Back to Long Tests report for BioC 3.21

This page was generated on 2025-03-01 23:55 -0500 (Sat, 01 Mar 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.1 LTS)x86_64R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" 4708
palomino7Windows Server 2022 Datacenterx64R Under development (unstable) (2025-01-21 r87610 ucrt) -- "Unsuffered Consequences" 4495
lconwaymacOS 12.7.1 Montereyx86_64R Under development (unstable) (2025-01-22 r87618) -- "Unsuffered Consequences" 4506
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 1.11.0  (landing page)
Pierrick Roger
Snapshot Date: 2025-03-01 09:55 -0500 (Sat, 01 Mar 2025)
git_url: https://git.bioconductor.org/packages/biodbNci
git_branch: devel
git_last_commit: 10e1a05
git_last_commit_date: 2024-10-29 11:09:24 -0500 (Tue, 29 Oct 2024)
nebbiolo1Linux (Ubuntu 24.04.1 LTS) / x86_64  OK  
palomino7Windows Server 2022 Datacenter / x64  ERROR  
lconwaymacOS 12.7.1 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: 1.11.0
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_1.11.0.tar.gz
StartedAt: 2025-03-01 16:04:33 -0500 (Sat, 01 Mar 2025)
EndedAt: 2025-03-01 16:05:32 -0500 (Sat, 01 Mar 2025)
EllapsedTime: 59.0 seconds
RetCode: 0
Status:   OK  
CheckDir: biodbNci.Rcheck
Warnings: 0

Tests output

biodbNci.Rcheck/tests/testthat.Rout


R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

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> # Script needed to run testthat automatically from ‘R CMD check’. See
> # testthat::test_dir documentation.
> library(testthat)
> library(biodbNci)
> Sys.setenv(TESTTHAT_REPORTER="summary")
> Sys.setenv(BIODB_LOG_DST="console")
> test_check("biodbNci")
biodb.INFO [2025-03-01 16:05:29.423][biodb::testContext]
biodb.INFO [2025-03-01 16:05:29.425][biodb::testContext] ********************************************************************************
biodb.INFO [2025-03-01 16:05:29.426][biodb::testContext] Test context - Generic long tests
biodb.INFO [2025-03-01 16:05:29.427][biodb::testContext] ********************************************************************************
biodb.INFO [2025-03-01 16:05:29.428][biodb::testContext]
biodb.INFO [2025-03-01 16:05:29.434][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.15.0.
biodb.DEBUG[2025-03-01 16:05:29.436][self$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.21-bioc/R/site-library/biodb/definitions.yml".
biodb.DEBUG[2025-03-01 16:05:29.442][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-03-01 16:05:29.443][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-03-01 16:05:29.444][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-03-01 16:05:29.445][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:05:29.446][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:05:29.447][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:05:29.448][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-03-01 16:05:29.465][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-03-01 16:05:29.466][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:05:29.466][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:05:29.467][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:05:29.468][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-03-01 16:05:29.469][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-03-01 16:05:29.470][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:05:29.471][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:05:29.472][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:05:29.473][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-03-01 16:05:29.473][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-03-01 16:05:29.474][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-03-01 16:05:29.475][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:05:29.476][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:05:29.477][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[2025-03-01 16:05:29.478][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-03-01 16:05:29.479][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-03-01 16:05:29.480][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-03-01 16:05:29.481][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:05:29.481][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:05:29.482][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:05:29.483][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-03-01 16:05:29.484][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-03-01 16:05:29.485][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:05:29.486][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:05:29.487][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:05:29.487][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-03-01 16:05:29.488][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-03-01 16:05:29.489][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-03-01 16:05:29.490][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:05:29.491][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:05:29.492][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:05:29.493][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-03-01 16:05:29.494][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-03-01 16:05:29.495][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:05:29.495][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:05:29.496][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:05:29.497][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-03-01 16:05:29.498][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-03-01 16:05:29.499][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-03-01 16:05:29.500][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:05:29.501][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:05:29.502][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:05:29.503][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-03-01 16:05:29.504][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-03-01 16:05:29.505][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-03-01 16:05:29.505][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-03-01 16:05:29.506][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-03-01 16:05:29.507][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-03-01 16:05:29.508][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:05:29.509][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:05:29.510][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:05:29.511][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-03-01 16:05:29.512][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-03-01 16:05:29.513][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:05:29.513][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:05:29.514][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:05:29.515][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-03-01 16:05:29.516][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-03-01 16:05:29.517][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:05:29.518][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:05:29.519][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:05:29.519][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-03-01 16:05:29.520][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-03-01 16:05:29.521][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:05:29.522][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:05:29.523][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:05:29.524][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-03-01 16:05:29.525][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2025-03-01 16:05:29.526][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:05:29.526][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:05:29.527][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:05:29.528][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-03-01 16:05:29.529][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-03-01 16:05:29.530][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:05:29.531][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:05:29.532][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:05:29.533][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-03-01 16:05:29.533][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-03-01 16:05:29.538][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-03-01 16:05:29.539][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:05:29.540][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:05:29.541][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:05:29.542][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-03-01 16:05:29.543][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-03-01 16:05:29.544][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-03-01 16:05:29.544][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:05:29.545][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:05:29.546][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:05:29.549][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-03-01 16:05:29.580][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-03-01 16:05:29.600][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2025-03-01 16:05:29.601][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-01 16:05:29.602][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-01 16:05:29.603][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-01 16:05:29.604][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-01 16:05:29.605][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-01 16:05:29.606][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-01 16:05:29.607][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-03-01 16:05:29.608][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-01 16:05:29.609][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-03-01 16:05:29.610][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-03-01 16:05:29.611][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-01 16:05:29.612][self$setPropertyValue]
biodb.DEBUG[2025-03-01 16:05:29.613][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-01 16:05:29.613][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-03-01 16:05:29.613][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-03-01 16:05:29.613][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-03-01 16:05:29.613][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-03-01 16:05:29.613][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-03-01 16:05:29.614][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-01 16:05:29.615][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-01 16:05:29.616][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-01 16:05:29.617][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-01 16:05:29.618][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-01 16:05:29.619][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-01 16:05:29.620][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-01 16:05:29.621][self$setPropertyValue]
biodb.DEBUG[2025-03-01 16:05:29.622][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-01 16:05:29.622][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-01 16:05:29.623][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-01 16:05:29.624][self$setPropertyValue]
biodb.DEBUG[2025-03-01 16:05:29.625][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-03-01 16:05:29.627][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-03-01 16:05:29.628][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-03-01 16:05:29.629][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-01 16:05:29.630][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-01 16:05:29.631][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-01 16:05:29.632][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-01 16:05:29.633][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-01 16:05:29.634][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-01 16:05:29.635][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-03-01 16:05:29.635][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-01 16:05:29.636][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-03-01 16:05:29.637][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-03-01 16:05:29.638][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-01 16:05:29.639][self$setPropertyValue]
biodb.DEBUG[2025-03-01 16:05:29.640][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-01 16:05:29.641][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-03-01 16:05:29.641][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-03-01 16:05:29.641][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-03-01 16:05:29.641][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-03-01 16:05:29.641][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-03-01 16:05:29.642][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-01 16:05:29.643][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-01 16:05:29.644][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-01 16:05:29.645][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-01 16:05:29.646][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-01 16:05:29.646][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-01 16:05:29.647][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-01 16:05:29.648][self$setPropertyValue]
biodb.DEBUG[2025-03-01 16:05:29.649][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-01 16:05:29.650][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-01 16:05:29.651][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-01 16:05:29.652][self$setPropertyValue]
biodb.DEBUG[2025-03-01 16:05:29.653][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-03-01 16:05:29.654][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-03-01 16:05:29.655][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2025-03-01 16:05:29.656][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-01 16:05:29.657][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-01 16:05:29.658][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-01 16:05:29.659][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-01 16:05:29.660][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-01 16:05:29.661][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-01 16:05:29.662][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-03-01 16:05:29.663][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-01 16:05:29.664][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-03-01 16:05:29.665][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-03-01 16:05:29.666][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-01 16:05:29.667][self$setPropertyValue]
biodb.DEBUG[2025-03-01 16:05:29.668][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-01 16:05:29.668][self$setPropertyValue]
biodb.DEBUG[2025-03-01 16:05:29.669][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-01 16:05:29.670][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-01 16:05:29.671][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-01 16:05:29.672][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-01 16:05:29.673][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-01 16:05:29.674][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-01 16:05:29.675][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-01 16:05:29.676][self$setPropertyValue]
biodb.DEBUG[2025-03-01 16:05:29.676][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-01 16:05:29.677][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-01 16:05:29.678][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-01 16:05:29.679][self$setPropertyValue]
biodb.DEBUG[2025-03-01 16:05:29.680][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-03-01 16:05:29.682][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-03-01 16:05:29.683][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-03-01 16:05:29.684][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-01 16:05:29.685][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-01 16:05:29.686][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-01 16:05:29.686][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-01 16:05:29.687][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-01 16:05:29.688][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-01 16:05:29.689][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-03-01 16:05:29.690][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-01 16:05:29.691][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-03-01 16:05:29.692][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-03-01 16:05:29.693][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-01 16:05:29.694][self$setPropertyValue]
biodb.DEBUG[2025-03-01 16:05:29.695][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-01 16:05:29.696][self$setPropertyValue]
biodb.DEBUG[2025-03-01 16:05:29.697][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-01 16:05:29.698][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-01 16:05:29.698][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-01 16:05:29.699][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-01 16:05:29.700][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-01 16:05:29.701][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-01 16:05:29.702][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-01 16:05:29.703][self$setPropertyValue]
biodb.DEBUG[2025-03-01 16:05:29.704][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-01 16:05:29.705][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-01 16:05:29.706][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-01 16:05:29.706][self$setPropertyValue]
