Back to Long Tests report for BioC 3.17

This page was generated on 2023-10-14 21:30:02 -0400 (Sat, 14 Oct 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.2 LTS)x86_644.3.1 (2023-06-16) -- "Beagle Scouts" 4626
palomino3Windows Server 2022 Datacenterx644.3.1 (2023-06-16 ucrt) -- "Beagle Scouts" 4379
merida1macOS 12.6.4 Montereyx86_644.3.1 (2023-06-16) -- "Beagle Scouts" 4395
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 7/31HostnameOS / ArchCHECK
biodbExpasy 1.4.0  (landing page)
Pierrick Roger
Snapshot Date: 2023-10-14 09:55:02 -0400 (Sat, 14 Oct 2023)
git_url: https://git.bioconductor.org/packages/biodbExpasy
git_branch: RELEASE_3_17
git_last_commit: 6a2064e
git_last_commit_date: 2023-04-25 11:36:51 -0400 (Tue, 25 Apr 2023)
nebbiolo1Linux (Ubuntu 22.04.2 LTS) / x86_64  OK  
palomino3Windows Server 2022 Datacenter / x64  OK  
merida1macOS 12.6.4 Monterey / x86_64  OK  

CHECK results for biodbExpasy on nebbiolo1


To the developers/maintainers of the biodbExpasy 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: biodbExpasy
Version: 1.4.0
Command: /home/biocbuild/bbs-3.17-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 biodbExpasy_1.4.0.tar.gz
StartedAt: 2023-10-14 11:04:32 -0400 (Sat, 14 Oct 2023)
EndedAt: 2023-10-14 11:05:21 -0400 (Sat, 14 Oct 2023)
EllapsedTime: 48.4 seconds
RetCode: 0
Status:   OK  
CheckDir: biodbExpasy.Rcheck
Warnings: 0

Tests output

biodbExpasy.Rcheck/tests/testthat.Rout


R version 4.3.1 (2023-06-16) -- "Beagle Scouts"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

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

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Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> # Script needed to run testthat automatically from ‘R CMD check’. See
> # testthat::test_dir documentation.
> library(testthat)
> library(biodbExpasy)
> Sys.setenv(TESTTHAT_REPORTER="summary")
> Sys.setenv(BIODB_LOG_DST="console")
> test_check("biodbExpasy")
biodb.INFO [2023-10-14 11:05:07.542][biodb::testContext]
biodb.INFO [2023-10-14 11:05:07.544][biodb::testContext] ********************************************************************************
biodb.INFO [2023-10-14 11:05:07.545][biodb::testContext] Test context - Generic long tests
biodb.INFO [2023-10-14 11:05:07.546][biodb::testContext] ********************************************************************************
biodb.INFO [2023-10-14 11:05:07.547][biodb::testContext]
biodb.INFO [2023-10-14 11:05:07.554][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.8.1.
biodb.DEBUG[2023-10-14 11:05:07.556][self$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.17-bioc/R/site-library/biodb/definitions.yml".
