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-16 16:17:36.264][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-16 16:17:36.265][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:17:36.266][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:17:36.267][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-08-16 16:17:36.268][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-08-16 16:17:36.269][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:17:36.270][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:17:36.271][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-16 16:17:36.272][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-16 16:17:36.273][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:17:36.275][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:17:36.276][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-16 16:17:36.277][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-16 16:17:36.278][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:17:36.279][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:17:36.280][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-16 16:17:36.281][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-16 16:17:36.282][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:17:36.283][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-16 16:17:36.284][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-16 16:17:36.285][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-16 16:17:36.286][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-16 16:17:36.291][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-16 16:17:36.292][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-16 16:17:36.293][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:17:36.294][FUN] Functions in observer BiodbConfig: [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[2025-08-16 16:17:36.305][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-16 16:17:36.306][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-16 16:17:36.307][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:17:36.308][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:17:36.309][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-16 16:17:36.310][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-16 16:17:36.311][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:17:36.312][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:17:36.315][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-08-16 16:17:36.316][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-08-16 16:17:36.317][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:17:36.318][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:17:36.319][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-08-16 16:17:36.320][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-08-16 16:17:36.328][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:17:36.329][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:17:36.331][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-08-16 16:17:36.332][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-16 16:17:36.333][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:17:36.334][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:17:36.335][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-08-16 16:17:36.336][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-16 16:17:36.337][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:17:36.338][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:17:36.340][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-16 16:17:36.341][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-16 16:17:36.342][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:17:36.343][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:17:36.344][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-16 16:17:36.345][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-16 16:17:36.346][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:17:36.347][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:17:36.349][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-16 16:17:36.350][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-16 16:17:36.351][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:17:36.352][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:17:36.353][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-16 16:17:36.354][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-16 16:17:36.355][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:17:36.356][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:17:36.358][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-16 16:17:36.359][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-16 16:17:36.360][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:17:36.361][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:17:36.362][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-16 16:17:36.363][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-16 16:17:36.364][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:17:36.365][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:17:36.366][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-16 16:17:36.367][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-16 16:17:36.368][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:17:36.369][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:17:36.371][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-16 16:17:36.372][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-16 16:17:36.373][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:17:36.374][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:17:36.375][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-16 16:17:36.376][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-16 16:17:36.377][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:17:36.378][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:17:36.381][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-08-16 16:17:36.382][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-16 16:17:36.383][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:17:36.384][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:17:36.385][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-08-16 16:17:36.386][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-16 16:17:36.387][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:17:36.388][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:17:36.390][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-16 16:17:36.391][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-16 16:17:36.392][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:17:36.393][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:17:36.394][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-16 16:17:36.395][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-16 16:17:36.396][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:17:36.397][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:17:36.399][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-08-16 16:17:36.401][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-08-16 16:17:36.402][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:17:36.403][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:17:36.404][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-08-16 16:17:36.405][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-08-16 16:17:36.406][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:17:36.407][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:17:36.408][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-16 16:17:36.409][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-16 16:17:36.410][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:17:36.411][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:17:36.413][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-08-16 16:17:36.414][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-08-16 16:17:36.415][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:17:36.416][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:17:36.417][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-16 16:17:36.418][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-16 16:17:36.419][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:17:36.420][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:17:36.422][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-16 16:17:36.423][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-16 16:17:36.424][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:17:36.425][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:17:36.426][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-16 16:17:36.427][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-16 16:17:36.428][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:17:36.429][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:17:36.430][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-16 16:17:36.432][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-16 16:17:36.433][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:17:36.434][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:17:36.435][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-16 16:17:36.436][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-16 16:17:36.437][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:17:36.438][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:17:36.439][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-16 16:17:36.440][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-16 16:17:36.441][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:17:36.442][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:17:36.444][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-16 16:17:36.445][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-16 16:17:36.446][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:17:36.447][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:17:36.448][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-16 16:17:36.449][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-16 16:17:36.450][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:17:36.451][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:17:36.452][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-16 16:17:36.453][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-16 16:17:36.454][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:17:36.455][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-16 16:17:36.456][self$createEntryFromContent] Accession numbers: 749674, 750690.