biodb.DEBUG[2025-03-01 16:05:29.710][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-03-01 16:05:29.711][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:05:29.712][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:05:29.713][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:05:29.713][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:05:29.714][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:05:29.715][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:05:29.716][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:05:29.717][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:05:29.717][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:05:29.718][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:05:29.719][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:05:29.720][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:05:29.721][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:05:29.722][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:05:29.722][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:05:29.723][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:05:29.724][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:05:29.725][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:05:29.726][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:05:29.727][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:05:29.727][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:05:29.728][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:05:29.729][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:05:29.730][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:05:29.731][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:05:29.732][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:05:29.732][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:05:29.733][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:05:29.734][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:05:29.735][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:05:29.736][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:05:29.737][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:05:29.737][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:05:29.738][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:05:29.739][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:05:29.740][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:05:29.741][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:05:29.742][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:05:29.742][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:05:29.743][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:05:29.744][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:05:29.745][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[2025-03-01 16:05:29.746][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:05:29.747][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:05:29.747][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:05:29.748][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:05:29.749][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:05:29.750][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:05:29.751][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:05:29.752][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:05:29.752][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:05:29.753][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:05:29.754][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:05:29.759][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:05:29.760][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:05:29.760][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:05:29.761][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:05:29.762][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:05:29.763][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:05:29.764][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:05:29.764][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:05:29.765][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:05:29.766][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:05:29.767][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:05:29.768][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:05:29.769][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:05:29.769][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:05:29.770][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:05:29.771][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:05:29.772][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:05:29.773][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:05:29.773][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[2025-03-01 16:05:29.774][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:05:29.775][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:05:29.776][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:05:29.777][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:05:29.778][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[2025-03-01 16:05:29.778][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:05:29.779][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:05:29.780][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:05:29.781][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:05:29.782][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:05:29.783][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:05:29.783][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:05:29.784][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:05:29.785][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:05:29.786][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:05:29.787][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-03-01 16:05:29.791][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-03-01 16:05:29.793][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-03-01 16:05:29.794][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-03-01 16:05:29.795][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-03-01 16:05:29.797][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-03-01 16:05:29.798][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-03-01 16:05:29.799][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-03-01 16:05:29.801][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-03-01 16:05:29.802][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-03-01 16:05:29.808][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-03-01 16:05:29.811][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-03-01 16:05:29.812][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-03-01 16:05:29.814][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-03-01 16:05:29.815][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-03-01 16:05:29.817][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-03-01 16:05:29.818][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-03-01 16:05:29.820][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-03-01 16:05:29.821][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-03-01 16:05:29.823][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-03-01 16:05:29.824][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-03-01 16:05:29.826][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-03-01 16:05:29.827][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-03-01 16:05:29.829][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-03-01 16:05:29.830][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-03-01 16:05:29.832][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-03-01 16:05:29.833][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-03-01 16:05:29.834][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-03-01 16:05:29.836][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-03-01 16:05:29.837][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-03-01 16:05:29.839][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-03-01 16:05:29.840][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-03-01 16:05:29.842][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-03-01 16:05:29.843][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-03-01 16:05:29.845][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-03-01 16:05:29.846][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-03-01 16:05:29.848][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-03-01 16:05:29.849][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-03-01 16:05:29.851][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-03-01 16:05:29.852][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-03-01 16:05:29.853][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-03-01 16:05:29.855][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-03-01 16:05:29.856][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-03-01 16:05:29.858][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-03-01 16:05:29.859][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-03-01 16:05:29.861][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-03-01 16:05:29.862][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-03-01 16:05:29.864][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-03-01 16:05:29.865][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-03-01 16:05:29.867][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-03-01 16:05:29.868][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-03-01 16:05:29.869][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-03-01 16:05:29.871][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-03-01 16:05:29.872][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-03-01 16:05:29.874][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-03-01 16:05:29.875][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-03-01 16:05:29.877][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-03-01 16:05:29.878][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-03-01 16:05:29.880][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-03-01 16:05:29.881][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-03-01 16:05:29.882][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-03-01 16:05:29.884][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-03-01 16:05:29.885][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-03-01 16:05:29.887][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-03-01 16:05:29.888][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-03-01 16:05:29.890][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-03-01 16:05:29.891][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-03-01 16:05:29.893][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-03-01 16:05:29.894][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-03-01 16:05:29.896][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-03-01 16:05:29.897][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-03-01 16:05:29.899][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-03-01 16:05:29.900][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-03-01 16:05:29.901][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-03-01 16:05:29.903][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-03-01 16:05:29.904][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-03-01 16:05:29.906][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-03-01 16:05:29.907][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-03-01 16:05:29.909][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-03-01 16:05:29.910][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-03-01 16:05:29.911][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-03-01 16:05:29.913][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-03-01 16:05:29.914][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-03-01 16:05:29.921][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-03-01 16:05:29.923][initialize] This is biodb version 1.15.0.
biodb.DEBUG[2025-03-01 16:05:29.927][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-03-01 16:05:29.928][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:05:29.929][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:05:29.930][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:05:29.931][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:05:29.936][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:05:29.937][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-01 16:05:29.938][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-01 16:05:29.939][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:05:29.940][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:05:29.941][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:05:29.942][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[2025-03-01 16:05:29.943][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:05:29.944][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-01 16:05:29.944][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-01 16:05:29.945][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:05:29.946][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:05:29.959][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:05:29.960][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:05:29.961][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:05:29.962][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-01 16:05:29.963][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-01 16:05:29.964][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:05:29.965][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:05:29.966][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:05:29.967][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:05:29.968][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:05:29.969][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-01 16:05:29.970][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-01 16:05:29.971][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:05:29.972][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:05:29.973][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:05:29.974][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[2025-03-01 16:05:29.975][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:05:29.976][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-01 16:05:29.977][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-01 16:05:29.978][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:05:29.979][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:05:29.980][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:05:29.981][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:05:29.982][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:05:29.983][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-01 16:05:29.983][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-01 16:05:29.984][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:05:29.986][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:05:29.987][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:05:29.988][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[2025-03-01 16:05:29.989][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:05:29.990][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-01 16:05:29.991][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-01 16:05:29.992][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:05:29.993][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:05:29.994][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:05:29.995][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:05:29.995][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:05:29.996][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-01 16:05:29.997][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-01 16:05:29.998][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:05:29.999][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:05:30.000][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:05:30.001][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:05:30.002][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:05:30.003][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-01 16:05:30.004][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-01 16:05:30.005][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:05:30.006][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:05:30.007][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:05:30.008][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:05:30.008][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:05:30.009][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-01 16:05:30.010][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-01 16:05:30.011][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:05:30.012][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:05:30.013][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:05:30.014][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:05:30.014][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:05:30.015][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-01 16:05:30.016][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-01 16:05:30.017][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:05:30.018][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:05:30.019][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:05:30.020][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:05:30.021][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:05:30.021][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-01 16:05:30.022][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-01 16:05:30.023][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:05:30.024][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:05:30.025][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:05:30.026][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:05:30.027][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:05:30.028][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-01 16:05:30.028][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-01 16:05:30.029][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:05:30.030][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:05:30.031][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:05:30.032][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:05:30.033][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:05:30.034][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-01 16:05:30.035][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-01 16:05:30.036][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:05:30.037][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:05:30.037][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:05:30.038][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:05:30.039][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:05:30.040][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-01 16:05:30.041][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-01 16:05:30.042][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:05:30.043][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:05:30.044][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:05:30.044][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:05:30.045][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:05:30.046][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-01 16:05:30.047][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-01 16:05:30.048][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:05:30.049][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:05:30.050][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:05:30.051][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:05:30.051][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:05:30.052][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-01 16:05:30.053][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-01 16:05:30.054][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:05:30.055][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:05:30.056][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:05:30.056][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:05:30.058][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.21-bioc-longtests/meat/biodbNci.Rcheck/biodbNci/definitions.yml".