biodb.DEBUG[2023-10-14 11:05:07.564][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-10-14 11:05:07.565][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2023-10-14 11:05:07.566][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2023-10-14 11:05:07.567][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:05:07.568][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:05:07.569][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:05:07.570][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2023-10-14 11:05:07.590][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2023-10-14 11:05:07.591][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:05:07.592][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:05:07.593][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:05:07.594][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2023-10-14 11:05:07.595][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2023-10-14 11:05:07.596][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:05:07.597][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:05:07.598][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:05:07.599][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2023-10-14 11:05:07.600][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2023-10-14 11:05:07.601][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2023-10-14 11:05:07.602][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:05:07.603][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:05:07.604][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:05:07.605][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2023-10-14 11:05:07.606][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2023-10-14 11:05:07.607][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2023-10-14 11:05:07.608][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:05:07.609][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:05:07.610][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:05:07.611][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2023-10-14 11:05:07.612][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2023-10-14 11:05:07.613][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:05:07.614][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:05:07.615][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:05:07.616][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2023-10-14 11:05:07.617][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2023-10-14 11:05:07.618][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2023-10-14 11:05:07.619][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:05:07.620][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:05:07.620][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:05:07.621][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2023-10-14 11:05:07.623][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2023-10-14 11:05:07.623][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:05:07.624][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:05:07.625][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:05:07.626][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2023-10-14 11:05:07.627][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2023-10-14 11:05:07.628][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2023-10-14 11:05:07.629][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:05:07.630][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:05:07.631][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:05:07.632][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2023-10-14 11:05:07.633][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2023-10-14 11:05:07.634][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2023-10-14 11:05:07.635][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2023-10-14 11:05:07.636][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2023-10-14 11:05:07.638][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2023-10-14 11:05:07.638][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:05:07.639][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:05:07.640][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:05:07.641][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2023-10-14 11:05:07.642][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2023-10-14 11:05:07.643][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:05:07.644][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:05:07.645][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:05:07.646][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2023-10-14 11:05:07.647][self$set] Set key entries.sep to "|".
biodb.DEBUG[2023-10-14 11:05:07.648][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:05:07.649][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:05:07.650][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:05:07.651][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2023-10-14 11:05:07.652][self$set] Set key offline to FALSE.
biodb.DEBUG[2023-10-14 11:05:07.653][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:05:07.654][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:05:07.655][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:05:07.656][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2023-10-14 11:05:07.657][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2023-10-14 11:05:07.658][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:05:07.659][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:05:07.660][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:05:07.661][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2023-10-14 11:05:07.662][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2023-10-14 11:05:07.663][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:05:07.664][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:05:07.665][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:05:07.666][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2023-10-14 11:05:07.667][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2023-10-14 11:05:07.670][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2023-10-14 11:05:07.671][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:05:07.672][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:05:07.673][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:05:07.674][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2023-10-14 11:05:07.675][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2023-10-14 11:05:07.676][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2023-10-14 11:05:07.677][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:05:07.678][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:05:07.679][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:05:07.683][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2023-10-14 11:05:07.719][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-10-14 11:05:07.736][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2023-10-14 11:05:07.737][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-10-14 11:05:07.738][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-10-14 11:05:07.739][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-10-14 11:05:07.741][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-10-14 11:05:07.742][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-10-14 11:05:07.743][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-10-14 11:05:07.744][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2023-10-14 11:05:07.745][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-10-14 11:05:07.746][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-10-14 11:05:07.752][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2023-10-14 11:05:07.753][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-10-14 11:05:07.754][self$setPropertyValue]
biodb.DEBUG[2023-10-14 11:05:07.755][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-10-14 11:05:07.756][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2023-10-14 11:05:07.756][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2023-10-14 11:05:07.756][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2023-10-14 11:05:07.756][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2023-10-14 11:05:07.756][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2023-10-14 11:05:07.757][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-10-14 11:05:07.758][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-10-14 11:05:07.759][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-10-14 11:05:07.759][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-10-14 11:05:07.760][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-10-14 11:05:07.761][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-10-14 11:05:07.762][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-10-14 11:05:07.763][self$setPropertyValue]
biodb.DEBUG[2023-10-14 11:05:07.764][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-10-14 11:05:07.765][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-10-14 11:05:07.765][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-10-14 11:05:07.766][self$setPropertyValue]