biodb.TRACE[2025-08-16 16:17:36.458][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2025-08-16 16:17:36.459][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2025-08-16 16:17:36.460][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:17:36.461][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:17:36.462][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2025-08-16 16:17:36.463][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2025-08-16 16:17:36.464][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:17:36.465][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:17:36.466][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2025-08-16 16:17:36.467][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2025-08-16 16:17:36.468][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:17:36.469][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:17:36.475][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2025-08-16 16:17:36.476][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2025-08-16 16:17:36.477][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:17:36.478][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:17:36.479][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2025-08-16 16:17:36.480][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2025-08-16 16:17:36.481][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:17:36.482][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:17:36.483][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2025-08-16 16:17:36.484][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2025-08-16 16:17:36.485][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:17:36.486][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2025-08-16 16:17:36.494][biodb::testThat]
biodb.INFO [2025-08-16 16:17:36.495][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2025-08-16 16:17:36.496][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-08-16 16:17:36.497][biodb::testThat]
biodb.INFO [2025-08-16 16:17:36.503][biodb::testThat]
biodb.INFO [2025-08-16 16:17:36.504][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2025-08-16 16:17:36.505][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-08-16 16:17:36.506][biodb::testThat]
biodb.WARN [2025-08-16 16:17:36.527][self$searchForEntries] This database is not searchable by field "name".
biodb.WARN [2025-08-16 16:17:36.548][self$searchForEntries] This database is not searchable by field "name".
biodb.INFO [2025-08-16 16:17:36.558][biodb::testThat]
biodb.INFO [2025-08-16 16:17:36.559][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2025-08-16 16:17:36.560][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-08-16 16:17:36.561][biodb::testThat]
biodb.TRACE[2025-08-16 16:17:36.586][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-08-16 16:17:36.587][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-08-16 16:17:36.588][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:17:36.590][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:17:36.591][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-08-16 16:17:36.592][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-08-16 16:17:36.593][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:17:36.594][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:17:36.595][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-08-16 16:17:36.596][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-08-16 16:17:36.597][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:17:36.598][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:17:36.599][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-08-16 16:17:36.600][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-08-16 16:17:36.601][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:17:36.602][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:17:36.638][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-08-16 16:17:36.640][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-08-16 16:17:36.641][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:17:36.642][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:17:36.643][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-08-16 16:17:36.644][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-08-16 16:17:36.645][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:17:36.646][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:17:36.647][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-08-16 16:17:36.649][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-08-16 16:17:36.650][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:17:36.651][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:17:36.652][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-08-16 16:17:36.653][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-08-16 16:17:36.654][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:17:36.655][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2025-08-16 16:17:36.661][biodb::testThat]
biodb.INFO [2025-08-16 16:17:36.662][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2025-08-16 16:17:36.663][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-08-16 16:17:36.664][biodb::testThat]
biodb.INFO [2025-08-16 16:17:36.672][biodb::testThat]
biodb.INFO [2025-08-16 16:17:36.673][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2025-08-16 16:17:36.674][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-08-16 16:17:36.675][biodb::testThat]
biodb.INFO [2025-08-16 16:17:36.683][biodb::testThat]
biodb.INFO [2025-08-16 16:17:36.684][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2025-08-16 16:17:36.685][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-08-16 16:17:36.686][biodb::testThat]
biodb.INFO [2025-08-16 16:17:36.692][biodb::testThat]
biodb.INFO [2025-08-16 16:17:36.694][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2025-08-16 16:17:36.695][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-08-16 16:17:36.696][biodb::testThat]
biodb.INFO [2025-08-16 16:17:36.702][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2025-08-16 16:17:36.703][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector nci.cactus from the request scheduler
biodb.INFO [2025-08-16 16:17:36.705][self$deleteConn] Connector "nci.cactus" deleted.