biodb.DEBUG[2025-03-01 16:05:30.068][self$getDbsInfo()$define] Define connector nci.cactus.
biodb.DEBUG[2025-03-01 16:05:30.069][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-03-01 16:05:30.070][self$setPropertyValue] Setting property "description" to "National Cancer Institute (USA) CACTUS Database.".
biodb.DEBUG[2025-03-01 16:05:30.071][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-01 16:05:30.072][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-01 16:05:30.073][self$setPropertyValue] Setting property "downloadable" to "TRUE".
biodb.DEBUG[2025-03-01 16:05:30.074][self$setPropertyValue] Setting property "dwnld.ext" to "gz".
biodb.DEBUG[2025-03-01 16:05:30.075][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-03-01 16:05:30.076][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-01 16:05:30.077][self$setPropertyValue] Setting property "entry.content.type" to "sdf".
biodb.DEBUG[2025-03-01 16:05:30.078][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-01 16:05:30.079][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-03-01 16:05:30.080][self$setPropertyValue] Setting property "name" to "NCI CACTUS".
biodb.DEBUG[2025-03-01 16:05:30.081][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-01 16:05:30.082][self$setPropertyValue] Setting property "parsing.expr" to "NSC".
biodb.DEBUG[2025-03-01 16:05:30.082][self$setPropertyValue] Setting property "parsing.expr" to "DTP names".
biodb.DEBUG[2025-03-01 16:05:30.082][self$setPropertyValue] Setting property "parsing.expr" to "Standard InChI".
biodb.DEBUG[2025-03-01 16:05:30.082][self$setPropertyValue] Setting property "parsing.expr" to "c("Standard InChIKey", "^InChIKey=(.*)$")".
biodb.DEBUG[2025-03-01 16:05:30.082][self$setPropertyValue] Setting property "parsing.expr" to "Formula".
biodb.DEBUG[2025-03-01 16:05:30.082][self$setPropertyValue] Setting property "parsing.expr" to "Molecular Weight".
biodb.DEBUG[2025-03-01 16:05:30.082][self$setPropertyValue] Setting property "parsing.expr" to "CAS".
biodb.DEBUG[2025-03-01 16:05:30.083][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-03-01 16:05:30.084][self$setPropertyValue]
biodb.DEBUG[2025-03-01 16:05:30.085][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-03-01 16:05:30.086][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-01 16:05:30.087][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-01 16:05:30.088][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-01 16:05:30.089][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-01 16:05:30.090][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-01 16:05:30.091][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-01 16:05:30.092][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/".
biodb.DEBUG[2025-03-01 16:05:30.092][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/".
biodb.DEBUG[2025-03-01 16:05:30.092][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/download/nci/".
biodb.DEBUG[2025-03-01 16:05:30.092][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/download/nci/NCI-Open_2012-05-01.sdf.gz".
biodb.DEBUG[2025-03-01 16:05:30.093][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-01 16:05:30.094][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-01 16:05:30.095][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-03-01 16:05:30.096][self$setPropertyValue]
biodb.DEBUG[2025-03-01 16:05:30.102][self$getEntryFields()$define] Define field nci.cactus.id.
biodb.DEBUG[2025-03-01 16:05:30.124][super$initialize] Initialize connector nci.cactus.
biodb.DEBUG[2025-03-01 16:05:30.125][super$initialize] Register connector nci.cactus with the request scheduler
biodb.DEBUG[2025-03-01 16:05:30.129][private$bdb$getRequestScheduler()$re ...] Register connector nci.cactus.
biodb.DEBUG[2025-03-01 16:05:30.133][private$addConnectorRules] Create new rule for URL "cactus.nci.nih.gov" of connector "nci.cactus".
biodb.DEBUG[2025-03-01 16:05:30.137][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-03-01 16:05:30.138][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-03-01 16:05:30.139][rule$addConnector] Connector "nci.cactus" is already listed in rule "cactus.nci.nih.gov".
biodb.DEBUG[2025-03-01 16:05:30.141][rule$addConnector] Connector "nci.cactus" is already listed in rule "cactus.nci.nih.gov".
biodb.DEBUG[2025-03-01 16:05:30.142][rule$addConnector] Connector "nci.cactus" is already listed in rule "cactus.nci.nih.gov".
biodb.DEBUG[2025-03-01 16:05:30.143][biodb$getFactory()$createConn] Creating new connector nci.cactus for database class nci.cactus .
biodb.INFO [2025-03-01 16:05:30.182][biodb::testThat]
biodb.INFO [2025-03-01 16:05:30.184][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2025-03-01 16:05:30.184][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-01 16:05:30.185][biodb::testThat]
biodb.TRACE[2025-03-01 16:05:30.189][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[2025-03-01 16:05:30.190][biodb$getFactory()$createEntryFromCo ...] Creating NCI CACTUS entries from 1 content(s).
biodb.DEBUG[2025-03-01 16:05:30.193][biodb$getFactory()$createEntryFromCo ...] Parsing 1 NCI CACTUS entries.
biodb.DEBUG[2025-03-01 16:05:30.201][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-01 16:05:30.202][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-01 16:05:30.203][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-01 16:05:30.215][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:05:30.216][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:05:30.217][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:05:30.217][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.TRACE[2025-03-01 16:05:30.234][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:05:30.235][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:05:30.236][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:30.237][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:30.238][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:05:30.251][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:05:30.252][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:30.253][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:30.255][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-01 16:05:30.256][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-01 16:05:30.257][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:30.258][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:30.283][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-01 16:05:30.284][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-01 16:05:30.285][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:30.286][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:30.288][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-01 16:05:30.289][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-01 16:05:30.290][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:30.291][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:30.292][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-01 16:05:30.293][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-01 16:05:30.294][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:30.295][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:30.297][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-01 16:05:30.298][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-01 16:05:30.299][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:30.300][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:30.301][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-01 16:05:30.302][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-01 16:05:30.303][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:30.304][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:30.305][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-01 16:05:30.306][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-01 16:05:30.307][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:30.308][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:30.309][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-01 16:05:30.310][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-01 16:05:30.311][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:30.312][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:30.314][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-03-01 16:05:30.315][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-03-01 16:05:30.315][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:30.316][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:30.317][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-03-01 16:05:30.318][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-03-01 16:05:30.319][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:30.320][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:30.321][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:05:30.322][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:05:30.323][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:30.324][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:30.325][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-03-01 16:05:30.326][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-03-01 16:05:30.327][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:30.328][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:30.329][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:05:30.330][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:05:30.330][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:30.331][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:30.332][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:05:30.333][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:05:30.334][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:30.335][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:30.336][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:05:30.337][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:05:30.338][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:30.339][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:30.376][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:05:30.377][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:05:30.378][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:30.379][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:30.380][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:05:30.381][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:05:30.382][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:30.383][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:30.384][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:05:30.385][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:05:30.386][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:30.387][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-01 16:05:30.387][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 749674.