biodb.DEBUG[2023-10-14 11:05:07.767][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2023-10-14 11:05:07.769][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-10-14 11:05:07.770][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2023-10-14 11:05:07.771][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-10-14 11:05:07.772][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-10-14 11:05:07.773][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-10-14 11:05:07.774][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-10-14 11:05:07.775][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-10-14 11:05:07.775][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-10-14 11:05:07.776][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2023-10-14 11:05:07.777][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-10-14 11:05:07.778][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-10-14 11:05:07.779][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2023-10-14 11:05:07.780][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-10-14 11:05:07.781][self$setPropertyValue]
biodb.DEBUG[2023-10-14 11:05:07.782][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-10-14 11:05:07.783][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2023-10-14 11:05:07.783][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2023-10-14 11:05:07.783][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2023-10-14 11:05:07.783][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2023-10-14 11:05:07.783][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2023-10-14 11:05:07.784][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-10-14 11:05:07.785][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-10-14 11:05:07.785][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-10-14 11:05:07.786][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-10-14 11:05:07.787][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-10-14 11:05:07.788][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-10-14 11:05:07.789][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-10-14 11:05:07.790][self$setPropertyValue]
biodb.DEBUG[2023-10-14 11:05:07.791][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-10-14 11:05:07.791][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-10-14 11:05:07.792][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-10-14 11:05:07.793][self$setPropertyValue]
biodb.DEBUG[2023-10-14 11:05:07.794][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2023-10-14 11:05:07.796][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2023-10-14 11:05:07.797][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2023-10-14 11:05:07.798][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-10-14 11:05:07.799][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-10-14 11:05:07.800][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-10-14 11:05:07.800][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-10-14 11:05:07.801][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-10-14 11:05:07.802][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-10-14 11:05:07.803][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2023-10-14 11:05:07.804][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-10-14 11:05:07.805][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2023-10-14 11:05:07.806][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2023-10-14 11:05:07.807][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-10-14 11:05:07.808][self$setPropertyValue]
biodb.DEBUG[2023-10-14 11:05:07.809][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-10-14 11:05:07.810][self$setPropertyValue]
biodb.DEBUG[2023-10-14 11:05:07.811][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-10-14 11:05:07.811][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-10-14 11:05:07.812][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-10-14 11:05:07.813][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-10-14 11:05:07.814][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-10-14 11:05:07.815][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-10-14 11:05:07.816][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-10-14 11:05:07.817][self$setPropertyValue]
biodb.DEBUG[2023-10-14 11:05:07.817][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-10-14 11:05:07.818][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-10-14 11:05:07.819][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-10-14 11:05:07.820][self$setPropertyValue]
biodb.DEBUG[2023-10-14 11:05:07.821][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2023-10-14 11:05:07.823][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2023-10-14 11:05:07.824][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2023-10-14 11:05:07.825][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-10-14 11:05:07.825][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-10-14 11:05:07.826][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-10-14 11:05:07.827][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-10-14 11:05:07.828][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-10-14 11:05:07.829][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-10-14 11:05:07.830][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2023-10-14 11:05:07.831][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-10-14 11:05:07.832][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2023-10-14 11:05:07.833][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2023-10-14 11:05:07.834][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-10-14 11:05:07.835][self$setPropertyValue]
biodb.DEBUG[2023-10-14 11:05:07.835][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-10-14 11:05:07.836][self$setPropertyValue]
biodb.DEBUG[2023-10-14 11:05:07.837][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-10-14 11:05:07.838][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-10-14 11:05:07.839][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-10-14 11:05:07.840][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-10-14 11:05:07.841][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-10-14 11:05:07.842][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-10-14 11:05:07.842][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-10-14 11:05:07.843][self$setPropertyValue]
biodb.DEBUG[2023-10-14 11:05:07.844][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-10-14 11:05:07.845][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-10-14 11:05:07.846][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-10-14 11:05:07.847][self$setPropertyValue]
biodb.DEBUG[2023-10-14 11:05:07.851][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-10-14 11:05:07.852][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:05:07.852][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:05:07.853][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:05:07.854][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:05:07.855][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-14 11:05:07.856][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:05:07.857][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:05:07.857][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:05:07.858][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:05:07.859][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-14 11:05:07.860][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:05:07.861][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:05:07.861][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:05:07.862][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:05:07.863][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-14 11:05:07.864][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:05:07.865][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:05:07.866][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:05:07.866][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:05:07.867][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-14 11:05:07.868][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:05:07.869][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:05:07.870][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:05:07.870][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:05:07.871][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-14 11:05:07.872][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:05:07.873][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:05:07.874][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:05:07.875][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:05:07.875][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-14 11:05:07.876][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:05:07.877][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:05:07.878][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:05:07.879][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:05:07.879][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-14 11:05:07.880][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:05:07.881][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:05:07.882][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:05:07.883][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:05:07.884][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-14 11:05:07.884][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:05:07.885][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:05:07.886][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:05:07.887][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:05:07.888][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-14 