biodb.DEBUG[2025-08-16 16:17:36.706][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-08-16 16:17:36.707][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-16 16:17:36.708][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-16 16:17:36.709][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-16 16:17:36.709][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-16 16:17:36.710][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:17:36.711][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2025-08-16 16:17:36.722][biodb::testContext]
biodb.INFO [2025-08-16 16:17:36.723][biodb::testContext] ********************************************************************************
biodb.INFO [2025-08-16 16:17:36.724][biodb::testContext] Test context - Example long tests
biodb.INFO [2025-08-16 16:17:36.725][biodb::testContext] ********************************************************************************
biodb.INFO [2025-08-16 16:17:36.726][biodb::testContext]
biodb.INFO [2025-08-16 16:17:36.729][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.16.0.
biodb.DEBUG[2025-08-16 16:17:36.730][self$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.21-bioc/R/site-library/biodb/definitions.yml".
biodb.DEBUG[2025-08-16 16:17:36.734][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-08-16 16:17:36.736][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-08-16 16:17:36.737][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-08-16 16:17:36.738][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:17:36.739][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:17:36.740][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-16 16:17:36.741][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-08-16 16:17:36.742][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-08-16 16:17:36.743][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:17:36.744][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:17:36.745][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-16 16:17:36.746][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-08-16 16:17:36.747][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-08-16 16:17:36.748][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:17:36.749][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:17:36.750][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-16 16:17:36.751][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-08-16 16:17:36.752][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-08-16 16:17:36.753][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-08-16 16:17:36.754][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:17:36.755][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:17:36.756][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-16 16:17:36.757][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-08-16 16:17:36.758][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-08-16 16:17:36.759][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-08-16 16:17:36.760][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:17:36.761][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:17:36.762][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-16 16:17:36.763][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-08-16 16:17:36.764][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-08-16 16:17:36.765][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:17:36.766][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:17:36.767][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-16 16:17:36.768][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-08-16 16:17:36.769][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-08-16 16:17:36.770][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-08-16 16:17:36.771][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:17:36.772][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:17:36.773][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-16 16:17:36.774][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-08-16 16:17:36.775][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-08-16 16:17:36.776][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:17:36.777][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:17:36.778][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-16 16:17:36.779][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-08-16 16:17:36.780][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-08-16 16:17:36.782][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-08-16 16:17:36.782][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:17:36.783][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:17:36.784][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-16 16:17:36.785][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-08-16 16:17:36.787][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-08-16 16:17:36.788][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-08-16 16:17:36.789][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-08-16 16:17:36.790][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-08-16 16:17:36.791][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-08-16 16:17:36.792][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:17:36.793][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:17:36.794][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-16 16:17:36.795][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-08-16 16:17:36.796][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-08-16 16:17:36.797][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:17:36.798][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:17:36.799][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[2025-08-16 16:17:36.800][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-08-16 16:17:36.801][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-08-16 16:17:36.802][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:17:36.803][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:17:36.804][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-16 16:17:36.805][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-08-16 16:17:36.806][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-08-16 16:17:36.807][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:17:36.808][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:17:36.809][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-16 16:17:36.810][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-08-16 16:17:36.811][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2025-08-16 16:17:36.812][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:17:36.813][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:17:36.814][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-16 16:17:36.815][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-08-16 16:17:36.816][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-08-16 16:17:36.817][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:17:36.818][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:17:36.819][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-16 16:17:36.820][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-08-16 16:17:36.821][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-08-16 16:17:36.826][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-08-16 16:17:36.827][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:17:36.828][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:17:36.829][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-16 16:17:36.830][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-08-16 16:17:36.831][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-08-16 16:17:36.832][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-08-16 16:17:36.833][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:17:36.834][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:17:36.835][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-16 16:17:36.836][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-08-16 16:17:36.838][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-08-16 16:17:36.839][self$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[2025-08-16 16:17:36.840][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-08-16 16:17:36.841][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-08-16 16:17:36.843][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-08-16 16:17:36.844][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-08-16 16:17:36.845][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-08-16 16:17:36.846][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-08-16 16:17:36.847][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-08-16 16:17:36.848][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-08-16 16:17:36.849][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-08-16 16:17:36.850][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-08-16 16:17:36.851][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-08-16 16:17:36.852][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-08-16 16:17:36.853][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-08-16 16:17:36.854][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-08-16 16:17:36.854][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-08-16 16:17:36.854][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-08-16 16:17:36.854][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-08-16 16:17:36.854][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-08-16 