biodb.TRACE[2025-03-01 16:05:30.390][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-03-01 16:05:30.391][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-03-01 16:05:30.392][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:30.392][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:30.393][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-03-01 16:05:30.394][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-03-01 16:05:30.395][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:30.396][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:30.397][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-03-01 16:05:30.398][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-03-01 16:05:30.399][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:30.400][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:30.401][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-03-01 16:05:30.402][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-03-01 16:05:30.403][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:30.404][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:30.417][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:05:30.418][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:05:30.419][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:30.420][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:30.432][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-03-01 16:05:30.433][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-03-01 16:05:30.434][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:30.435][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:30.439][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:05:30.440][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:05:30.441][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:30.442][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:30.443][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:05:30.444][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:05:30.445][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:30.445][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:30.446][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:05:30.447][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:05:30.448][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:30.449][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:30.451][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:05:30.452][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:05:30.453][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:30.454][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:30.455][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:05:30.456][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:05:30.457][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:30.458][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:30.459][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:05:30.460][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:05:30.461][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:30.462][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:30.463][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-03-01 16:05:30.464][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-03-01 16:05:30.465][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:30.465][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:30.466][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-03-01 16:05:30.467][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-03-01 16:05:30.468][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:30.469][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:30.470][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-03-01 16:05:30.471][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-03-01 16:05:30.472][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:30.477][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:30.483][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:05:30.484][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:05:30.485][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:30.486][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:30.487][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:05:30.488][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:05:30.489][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:30.490][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:30.491][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:05:30.492][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:05:30.492][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:30.493][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:30.494][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:05:30.495][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:05:30.496][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:30.497][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:30.498][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:05:30.499][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:05:30.500][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:30.501][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:30.508][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-01 16:05:30.509][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-01 16:05:30.510][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:30.511][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:30.512][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-01 16:05:30.513][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-01 16:05:30.514][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:30.515][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:30.516][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-01 16:05:30.517][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-01 16:05:30.518][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:30.518][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:30.519][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-01 16:05:30.520][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-01 16:05:30.521][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:30.522][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:30.523][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-01 16:05:30.524][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-01 16:05:30.525][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:30.526][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:30.533][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-01 16:05:30.534][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-01 16:05:30.535][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:30.536][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:30.537][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-01 16:05:30.538][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-01 16:05:30.539][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:30.540][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:30.540][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-01 16:05:30.541][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-01 16:05:30.542][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:30.543][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:30.544][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-01 16:05:30.545][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-01 16:05:30.546][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:30.547][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:30.548][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-01 16:05:30.549][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-01 16:05:30.550][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:30.551][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:30.558][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-01 16:05:30.559][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-01 16:05:30.560][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:30.561][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:30.562][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-01 16:05:30.563][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-01 16:05:30.563][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:30.564][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:30.565][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-01 16:05:30.566][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-01 16:05:30.567][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:30.568][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:30.569][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-01 16:05:30.570][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-01 16:05:30.571][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:30.572][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:30.573][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-01 16:05:30.574][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-01 16:05:30.574][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:30.575][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:30.582][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-01 16:05:30.583][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-01 16:05:30.584][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:30.585][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:30.586][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-01 16:05:30.587][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-01 16:05:30.588][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:30.589][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:30.590][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-01 16:05:30.591][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-01 16:05:30.592][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:30.593][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:30.594][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-01 16:05:30.594][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-01 16:05:30.595][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:30.596][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:30.597][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-01 16:05:30.598][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-01 16:05:30.599][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:30.600][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:30.607][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:05:30.608][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:05:30.613][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:30.614][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:30.617][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-01 16:05:30.618][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-01 16:05:30.619][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:30.620][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:30.624][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-01 16:05:30.625][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-01 16:05:30.626][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:30.627][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:30.630][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-01 16:05:30.631][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-01 16:05:30.632][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:30.633][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:30.637][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-01 16:05:30.638][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-01 16:05:30.639][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:30.640][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:30.655][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[2025-03-01 16:05:30.688][biodb$getFactory()$createEntryFromCo ...] Creating NCI CACTUS entries from 1 content(s).
biodb.DEBUG[2025-03-01 16:05:30.689][biodb$getFactory()$createEntryFromCo ...] Parsing 1 NCI CACTUS entries.
biodb.DEBUG[2025-03-01 16:05:30.690][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-01 16:05:30.691][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-01 16:05:30.692][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-01 16:05:30.696][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:05:30.697][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:05:30.698][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:05:30.698][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-01 16:05:30.707][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:05:30.708][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:05:30.709][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:30.710][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:30.711][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:05:30.712][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:05:30.713][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:30.714][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:30.735][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-03-01 16:05:30.736][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-03-01 16:05:30.737][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:30.738][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:30.738][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-03-01 16:05:30.739][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-03-01 16:05:30.740][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:30.741][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:30.743][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-01 16:05:30.744][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-01 16:05:30.745][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:30.745][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:30.746][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-01 16:05:30.747][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-01 16:05:30.748][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:30.749][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:30.750][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-01 16:05:30.751][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-01 16:05:30.752][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:30.753][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:30.754][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-01 16:05:30.755][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-01 16:05:30.756][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:30.757][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:30.758][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-01 16:05:30.759][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-01 16:05:30.760][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:30.761][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:30.762][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-01 16:05:30.763][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-01 16:05:30.764][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:30.765][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:30.766][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-01 16:05:30.767][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-01 16:05:30.768][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:30.769][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:30.770][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-01 16:05:30.771][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-01 16:05:30.771][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:30.772][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:30.773][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-01 16:05:30.774][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-01 16:05:30.775][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:30.776][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:30.777][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-01 16:05:30.778][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-01 16:05:30.779][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:30.780][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:30.781][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-01 16:05:30.782][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-01 16:05:30.783][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:30.783][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:30.785][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-01 16:05:30.786][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-01 16:05:30.787][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:30.788][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:30.789][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-01 16:05:30.790][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-01 16:05:30.791][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:30.792][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:30.793][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-01 16:05:30.794][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-01 16:05:30.795][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:30.796][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:30.797][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-01 16:05:30.798][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-01 16:05:30.799][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:30.799][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:30.801][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-03-01 16:05:30.802][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-03-01 16:05:30.803][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:30.804][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:30.805][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-03-01 16:05:30.806][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-03-01 16:05:30.807][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:30.808][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:30.809][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:05:30.810][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:05:30.810][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:30.811][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:30.812][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-03-01 16:05:30.813][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-03-01 16:05:30.814][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:30.815][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:30.816][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:05:30.817][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:05:30.818][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:30.819][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:30.820][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:05:30.821][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:05:30.822][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:30.823][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:30.824][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:05:30.825][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:05:30.825][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:30.826][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:30.827][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:05:30.828][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:05:30.829][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:30.830][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:30.831][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:05:30.832][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:05:30.833][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:30.834][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:30.835][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:05:30.836][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:05:30.837][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:30.838][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-01 16:05:30.839][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 750690.
biodb.TRACE[2025-03-01 16:05:30.858][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-03-01 16:05:30.859][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-03-01 16:05:30.860][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:30.861][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:30.862][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-03-01 16:05:30.863][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-03-01 16:05:30.867][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:30.868][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:30.869][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-03-01 16:05:30.870][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-03-01 16:05:30.871][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:30.872][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:30.873][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-03-01 16:05:30.874][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-03-01 16:05:30.875][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:30.875][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:30.877][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:05:30.878][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:05:30.879][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:30.880][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:30.884][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-03-01 16:05:30.885][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-03-01 16:05:30.886][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:30.887][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:30.891][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:05:30.892][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:05:30.893][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:30.894][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:30.895][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:05:30.896][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:05:30.896][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:30.897][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:30.898][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:05:30.899][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:05:30.900][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:30.901][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:30.903][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:05:30.904][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:05:30.905][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:30.906][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:30.907][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:05:30.908][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:05:30.909][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:30.910][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:30.911][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:05:30.912][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:05:30.913][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:30.914][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:30.915][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-03-01 16:05:30.916][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-03-01 16:05:30.917][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:30.917][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:30.918][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-03-01 16:05:30.919][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-03-01 16:05:30.920][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:30.921][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:30.922][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-03-01 16:05:30.923][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-03-01 16:05:30.924][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:30.925][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:30.940][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:05:30.941][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:05:30.942][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:30.943][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:30.944][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:05:30.945][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:05:30.946][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:30.947][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:30.948][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:05:30.949][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:05:30.949][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:30.950][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:30.951][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:05:30.952][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:05:30.953][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:30.954][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:30.955][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:05:30.956][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:05:30.957][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:30.958][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:30.965][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-03-01 16:05:30.966][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-03-01 16:05:30.967][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:30.968][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:30.969][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-03-01 16:05:30.970][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-03-01 16:05:30.971][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:30.972][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:30.973][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-03-01 16:05:30.974][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-03-01 16:05:30.975][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:30.975][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:30.976][ef$get] Asked field names are: cas.id.