11:05:07.888][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:05:07.889][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:05:07.890][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:05:07.891][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:05:07.892][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-14 11:05:07.893][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:05:07.893][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:05:07.894][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:05:07.895][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:05:07.896][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-14 11:05:07.897][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:05:07.897][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:05:07.898][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:05:07.899][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:05:07.900][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-14 11:05:07.901][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:05:07.902][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:05:07.902][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:05:07.903][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:05:07.904][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-14 11:05:07.905][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:05:07.906][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:05:07.906][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:05:07.907][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:05:07.908][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-14 11:05:07.909][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:05:07.910][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:05:07.911][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:05:07.911][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:05:07.912][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-14 11:05:07.913][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:05:07.914][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:05:07.915][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:05:07.915][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:05:07.916][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-14 11:05:07.917][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:05:07.918][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:05:07.923][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:05:07.924][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:05:07.925][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-14 11:05:07.926][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:05:07.927][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:05:07.928][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2023-10-14 11:05:07.934][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2023-10-14 11:05:07.936][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2023-10-14 11:05:07.937][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2023-10-14 11:05:07.938][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2023-10-14 11:05:07.940][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2023-10-14 11:05:07.941][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2023-10-14 11:05:07.943][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2023-10-14 11:05:07.944][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2023-10-14 11:05:07.945][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2023-10-14 11:05:07.947][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2023-10-14 11:05:07.948][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2023-10-14 11:05:07.950][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2023-10-14 11:05:07.951][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2023-10-14 11:05:07.952][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2023-10-14 11:05:07.954][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2023-10-14 11:05:07.955][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2023-10-14 11:05:07.957][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2023-10-14 11:05:07.958][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2023-10-14 11:05:07.959][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2023-10-14 11:05:07.961][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2023-10-14 11:05:07.962][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2023-10-14 11:05:07.964][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2023-10-14 11:05:07.965][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2023-10-14 11:05:07.966][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2023-10-14 11:05:07.968][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2023-10-14 11:05:07.969][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2023-10-14 11:05:07.971][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2023-10-14 11:05:07.972][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2023-10-14 11:05:07.973][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2023-10-14 11:05:07.975][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2023-10-14 11:05:07.976][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2023-10-14 11:05:07.978][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2023-10-14 11:05:07.979][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2023-10-14 11:05:07.980][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2023-10-14 11:05:07.982][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2023-10-14 11:05:07.983][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2023-10-14 11:05:07.984][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2023-10-14 11:05:07.986][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2023-10-14 11:05:07.987][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2023-10-14 11:05:07.989][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2023-10-14 11:05:07.990][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2023-10-14 11:05:07.991][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2023-10-14 11:05:07.993][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2023-10-14 11:05:07.994][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2023-10-14 11:05:07.996][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2023-10-14 11:05:07.997][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2023-10-14 11:05:07.998][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2023-10-14 11:05:08.000][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2023-10-14 11:05:08.001][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2023-10-14 11:05:08.003][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2023-10-14 11:05:08.004][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2023-10-14 11:05:08.018][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2023-10-14 11:05:08.020][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2023-10-14 11:05:08.021][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2023-10-14 11:05:08.023][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2023-10-14 11:05:08.024][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2023-10-14 11:05:08.025][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2023-10-14 11:05:08.027][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2023-10-14 11:05:08.028][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2023-10-14 11:05:08.030][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2023-10-14 11:05:08.031][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2023-10-14 11:05:08.032][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2023-10-14 11:05:08.034][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2023-10-14 11:05:08.035][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2023-10-14 11:05:08.037][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2023-10-14 11:05:08.038][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2023-10-14 11:05:08.039][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2023-10-14 11:05:08.041][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2023-10-14 11:05:08.042][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2023-10-14 11:05:08.044][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2023-10-14 11:05:08.045][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2023-10-14 11:05:08.046][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2023-10-14 11:05:08.048][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2023-10-14 11:05:08.049][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2023-10-14 11:05:08.050][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2023-10-14 11:05:08.052][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2023-10-14 11:05:08.053][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2023-10-14 11:05:08.055][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2023-10-14 11:05:08.056][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2023-10-14 11:05:08.058][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2023-10-14 11:05:08.059][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2023-10-14 11:05:08.060][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2023-10-14 11:05:08.067][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2023-10-14 11:05:08.068][initialize] This is biodb version 1.8.1.