16:17:36.855][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-08-16 16:17:36.856][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-16 16:17:36.857][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-16 16:17:36.858][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-08-16 16:17:36.859][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-16 16:17:36.860][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-16 16:17:36.861][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-08-16 16:17:36.862][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-08-16 16:17:36.863][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-08-16 16:17:36.864][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-08-16 16:17:36.865][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-08-16 16:17:36.867][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-08-16 16:17:36.868][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-08-16 16:17:36.870][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-08-16 16:17:36.871][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-08-16 16:17:36.872][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-08-16 16:17:36.873][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-08-16 16:17:36.874][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-08-16 16:17:36.875][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-08-16 16:17:36.876][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-08-16 16:17:36.877][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-08-16 16:17:36.878][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-08-16 16:17:36.879][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-08-16 16:17:36.880][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-08-16 16:17:36.882][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-08-16 16:17:36.883][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-08-16 16:17:36.884][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-08-16 16:17:36.885][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-08-16 16:17:36.886][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-08-16 16:17:36.886][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-08-16 16:17:36.886][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-08-16 16:17:36.886][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-08-16 16:17:36.886][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-08-16 16:17:36.887][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-08-16 16:17:36.888][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-16 16:17:36.889][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-16 16:17:36.890][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-08-16 16:17:36.891][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-16 16:17:36.892][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-16 16:17:36.893][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-08-16 16:17:36.894][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-08-16 16:17:36.895][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-08-16 16:17:36.896][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-08-16 16:17:36.897][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-08-16 16:17:36.898][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-08-16 16:17:36.899][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-08-16 16:17:36.901][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-08-16 16:17:36.902][self$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[2025-08-16 16:17:36.903][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-08-16 16:17:36.905][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-08-16 16:17:36.906][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-08-16 16:17:36.907][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-08-16 16:17:36.908][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-08-16 16:17:36.909][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-08-16 16:17:36.910][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-08-16 16:17:36.911][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-08-16 16:17:36.912][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-08-16 16:17:36.913][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-08-16 16:17:36.914][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-08-16 16:17:36.915][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-08-16 16:17:36.916][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-08-16 16:17:36.917][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-08-16 16:17:36.918][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-08-16 16:17:36.919][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-16 16:17:36.920][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-16 16:17:36.921][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-08-16 16:17:36.922][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-16 16:17:36.923][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-16 16:17:36.924][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-08-16 16:17:36.926][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-08-16 16:17:36.927][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-08-16 16:17:36.927][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-08-16 16:17:36.929][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-08-16 16:17:36.930][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-08-16 16:17:36.931][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-08-16 16:17:36.933][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-08-16 16:17:36.934][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-08-16 16:17:36.935][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-08-16 16:17:36.936][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-08-16 16:17:36.937][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-08-16 16:17:36.938][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-08-16 16:17:36.939][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-08-16 16:17:36.940][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-08-16 16:17:36.941][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-08-16 16:17:36.942][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-08-16 16:17:36.943][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-08-16 16:17:36.944][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-08-16 16:17:36.946][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-08-16 16:17:36.947][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-08-16 16:17:36.948][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-08-16 16:17:36.949][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-08-16 16:17:36.950][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-08-16 16:17:36.951][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-16 16:17:36.952][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-16 16:17:36.953][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-08-16 16:17:36.954][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-16 16:17:36.955][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-16 16:17:36.956][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-08-16 16:17:36.957][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-08-16 16:17:36.958][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-08-16 16:17:36.959][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-08-16 16:17:36.960][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-08-16 16:17:36.961][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-08-16 16:17:36.962][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-08-16 16:17:36.963][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:17:36.964][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-16 16:17:36.965][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:17:36.966][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-16 16:17:36.967][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-16 16:17:36.968][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:17:36.969][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-16 16:17:36.970][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:17:36.971][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-16 16:17:36.972][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-16 16:17:36.973][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:17:36.974][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-16 16:17:36.975][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:17:36.976][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-16 16:17:36.977][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-16 16:17:36.978][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:17:36.979][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-16 16:17:36.980][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:17:36.981][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-16 16:17:36.981][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-16 16:17:36.982][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:17:36.983][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[2025-08-16 16:17:36.984][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:17:36.985][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-16 16:17:36.986][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-16 16:17:36.987][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:17:36.988][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-16 