biodb.TRACE[2025-03-01 16:05:30.977][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-03-01 16:05:30.978][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:30.979][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:30.980][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-03-01 16:05:30.981][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-03-01 16:05:30.982][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:30.983][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:30.990][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-01 16:05:30.991][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-01 16:05:30.992][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:30.993][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:30.994][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-01 16:05:30.995][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-01 16:05:30.996][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:30.997][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:31.001][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-01 16:05:31.003][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-01 16:05:31.003][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:31.004][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:31.005][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-01 16:05:31.006][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-01 16:05:31.007][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:31.008][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:31.009][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-01 16:05:31.010][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-01 16:05:31.011][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:31.012][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:31.019][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-01 16:05:31.020][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-01 16:05:31.021][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:31.022][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:31.023][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-01 16:05:31.024][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-01 16:05:31.025][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:31.026][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:31.027][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-01 16:05:31.028][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-01 16:05:31.029][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:31.030][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:31.031][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-01 16:05:31.032][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-01 16:05:31.033][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:31.033][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:31.034][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-01 16:05:31.035][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-01 16:05:31.036][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:31.037][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:31.045][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-01 16:05:31.046][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-01 16:05:31.046][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:31.047][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:31.048][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-01 16:05:31.049][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-01 16:05:31.050][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:31.051][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:31.052][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-01 16:05:31.053][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-01 16:05:31.054][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:31.055][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:31.056][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-01 16:05:31.057][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-01 16:05:31.058][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:31.059][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:31.060][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-01 16:05:31.061][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-01 16:05:31.061][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:31.062][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:31.070][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-01 16:05:31.071][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-01 16:05:31.072][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:31.073][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:31.074][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-01 16:05:31.075][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-01 16:05:31.075][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:31.076][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:31.077][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-01 16:05:31.078][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-01 16:05:31.079][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:31.080][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:31.081][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-01 16:05:31.082][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-01 16:05:31.083][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:31.084][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:31.085][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-01 16:05:31.086][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-01 16:05:31.087][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:31.088][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:31.095][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-01 16:05:31.096][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-01 16:05:31.097][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:31.098][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:31.099][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-01 16:05:31.100][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-01 16:05:31.101][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:31.102][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:31.103][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-01 16:05:31.104][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-01 16:05:31.104][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:31.105][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:31.106][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-01 16:05:31.107][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-01 16:05:31.108][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:31.109][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:31.110][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-01 16:05:31.111][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-01 16:05:31.112][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:31.113][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:31.120][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:05:31.121][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:05:31.122][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:31.123][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:31.127][ef$get] Asked field names are: cas.id.
biodb.TRACE[2025-03-01 16:05:31.128][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-03-01 16:05:31.129][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:31.130][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:31.133][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-01 16:05:31.138][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-01 16:05:31.139][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:31.140][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:31.144][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-01 16:05:31.145][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-01 16:05:31.146][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:31.146][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:31.150][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-01 16:05:31.151][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-01 16:05:31.152][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:31.153][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:31.157][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-01 16:05:31.158][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-01 16:05:31.159][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:31.159][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:31.163][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-01 16:05:31.164][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-01 16:05:31.165][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:31.166][ef$get] fields variable is a list.
biodb.INFO [2025-03-01 16:05:31.173][biodb::testThat]
biodb.INFO [2025-03-01 16:05:31.173][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2025-03-01 16:05:31.174][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-01 16:05:31.175][biodb::testThat]
biodb.DEBUG[2025-03-01 16:05:31.177][private$loadEntries] Creating entries from ids [2]: "749674, 750690".
biodb.DEBUG[2025-03-01 16:05:31.184][conn$getEntryContent] Get NCI CACTUS entry content(s) for 2 id(s)...
biodb.DEBUG[2025-03-01 16:05:31.187][self$isDownloaded] Database nci.cactus has already been downloaded.
biodb.DEBUG[2025-03-01 16:05:31.189][self$isDownloaded] Database nci.cactus has already been downloaded.
biodb.TRACE[2025-03-01 16:05:31.191][cch$loadFileContent] Trying to load 2 files from cache: [2]: "749674, 750690".
biodb.TRACE[2025-03-01 16:05:31.192][cch$loadFileContent] file.exist = [2]: "TRUE, TRUE".
biodb.TRACE[2025-03-01 16:05:31.194][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[2025-03-01 16:05:31.195][conn$getEntryContent] 2 NCI CACTUS entry content(s) loaded from cache.
biodb.DEBUG[2025-03-01 16:05:31.196][self$createEntryFromContent] Creating NCI CACTUS entries from 2 content(s).
biodb.DEBUG[2025-03-01 16:05:31.197][self$createEntryFromContent] Parsing 2 NCI CACTUS entries.
biodb.DEBUG[2025-03-01 16:05:31.198][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-01 16:05:31.199][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-01 16:05:31.200][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-01 16:05:31.204][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:05:31.205][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:05:31.205][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:05:31.206][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-01 16:05:31.212][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:05:31.213][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:05:31.214][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:31.215][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:31.216][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:05:31.217][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:05:31.218][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:31.219][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:31.221][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-01 16:05:31.222][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-01 16:05:31.223][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:31.224][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:31.225][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-01 16:05:31.226][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-01 16:05:31.227][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:31.228][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:31.229][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-01 16:05:31.230][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-01 16:05:31.231][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:31.232][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:31.233][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-01 16:05:31.234][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-01 16:05:31.234][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:31.235][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:31.237][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-01 16:05:31.238][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-01 16:05:31.239][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:31.240][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:31.241][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-01 16:05:31.242][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-01 16:05:31.243][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:31.244][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:31.245][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-01 16:05:31.246][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-01 16:05:31.247][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:31.248][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:31.248][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-01 16:05:31.249][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-01 16:05:31.250][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:31.251][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:31.253][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-03-01 16:05:31.254][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-03-01 16:05:31.255][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:31.256][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:31.256][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-03-01 16:05:31.257][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-03-01 16:05:31.258][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:31.259][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:31.260][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:05:31.261][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:05:31.262][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:31.263][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:31.264][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-03-01 16:05:31.265][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-03-01 16:05:31.266][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:31.267][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:31.268][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:05:31.268][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:05:31.269][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:31.270][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:31.271][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:05:31.272][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:05:31.273][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:31.274][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:31.275][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:05:31.276][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:05:31.281][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:31.282][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-01 16:05:31.283][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-01 16:05:31.284][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-01 16:05:31.285][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-01 16:05:31.289][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:05:31.290][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:05:31.291][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:05:31.291][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-01 16:05:31.300][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:05:31.301][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:05:31.302][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:31.302][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:31.303][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:05:31.304][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:05:31.305][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:31.306][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:31.308][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-03-01 16:05:31.309][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-03-01 16:05:31.310][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:31.311][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:31.312][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-03-01 16:05:31.313][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-03-01 16:05:31.314][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:31.315][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:31.316][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-01 16:05:31.317][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-01 16:05:31.318][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:31.319][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:31.320][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-01 16:05:31.321][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-01 16:05:31.322][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:31.323][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:31.324][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-01 16:05:31.325][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-01 16:05:31.326][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:31.327][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:31.328][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-01 16:05:31.329][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-01 16:05:31.330][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:31.330][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:31.332][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-01 16:05:31.333][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-01 16:05:31.334][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:31.335][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:31.335][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-01 16:05:31.336][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-01 16:05:31.337][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:31.338][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:31.339][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-01 16:05:31.340][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-01 16:05:31.341][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:31.342][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:31.343][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-01 16:05:31.344][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-01 16:05:31.345][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:31.346][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:31.347][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-01 16:05:31.348][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-01 16:05:31.349][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:31.350][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:31.350][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-01 16:05:31.351][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-01 16:05:31.352][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:31.353][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:31.354][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-01 16:05:31.355][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-01 16:05:31.356][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:31.357][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:31.359][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-01 16:05:31.360][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-01 16:05:31.361][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:31.361][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:31.362][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-01 16:05:31.363][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-01 16:05:31.364][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:31.365][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:31.366][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-01 16:05:31.367][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-01 16:05:31.368][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:31.369][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:31.370][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-01 16:05:31.371][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-01 16:05:31.372][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:31.373][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:31.374][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-03-01 16:05:31.375][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-03-01 16:05:31.376][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:31.377][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:31.378][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-03-01 16:05:31.379][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-03-01 16:05:31.380][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:31.381][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:31.382][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:05:31.383][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:05:31.384][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:31.385][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:31.386][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-03-01 16:05:31.387][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-03-01 16:05:31.387][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:31.388][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:31.389][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:05:31.390][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:05:31.391][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:31.392][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:31.393][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:05:31.394][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:05:31.395][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:31.396][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:31.397][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:05:31.398][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:05:31.399][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:31.400][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:31.401][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:05:31.402][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:05:31.402][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:31.403][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:31.404][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:05:31.405][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:05:31.406][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:31.407][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:31.408][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:05:31.409][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:05:31.410][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:31.411][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:31.412][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:05:31.416][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:05:31.417][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:31.418][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:31.419][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:05:31.420][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:05:31.421][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:31.422][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:31.423][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:05:31.424][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:05:31.424][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:31.425][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-01 16:05:31.426][self$createEntryFromContent] Accession numbers: 749674, 750690.
biodb.TRACE[2025-03-01 16:05:31.427][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2025-03-01 16:05:31.428][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2025-03-01 16:05:31.429][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:31.430][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:31.431][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2025-03-01 16:05:31.432][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2025-03-01 16:05:31.433][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:31.434][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:31.435][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2025-03-01 16:05:31.436][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2025-03-01 16:05:31.436][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:31.437][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:31.442][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2025-03-01 16:05:31.443][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2025-03-01 16:05:31.444][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:31.445][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:31.446][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2025-03-01 16:05:31.447][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2025-03-01 16:05:31.447][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:31.448][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:31.449][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2025-03-01 16:05:31.450][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2025-03-01 16:05:31.451][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:31.452][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2025-03-01 16:05:31.459][biodb::testThat]
biodb.INFO [2025-03-01 16:05:31.460][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2025-03-01 16:05:31.460][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-01 16:05:31.461][biodb::testThat]
biodb.INFO [2025-03-01 16:05:31.466][biodb::testThat]
biodb.INFO [2025-03-01 16:05:31.467][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2025-03-01 16:05:31.468][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-01 16:05:31.469][biodb::testThat]
biodb.WARN [2025-03-01 16:05:31.487][self$searchForEntries] This database is not searchable by field "name".
biodb.WARN [2025-03-01 16:05:31.505][self$searchForEntries] This database is not searchable by field "name".
biodb.INFO [2025-03-01 16:05:31.512][biodb::testThat]
biodb.INFO [2025-03-01 16:05:31.513][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2025-03-01 16:05:31.514][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-01 16:05:31.515][biodb::testThat]
biodb.TRACE[2025-03-01 16:05:31.539][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-03-01 16:05:31.540][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-03-01 16:05:31.541][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:31.542][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:31.543][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-03-01 16:05:31.544][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-03-01 16:05:31.545][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:31.546][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:31.547][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-03-01 16:05:31.548][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-03-01 16:05:31.549][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:31.549][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:31.550][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-03-01 16:05:31.551][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-03-01 16:05:31.552][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:31.553][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:31.584][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-03-01 16:05:31.585][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-03-01 16:05:31.586][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:31.587][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:31.588][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-03-01 16:05:31.589][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-03-01 16:05:31.589][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:31.590][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:31.591][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-03-01 16:05:31.592][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-03-01 16:05:31.593][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:31.594][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:31.595][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-03-01 16:05:31.596][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-03-01 16:05:31.597][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:31.598][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2025-03-01 16:05:31.603][biodb::testThat]
biodb.INFO [2025-03-01 16:05:31.604][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2025-03-01 16:05:31.605][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-01 16:05:31.606][biodb::testThat]
biodb.INFO [2025-03-01 16:05:31.612][biodb::testThat]
biodb.INFO [2025-03-01 16:05:31.613][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2025-03-01 16:05:31.614][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-01 16:05:31.615][biodb::testThat]
biodb.INFO [2025-03-01 16:05:31.621][biodb::testThat]
biodb.INFO [2025-03-01 16:05:31.622][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2025-03-01 16:05:31.623][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-01 16:05:31.623][biodb::testThat]
biodb.INFO [2025-03-01 16:05:31.629][biodb::testThat]
biodb.INFO [2025-03-01 16:05:31.630][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2025-03-01 16:05:31.630][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-01 16:05:31.631][biodb::testThat]
biodb.INFO [2025-03-01 16:05:31.636][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2025-03-01 16:05:31.637][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector nci.cactus from the request scheduler
biodb.INFO [2025-03-01 16:05:31.638][self$deleteConn] Connector "nci.cactus" deleted.
biodb.DEBUG[2025-03-01 16:05:31.639][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-03-01 16:05:31.640][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-01 16:05:31.641][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-01 16:05:31.642][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:05:31.642][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:05:31.643][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:05:31.644][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2025-03-01 16:05:31.652][biodb::testContext]
biodb.INFO [2025-03-01 16:05:31.653][biodb::testContext] ********************************************************************************
biodb.INFO [2025-03-01 16:05:31.654][biodb::testContext] Test context - Example long tests
biodb.INFO [2025-03-01 16:05:31.659][biodb::testContext] ********************************************************************************
biodb.INFO [2025-03-01 16:05:31.660][biodb::testContext]
biodb.INFO [2025-03-01 16:05:31.662][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.15.0.
biodb.DEBUG[2025-03-01 16:05:31.663][self$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.21-bioc/R/site-library/biodb/definitions.yml".
biodb.DEBUG[2025-03-01 16:05:31.667][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-03-01 16:05:31.667][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-03-01 16:05:31.668][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-03-01 16:05:31.669][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:05:31.670][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:05:31.671][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:05:31.672][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-03-01 16:05:31.673][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-03-01 16:05:31.674][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:05:31.674][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:05:31.675][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:05:31.676][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-03-01 16:05:31.677][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-03-01 16:05:31.678][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:05:31.679][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:05:31.680][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:05:31.680][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-03-01 16:05:31.681][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-03-01 16:05:31.682][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-03-01 16:05:31.683][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:05:31.684][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:05:31.685][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:05:31.686][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-03-01 16:05:31.687][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-03-01 16:05:31.688][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-03-01 16:05:31.688][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:05:31.689][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:05:31.690][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:05:31.691][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-03-01 16:05:31.692][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-03-01 16:05:31.693][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:05:31.694][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:05:31.694][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:05:31.695][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-03-01 16:05:31.696][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-03-01 16:05:31.697][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-03-01 16:05:31.698][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:05:31.699][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:05:31.700][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:05:31.701][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-03-01 16:05:31.702][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-03-01 16:05:31.702][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:05:31.703][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:05:31.704][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:05:31.705][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-03-01 16:05:31.706][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-03-01 16:05:31.707][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-03-01 16:05:31.708][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:05:31.709][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:05:31.709][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:05:31.710][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-03-01 16:05:31.711][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-03-01 16:05:31.712][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-03-01 16:05:31.713][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-03-01 16:05:31.714][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-03-01 16:05:31.715][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-03-01 16:05:31.716][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:05:31.717][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:05:31.718][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[2025-03-01 16:05:31.718][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-03-01 16:05:31.719][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-03-01 16:05:31.720][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:05:31.721][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:05:31.722][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:05:31.723][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-03-01 16:05:31.724][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-03-01 16:05:31.725][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:05:31.725][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:05:31.726][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:05:31.727][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-03-01 16:05:31.728][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-03-01 16:05:31.729][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:05:31.730][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:05:31.731][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:05:31.731][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-03-01 16:05:31.732][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2025-03-01 16:05:31.733][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:05:31.734][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:05:31.735][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[2025-03-01 16:05:31.736][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-03-01 16:05:31.737][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-03-01 16:05:31.738][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:05:31.738][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:05:31.739][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:05:31.740][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-03-01 16:05:31.741][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-03-01 16:05:31.745][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-03-01 16:05:31.745][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:05:31.746][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:05:31.747][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:05:31.748][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-03-01 16:05:31.749][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-03-01 16:05:31.750][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-03-01 16:05:31.751][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:05:31.751][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:05:31.752][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:05:31.753][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-03-01 16:05:31.755][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-03-01 16:05:31.756][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2025-03-01 16:05:31.757][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-01 16:05:31.758][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-01 16:05:31.759][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-01 16:05:31.760][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-01 16:05:31.761][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-01 16:05:31.761][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-01 16:05:31.762][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-03-01 16:05:31.763][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-01 16:05:31.764][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-03-01 16:05:31.765][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-03-01 16:05:31.766][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-01 16:05:31.767][self$setPropertyValue]
biodb.DEBUG[2025-03-01 16:05:31.768][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-01 16:05:31.769][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-03-01 16:05:31.769][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-03-01 16:05:31.769][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-03-01 16:05:31.769][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-03-01 16:05:31.769][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-03-01 16:05:31.770][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-01 16:05:31.771][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-01 16:05:31.772][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-01 16:05:31.772][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-01 16:05:31.773][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-01 16:05:31.774][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-01 16:05:31.775][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-01 16:05:31.776][self$setPropertyValue]
biodb.DEBUG[2025-03-01 16:05:31.777][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-01 16:05:31.778][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-01 16:05:31.779][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-01 16:05:31.779][self$setPropertyValue]
biodb.DEBUG[2025-03-01 16:05:31.781][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-03-01 16:05:31.782][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-03-01 16:05:31.783][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-03-01 16:05:31.784][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-01 16:05:31.785][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-01 16:05:31.786][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-01 16:05:31.787][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-01 16:05:31.791][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-01 16:05:31.792][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-01 16:05:31.793][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-03-01 16:05:31.794][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-01 16:05:31.795][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-03-01 16:05:31.796][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-03-01 16:05:31.797][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-01 16:05:31.798][self$setPropertyValue]