16:17:36.989][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:17:36.990][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-16 16:17:36.991][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-16 16:17:36.992][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:17:36.993][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-16 16:17:36.994][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:17:36.995][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-16 16:17:36.996][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-16 16:17:36.997][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:17:36.998][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[2025-08-16 16:17:36.999][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:17:37.000][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-16 16:17:37.001][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-16 16:17:37.002][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:17:37.003][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-16 16:17:37.004][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:17:37.005][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-16 16:17:37.006][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-16 16:17:37.006][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:17:37.007][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-16 16:17:37.008][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:17:37.009][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-16 16:17:37.010][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-16 16:17:37.011][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:17:37.012][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-16 16:17:37.013][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:17:37.014][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-16 16:17:37.015][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-16 16:17:37.016][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:17:37.017][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-16 16:17:37.018][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:17:37.019][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-16 16:17:37.020][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-16 16:17:37.021][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:17:37.022][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[2025-08-16 16:17:37.023][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:17:37.024][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-16 16:17:37.025][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-16 16:17:37.026][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:17:37.027][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-16 16:17:37.028][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:17:37.029][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-16 16:17:37.030][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-16 16:17:37.030][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:17:37.031][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[2025-08-16 16:17:37.032][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:17:37.033][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-16 16:17:37.034][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-16 16:17:37.035][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:17:37.036][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-16 16:17:37.037][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:17:37.038][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-16 16:17:37.039][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-16 16:17:37.040][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:17:37.041][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-16 16:17:37.042][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:17:37.043][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-16 16:17:37.044][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-16 16:17:37.045][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:17:37.046][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[2025-08-16 16:17:37.047][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-08-16 16:17:37.049][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-08-16 16:17:37.050][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-08-16 16:17:37.052][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-08-16 16:17:37.053][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-08-16 16:17:37.055][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-08-16 16:17:37.056][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-08-16 16:17:37.058][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-08-16 16:17:37.059][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-08-16 16:17:37.061][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-08-16 16:17:37.062][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-08-16 16:17:37.063][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-08-16 16:17:37.065][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-08-16 16:17:37.066][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-08-16 16:17:37.068][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-08-16 16:17:37.069][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-08-16 16:17:37.071][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-08-16 16:17:37.072][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-08-16 16:17:37.074][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-08-16 16:17:37.075][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-08-16 16:17:37.077][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-08-16 16:17:37.078][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-08-16 16:17:37.080][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-08-16 16:17:37.081][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-08-16 16:17:37.083][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-08-16 16:17:37.084][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-08-16 16:17:37.086][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-08-16 16:17:37.087][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-08-16 16:17:37.089][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-08-16 16:17:37.090][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-08-16 16:17:37.092][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-08-16 16:17:37.093][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-08-16 16:17:37.094][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-08-16 16:17:37.096][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-08-16 16:17:37.097][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-08-16 16:17:37.099][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-08-16 16:17:37.100][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-08-16 16:17:37.102][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-08-16 16:17:37.103][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-08-16 16:17:37.105][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-08-16 16:17:37.106][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-08-16 16:17:37.108][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-08-16 16:17:37.109][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-08-16 16:17:37.111][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-08-16 16:17:37.112][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-08-16 16:17:37.114][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-08-16 16:17:37.115][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-08-16 16:17:37.117][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-08-16 16:17:37.118][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-08-16 16:17:37.119][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-08-16 16:17:37.121][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-08-16 16:17:37.122][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-08-16 16:17:37.124][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-08-16 16:17:37.125][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-08-16 16:17:37.127][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-08-16 16:17:37.128][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-08-16 16:17:37.130][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-08-16 16:17:37.131][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-08-16 16:17:37.133][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-08-16 16:17:37.134][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-08-16 16:17:37.136][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-08-16 16:17:37.137][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-08-16 16:17:37.139][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-08-16 16:17:37.140][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-08-16 16:17:37.142][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-08-16 16:17:37.143][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-08-16 16:17:37.145][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-08-16 16:17:37.146][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-08-16 16:17:37.148][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-08-16 16:17:37.149][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-08-16 16:17:37.151][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-08-16 16:17:37.152][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-08-16 16:17:37.154][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-08-16 16:17:37.155][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-08-16 16:17:37.156][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-08-16 16:17:37.158][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-08-16 16:17:37.159][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-08-16 16:17:37.161][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-08-16 16:17:37.162][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-08-16 16:17:37.164][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-08-16 16:17:37.165][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-08-16 16:17:37.167][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-08-16 16:17:37.168][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-08-16 16:17:37.170][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-08-16 16:17:37.171][initialize] This is biodb version 1.16.0.