biodb.DEBUG[2025-03-01 16:05:31.799][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-01 16:05:31.800][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-03-01 16:05:31.800][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-03-01 16:05:31.800][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-03-01 16:05:31.800][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-03-01 16:05:31.800][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-03-01 16:05:31.801][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-01 16:05:31.801][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-01 16:05:31.802][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-01 16:05:31.803][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-01 16:05:31.804][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-01 16:05:31.805][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-01 16:05:31.806][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-01 16:05:31.807][self$setPropertyValue]
biodb.DEBUG[2025-03-01 16:05:31.808][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-01 16:05:31.808][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-01 16:05:31.809][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-01 16:05:31.810][self$setPropertyValue]
biodb.DEBUG[2025-03-01 16:05:31.811][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-03-01 16:05:31.813][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-03-01 16:05:31.814][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2025-03-01 16:05:31.815][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-01 16:05:31.816][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-01 16:05:31.816][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-01 16:05:31.817][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-01 16:05:31.818][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-01 16:05:31.819][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-01 16:05:31.820][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-03-01 16:05:31.821][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-01 16:05:31.822][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-03-01 16:05:31.823][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-03-01 16:05:31.824][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-01 16:05:31.825][self$setPropertyValue]
biodb.DEBUG[2025-03-01 16:05:31.826][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-01 16:05:31.827][self$setPropertyValue]
biodb.DEBUG[2025-03-01 16:05:31.828][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-01 16:05:31.828][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-01 16:05:31.829][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-01 16:05:31.830][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-01 16:05:31.831][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-01 16:05:31.832][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-01 16:05:31.833][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-01 16:05:31.834][self$setPropertyValue]
biodb.DEBUG[2025-03-01 16:05:31.835][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-01 16:05:31.835][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-01 16:05:31.836][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-01 16:05:31.837][self$setPropertyValue]
biodb.DEBUG[2025-03-01 16:05:31.838][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-03-01 16:05:31.840][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-03-01 16:05:31.841][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-03-01 16:05:31.842][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-01 16:05:31.843][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-01 16:05:31.844][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-01 16:05:31.844][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-01 16:05:31.845][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-01 16:05:31.846][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-01 16:05:31.847][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-03-01 16:05:31.848][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-01 16:05:31.849][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-03-01 16:05:31.850][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-03-01 16:05:31.851][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-01 16:05:31.852][self$setPropertyValue]
biodb.DEBUG[2025-03-01 16:05:31.853][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-01 16:05:31.854][self$setPropertyValue]
biodb.DEBUG[2025-03-01 16:05:31.855][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-01 16:05:31.855][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-01 16:05:31.856][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-01 16:05:31.857][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-01 16:05:31.858][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-01 16:05:31.859][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-01 16:05:31.860][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-01 16:05:31.861][self$setPropertyValue]
biodb.DEBUG[2025-03-01 16:05:31.862][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-01 16:05:31.862][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-01 16:05:31.863][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-01 16:05:31.864][self$setPropertyValue]
biodb.DEBUG[2025-03-01 16:05:31.865][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-03-01 16:05:31.866][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:05:31.867][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:05:31.868][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:05:31.869][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:05:31.870][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:05:31.870][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:05:31.871][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:05:31.872][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:05:31.873][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:05:31.874][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:05:31.875][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:05:31.875][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:05:31.876][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:05:31.877][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:05:31.878][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:05:31.879][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:05:31.879][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:05:31.880][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:05:31.881][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:05:31.882][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:05:31.883][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:05:31.884][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:05:31.884][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:05:31.885][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:05:31.886][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:05:31.887][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:05:31.888][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:05:31.889][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:05:31.889][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:05:31.890][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:05:31.891][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:05:31.892][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:05:31.893][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:05:31.893][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:05:31.894][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:05:31.895][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:05:31.896][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:05:31.897][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:05:31.898][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:05:31.898][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:05:31.899][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:05:31.900][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:05:31.901][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:05:31.902][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:05:31.902][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:05:31.903][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:05:31.904][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:05:31.905][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:05:31.906][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:05:31.907][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:05:31.907][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:05:31.908][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:05:31.909][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:05:31.910][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:05:31.911][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:05:31.912][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:05:31.912][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:05:31.913][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:05:31.917][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:05:31.918][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:05:31.919][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:05:31.920][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:05:31.921][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:05:31.922][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:05:31.922][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:05:31.923][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:05:31.924][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:05:31.925][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:05:31.926][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:05:31.926][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:05:31.927][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:05:31.928][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:05:31.929][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:05:31.930][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:05:31.931][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:05:31.931][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:05:31.932][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:05:31.933][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:05:31.934][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:05:31.935][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:05:31.935][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:05:31.936][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:05:31.942][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:05:31.943][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:05:31.944][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:05:31.945][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:05:31.946][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:05:31.948][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-03-01 16:05:31.949][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-03-01 16:05:31.951][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-03-01 16:05:31.952][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-03-01 16:05:31.954][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-03-01 16:05:31.955][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-03-01 16:05:31.957][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-03-01 16:05:31.958][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-03-01 16:05:31.959][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-03-01 16:05:31.961][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-03-01 16:05:31.962][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-03-01 16:05:31.964][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-03-01 16:05:31.965][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-03-01 16:05:31.967][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-03-01 16:05:31.968][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-03-01 16:05:31.970][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-03-01 16:05:31.971][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-03-01 16:05:31.973][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-03-01 16:05:31.974][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-03-01 16:05:31.976][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-03-01 16:05:31.977][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-03-01 16:05:31.979][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-03-01 16:05:31.980][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-03-01 16:05:31.982][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-03-01 16:05:31.983][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-03-01 16:05:31.985][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-03-01 16:05:31.986][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-03-01 16:05:31.987][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-03-01 16:05:31.989][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-03-01 16:05:31.990][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-03-01 16:05:31.992][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-03-01 16:05:31.993][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-03-01 16:05:31.995][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-03-01 16:05:31.996][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-03-01 16:05:31.998][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-03-01 16:05:31.999][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-03-01 16:05:32.001][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-03-01 16:05:32.002][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-03-01 16:05:32.003][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-03-01 16:05:32.005][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-03-01 16:05:32.006][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-03-01 16:05:32.008][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-03-01 16:05:32.009][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-03-01 16:05:32.011][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-03-01 16:05:32.012][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-03-01 16:05:32.014][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-03-01 16:05:32.015][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-03-01 16:05:32.017][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-03-01 16:05:32.018][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-03-01 16:05:32.019][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-03-01 16:05:32.021][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-03-01 16:05:32.022][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-03-01 16:05:32.024][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-03-01 16:05:32.025][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-03-01 16:05:32.027][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-03-01 16:05:32.028][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-03-01 16:05:32.030][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-03-01 16:05:32.031][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-03-01 16:05:32.032][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-03-01 16:05:32.034][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-03-01 16:05:32.035][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-03-01 16:05:32.037][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-03-01 16:05:32.038][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-03-01 16:05:32.040][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-03-01 16:05:32.041][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-03-01 16:05:32.042][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-03-01 16:05:32.044][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-03-01 16:05:32.045][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-03-01 16:05:32.047][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-03-01 16:05:32.048][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-03-01 16:05:32.050][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-03-01 16:05:32.051][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-03-01 16:05:32.053][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-03-01 16:05:32.054][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-03-01 16:05:32.056][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-03-01 16:05:32.070][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-03-01 16:05:32.071][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-03-01 16:05:32.072][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-03-01 16:05:32.074][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-03-01 16:05:32.075][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-03-01 16:05:32.077][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-03-01 16:05:32.078][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-03-01 16:05:32.079][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-03-01 16:05:32.081][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-03-01 16:05:32.083][initialize] This is biodb version 1.15.0.
biodb.DEBUG[2025-03-01 16:05:32.084][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-03-01 16:05:32.085][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:05:32.086][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:05:32.086][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:05:32.087][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:05:32.088][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:05:32.089][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-01 16:05:32.090][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-01 16:05:32.091][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:05:32.092][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:05:32.093][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:05:32.094][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:05:32.094][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:05:32.095][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-01 16:05:32.096][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-01 16:05:32.097][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:05:32.098][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:05:32.098][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:05:32.099][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:05:32.100][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:05:32.101][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-01 16:05:32.102][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-01 16:05:32.103][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:05:32.103][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:05:32.104][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:05:32.105][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:05:32.106][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:05:32.107][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-01 16:05:32.108][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-01 16:05:32.108][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:05:32.109][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:05:32.110][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:05:32.111][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:05:32.112][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:05:32.112][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-01 16:05:32.113][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-01 16:05:32.114][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:05:32.115][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:05:32.116][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:05:32.117][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:05:32.117][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:05:32.118][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-01 16:05:32.119][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-01 16:05:32.120][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:05:32.121][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:05:32.122][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:05:32.122][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:05:32.123][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:05:32.124][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-01 16:05:32.125][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-01 16:05:32.126][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:05:32.126][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:05:32.127][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:05:32.128][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:05:32.129][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:05:32.130][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-01 16:05:32.131][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-01 16:05:32.131][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:05:32.132][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:05:32.133][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:05:32.134][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:05:32.135][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:05:32.135][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-01 16:05:32.136][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-01 16:05:32.137][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:05:32.138][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:05:32.139][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:05:32.140][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:05:32.140][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:05:32.141][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-01 16:05:32.142][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-01 16:05:32.143][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:05:32.144][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:05:32.144][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:05:32.145][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:05:32.146][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:05:32.147][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-01 16:05:32.148][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-01 16:05:32.149][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:05:32.149][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:05:32.150][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:05:32.151][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:05:32.152][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:05:32.153][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-01 16:05:32.153][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-01 16:05:32.154][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:05:32.155][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:05:32.156][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:05:32.157][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:05:32.158][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:05:32.158][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-01 16:05:32.159][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-01 16:05:32.160][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:05:32.161][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:05:32.162][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:05:32.163][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:05:32.163][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:05:32.164][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-01 16:05:32.165][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-01 16:05:32.166][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:05:32.167][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:05:32.167][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:05:32.168][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:05:32.169][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:05:32.170][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-01 16:05:32.171][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-01 16:05:32.172][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:05:32.172][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:05:32.173][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:05:32.174][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:05:32.175][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:05:32.176][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-01 16:05:32.177][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-01 16:05:32.177][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:05:32.178][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:05:32.179][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:05:32.180][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:05:32.181][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:05:32.182][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-01 16:05:32.182][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-01 16:05:32.183][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:05:32.184][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:05:32.185][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:05:32.186][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:05:32.187][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.21-bioc-longtests/meat/biodbNci.Rcheck/biodbNci/definitions.yml".
biodb.DEBUG[2025-03-01 16:05:32.188][self$getDbsInfo()$define] Define connector nci.cactus.
biodb.DEBUG[2025-03-01 16:05:32.190][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-03-01 16:05:32.191][self$setPropertyValue] Setting property "description" to "National Cancer Institute (USA) CACTUS Database.".
biodb.DEBUG[2025-03-01 16:05:32.192][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-01 16:05:32.193][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-01 16:05:32.198][self$setPropertyValue] Setting property "downloadable" to "TRUE".
biodb.DEBUG[2025-03-01 16:05:32.199][self$setPropertyValue] Setting property "dwnld.ext" to "gz".
biodb.DEBUG[2025-03-01 16:05:32.200][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-03-01 16:05:32.200][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-01 16:05:32.201][self$setPropertyValue] Setting property "entry.content.type" to "sdf".
biodb.DEBUG[2025-03-01 16:05:32.202][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-01 16:05:32.203][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-03-01 16:05:32.204][self$setPropertyValue] Setting property "name" to "NCI CACTUS".
biodb.DEBUG[2025-03-01 16:05:32.205][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-01 16:05:32.206][self$setPropertyValue] Setting property "parsing.expr" to "NSC".
biodb.DEBUG[2025-03-01 16:05:32.206][self$setPropertyValue] Setting property "parsing.expr" to "DTP names".
biodb.DEBUG[2025-03-01 16:05:32.206][self$setPropertyValue] Setting property "parsing.expr" to "Standard InChI".
biodb.DEBUG[2025-03-01 16:05:32.206][self$setPropertyValue] Setting property "parsing.expr" to "c("Standard InChIKey", "^InChIKey=(.*)$")".
biodb.DEBUG[2025-03-01 16:05:32.206][self$setPropertyValue] Setting property "parsing.expr" to "Formula".
biodb.DEBUG[2025-03-01 16:05:32.206][self$setPropertyValue] Setting property "parsing.expr" to "Molecular Weight".
biodb.DEBUG[2025-03-01 16:05:32.206][self$setPropertyValue] Setting property "parsing.expr" to "CAS".
biodb.DEBUG[2025-03-01 16:05:32.207][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-03-01 16:05:32.208][self$setPropertyValue]
biodb.DEBUG[2025-03-01 16:05:32.209][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-03-01 16:05:32.210][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-01 16:05:32.211][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-01 16:05:32.211][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-01 16:05:32.212][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-01 16:05:32.213][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-01 16:05:32.214][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-01 16:05:32.215][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/".
biodb.DEBUG[2025-03-01 16:05:32.215][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/".
biodb.DEBUG[2025-03-01 16:05:32.215][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/download/nci/".
biodb.DEBUG[2025-03-01 16:05:32.215][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/download/nci/NCI-Open_2012-05-01.sdf.gz".
biodb.DEBUG[2025-03-01 16:05:32.216][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-01 16:05:32.217][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-01 16:05:32.218][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-03-01 16:05:32.219][self$setPropertyValue]
biodb.DEBUG[2025-03-01 16:05:32.220][self$getEntryFields()$define] Define field nci.cactus.id.
biodb.DEBUG[2025-03-01 16:05:32.223][super$initialize] Initialize connector nci.cactus.
biodb.DEBUG[2025-03-01 16:05:32.224][super$initialize] Register connector nci.cactus with the request scheduler
biodb.DEBUG[2025-03-01 16:05:32.225][private$bdb$getRequestScheduler()$re ...] Register connector nci.cactus.
biodb.DEBUG[2025-03-01 16:05:32.226][private$addConnectorRules] Create new rule for URL "cactus.nci.nih.gov" of connector "nci.cactus".
biodb.DEBUG[2025-03-01 16:05:32.227][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-03-01 16:05:32.228][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-03-01 16:05:32.229][rule$addConnector] Connector "nci.cactus" is already listed in rule "cactus.nci.nih.gov".
biodb.DEBUG[2025-03-01 16:05:32.230][rule$addConnector] Connector "nci.cactus" is already listed in rule "cactus.nci.nih.gov".
biodb.DEBUG[2025-03-01 16:05:32.232][rule$addConnector] Connector "nci.cactus" is already listed in rule "cactus.nci.nih.gov".
biodb.DEBUG[2025-03-01 16:05:32.233][biodb$getFactory()$createConn] Creating new connector nci.cactus for database class nci.cactus .
biodb.INFO [2025-03-01 16:05:32.233][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2025-03-01 16:05:32.235][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector nci.cactus from the request scheduler
biodb.INFO [2025-03-01 16:05:32.235][self$deleteConn] Connector "nci.cactus" deleted.
biodb.DEBUG[2025-03-01 16:05:32.236][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-03-01 16:05:32.237][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-01 16:05:32.238][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-01 16:05:32.239][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:05:32.240][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:05:32.240][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:05:32.241][FUN] Functions in observer 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 
  4.237   0.239   4.465

'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_1.11.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.21-bioc-longtests/meat/biodbNci.Rcheck’
* using R Under development (unstable) (2025-02-19 r87757)
* 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 24.04.2 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 ‘1.11.0’
* 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 ‘1.11.0’
** 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   -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   -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   -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   -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)