biodb.DEBUG[2025-08-16 16:17:37.173][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-08-16 16:17:37.173][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-08-16 16:17:37.174][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-16 16:17:37.175][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:17:37.176][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-16 16:17:37.177][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:17:37.178][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-16 16:17:37.179][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-16 16:17:37.180][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-16 16:17:37.181][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-16 16:17:37.182][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:17:37.183][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-16 16:17:37.184][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:17:37.185][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-16 16:17:37.186][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-16 16:17:37.187][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-16 16:17:37.188][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-16 16:17:37.189][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:17:37.190][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-16 16:17:37.191][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:17:37.192][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-16 16:17:37.193][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-16 16:17:37.194][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-16 16:17:37.195][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-16 16:17:37.196][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:17:37.197][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-16 16:17:37.198][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:17:37.198][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-16 16:17:37.199][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-16 16:17:37.200][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-16 16:17:37.201][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-16 16:17:37.202][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:17:37.203][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-16 16:17:37.204][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:17:37.205][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-16 16:17:37.206][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-16 16:17:37.207][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-16 16:17:37.208][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-16 16:17:37.209][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:17:37.210][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-16 16:17:37.211][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:17:37.212][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-16 16:17:37.213][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-16 16:17:37.214][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-16 16:17:37.215][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-16 16:17:37.216][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:17:37.217][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-16 16:17:37.218][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:17:37.219][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-16 16:17:37.220][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-16 16:17:37.220][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-16 16:17:37.221][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-16 16:17:37.222][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:17:37.223][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-16 16:17:37.224][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:17:37.225][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-16 16:17:37.226][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-16 16:17:37.227][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-16 16:17:37.228][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-16 16:17:37.229][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:17:37.230][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-16 16:17:37.231][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:17:37.232][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-16 16:17:37.233][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-16 16:17:37.234][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-16 16:17:37.235][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-16 16:17:37.236][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:17:37.237][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-16 16:17:37.238][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:17:37.239][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-16 16:17:37.239][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-16 16:17:37.240][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-16 16:17:37.241][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-16 16:17:37.242][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:17:37.243][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-16 16:17:37.244][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:17:37.245][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-16 16:17:37.246][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-16 16:17:37.247][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-16 16:17:37.248][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-16 16:17:37.249][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:17:37.250][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-16 16:17:37.251][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:17:37.252][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-16 16:17:37.253][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-16 16:17:37.254][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-16 16:17:37.255][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-16 16:17:37.256][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:17:37.257][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-16 16:17:37.258][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:17:37.259][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-16 16:17:37.260][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-16 16:17:37.260][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-16 16:17:37.261][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-16 16:17:37.262][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:17:37.263][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-16 16:17:37.264][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:17:37.265][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-16 16:17:37.266][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-16 16:17:37.267][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-16 16:17:37.268][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-16 16:17:37.269][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:17:37.270][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-16 16:17:37.271][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:17:37.272][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-16 16:17:37.273][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-16 16:17:37.274][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-16 16:17:37.275][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-16 16:17:37.276][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:17:37.277][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-16 16:17:37.278][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:17:37.279][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-16 16:17:37.280][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-16 16:17:37.281][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-16 16:17:37.281][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-16 16:17:37.282][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:17:37.283][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-16 16:17:37.284][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:17:37.285][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-16 16:17:37.286][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-16 16:17:37.287][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-16 16:17:37.288][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-16 16:17:37.289][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:17:37.290][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-16 16:17:37.292][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.21-bioc-longtests/meat/biodbNci.Rcheck/biodbNci/definitions.yml".
biodb.DEBUG[2025-08-16 16:17:37.293][self$getDbsInfo()$define] Define connector nci.cactus.
biodb.DEBUG[2025-08-16 16:17:37.295][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-08-16 16:17:37.296][self$setPropertyValue] Setting property "description" to "National Cancer Institute (USA) CACTUS Database.".
biodb.DEBUG[2025-08-16 16:17:37.298][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-08-16 16:17:37.299][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-08-16 16:17:37.300][self$setPropertyValue] Setting property "downloadable" to "TRUE".
biodb.DEBUG[2025-08-16 16:17:37.301][self$setPropertyValue] Setting property "dwnld.ext" to "gz".
biodb.DEBUG[2025-08-16 16:17:37.302][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-08-16 16:17:37.303][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-08-16 16:17:37.304][self$setPropertyValue] Setting property "entry.content.type" to "sdf".
biodb.DEBUG[2025-08-16 16:17:37.305][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-08-16 16:17:37.306][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-08-16 16:17:37.307][self$setPropertyValue] Setting property "name" to "NCI CACTUS".
biodb.DEBUG[2025-08-16 16:17:37.308][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-08-16 16:17:37.309][self$setPropertyValue] Setting property "parsing.expr" to "NSC".
biodb.DEBUG[2025-08-16 16:17:37.309][self$setPropertyValue] Setting property "parsing.expr" to "DTP names".
biodb.DEBUG[2025-08-16 16:17:37.309][self$setPropertyValue] Setting property "parsing.expr" to "Standard InChI".
biodb.DEBUG[2025-08-16 16:17:37.309][self$setPropertyValue] Setting property "parsing.expr" to "c("Standard InChIKey", "^InChIKey=(.*)$")".
biodb.DEBUG[2025-08-16 16:17:37.309][self$setPropertyValue] Setting property "parsing.expr" to "Formula".
biodb.DEBUG[2025-08-16 16:17:37.309][self$setPropertyValue] Setting property "parsing.expr" to "Molecular Weight".
biodb.DEBUG[2025-08-16 16:17:37.309][self$setPropertyValue] Setting property "parsing.expr" to "CAS".
biodb.DEBUG[2025-08-16 16:17:37.310][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-08-16 16:17:37.311][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-08-16 16:17:37.312][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-08-16 16:17:37.313][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-16 16:17:37.314][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-16 16:17:37.315][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-08-16 16:17:37.316][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-16 16:17:37.317][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-16 16:17:37.318][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-08-16 16:17:37.320][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/".
biodb.DEBUG[2025-08-16 16:17:37.320][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/".
biodb.DEBUG[2025-08-16 16:17:37.320][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/download/nci/".
biodb.DEBUG[2025-08-16 16:17:37.320][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/download/nci/NCI-Open_2012-05-01.sdf.gz".
biodb.DEBUG[2025-08-16 16:17:37.321][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-08-16 16:17:37.322][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-08-16 16:17:37.323][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-08-16 16:17:37.324][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-08-16 16:17:37.325][self$getEntryFields()$define] Define field nci.cactus.id.
biodb.DEBUG[2025-08-16 16:17:37.329][super$initialize] Initialize connector nci.cactus.
biodb.DEBUG[2025-08-16 16:17:37.330][super$initialize] Register connector nci.cactus with the request scheduler
biodb.DEBUG[2025-08-16 16:17:37.331][private$bdb$getRequestScheduler()$re ...] Register connector nci.cactus.
biodb.DEBUG[2025-08-16 16:17:37.333][private$addConnectorRules] Create new rule for URL "cactus.nci.nih.gov" of connector "nci.cactus".
biodb.DEBUG[2025-08-16 16:17:37.334][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-08-16 16:17:37.335][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-08-16 16:17:37.336][rule$addConnector] Connector "nci.cactus" is already listed in rule "cactus.nci.nih.gov".
biodb.DEBUG[2025-08-16 16:17:37.338][rule$addConnector] Connector "nci.cactus" is already listed in rule "cactus.nci.nih.gov".
biodb.DEBUG[2025-08-16 16:17:37.339][rule$addConnector] Connector "nci.cactus" is already listed in rule "cactus.nci.nih.gov".
biodb.DEBUG[2025-08-16 16:17:37.340][biodb$getFactory()$createConn] Creating new connector nci.cactus for database class nci.cactus .
biodb.INFO [2025-08-16 16:17:37.341][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2025-08-16 16:17:37.342][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector nci.cactus from the request scheduler
biodb.INFO [2025-08-16 16:17:37.343][self$deleteConn] Connector "nci.cactus" deleted.
biodb.DEBUG[2025-08-16 16:17:37.344][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-08-16 16:17:37.345][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-16 16:17:37.346][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-16 16:17:37.347][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-16 16:17:37.348][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-16 16:17:37.349][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:17:37.350][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 92 ]
> 
> proc.time()
   user  system elapsed 
627.203  59.300 717.637 

'R CMD check' output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --test-dir=longtests --no-stop-on-test-error --no-codoc --no-examples --no-manual --ignore-vignettes --check-subdirs=no biodbNci_1.12.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.21-bioc-longtests/meat/biodbNci.Rcheck’
* using R version 4.5.1 (2025-06-13)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* using options ‘--no-codoc --no-examples --no-manual --ignore-vignettes --no-stop-on-test-error’
* checking for file ‘biodbNci/DESCRIPTION’ ... OK
* this is package ‘biodbNci’ version ‘1.12.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘biodbNci’ can be installed ... OK
* used C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  NciCactusConn.Rd: BiodbConn
  NciCactusEntry.Rd: BiodbSdfEntry
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... SKIPPED
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... OK
* checking files in ‘vignettes’ ... SKIPPED
* checking examples ... SKIPPED
* checking for unstated dependencies in ‘longtests’ ... OK
* checking tests in ‘longtests’ ...
  Running ‘testthat.R’
 OK
* DONE

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


Installation output

biodbNci.Rcheck/00install.out

* installing *source* package ‘biodbNci’ ...
** this is package ‘biodbNci’ version ‘1.12.0’
** using staged installation
** libs
using C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/testthat/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/testthat/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c extractEntries.cpp -o extractEntries.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/testthat/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c test-100-example.cpp -o test-100-example.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/testthat/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c test-runner.cpp -o test-runner.o
g++ -std=gnu++17 -shared -L/home/biocbuild/bbs-3.21-bioc/R/lib -L/usr/local/lib -o biodbNci.so RcppExports.o extractEntries.o test-100-example.o test-runner.o -L/home/biocbuild/bbs-3.21-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.21-bioc-longtests/meat/biodbNci.Rcheck/00LOCK-biodbNci/00new/biodbNci/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (biodbNci)