biodb.DEBUG[2023-10-14 11:05:08.072][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-10-14 11:05:08.073][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:05:08.073][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-14 11:05:08.074][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:05:08.075][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:05:08.080][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:05:08.081][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-14 11:05:08.082][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-14 11:05:08.083][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:05:08.084][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-14 11:05:08.084][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:05:08.085][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:05:08.086][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:05:08.087][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-14 11:05:08.088][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-14 11:05:08.089][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:05:08.090][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-14 11:05:08.091][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:05:08.092][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:05:08.093][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:05:08.093][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-14 11:05:08.094][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-14 11:05:08.095][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:05:08.096][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-14 11:05:08.097][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:05:08.098][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:05:08.099][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:05:08.100][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-14 11:05:08.100][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-14 11:05:08.101][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:05:08.102][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-14 11:05:08.103][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:05:08.104][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:05:08.105][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:05:08.106][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-14 11:05:08.107][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-14 11:05:08.107][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:05:08.108][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-14 11:05:08.109][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:05:08.110][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:05:08.111][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:05:08.112][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-14 11:05:08.113][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-14 11:05:08.114][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:05:08.115][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-14 11:05:08.115][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:05:08.116][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:05:08.117][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:05:08.118][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-14 11:05:08.119][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-14 11:05:08.120][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:05:08.121][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-14 11:05:08.122][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:05:08.123][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:05:08.123][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:05:08.124][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-14 11:05:08.125][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-14 11:05:08.126][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:05:08.127][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-14 11:05:08.128][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:05:08.129][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:05:08.130][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:05:08.131][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-14 11:05:08.131][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-14 11:05:08.132][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:05:08.133][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-14 11:05:08.134][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:05:08.135][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:05:08.136][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:05:08.137][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-14 11:05:08.138][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-14 11:05:08.139][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:05:08.139][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-14 11:05:08.140][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:05:08.141][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:05:08.142][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:05:08.143][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-14 11:05:08.144][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-14 11:05:08.145][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:05:08.146][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-14 11:05:08.147][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:05:08.147][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:05:08.148][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:05:08.149][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-14 11:05:08.150][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-14 11:05:08.151][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:05:08.152][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-14 11:05:08.153][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:05:08.154][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:05:08.154][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:05:08.155][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-14 11:05:08.156][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-14 11:05:08.157][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:05:08.158][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-14 11:05:08.159][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:05:08.160][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:05:08.161][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:05:08.162][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-14 11:05:08.162][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-14 11:05:08.163][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:05:08.164][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-14 11:05:08.165][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:05:08.166][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:05:08.167][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:05:08.168][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-14 11:05:08.169][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-14 11:05:08.169][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:05:08.170][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-14 11:05:08.171][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:05:08.172][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:05:08.173][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:05:08.174][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-14 11:05:08.175][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-14 11:05:08.176][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:05:08.177][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-14 11:05:08.177][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:05:08.178][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:05:08.179][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:05:08.180][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-14 11:05:08.181][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-14 11:05:08.182][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:05:08.183][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-14 11:05:08.184][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:05:08.184][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:05:08.186][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.17-bioc-longtests/meat/biodbExpasy.Rcheck/biodbExpasy/definitions.yml".
biodb.DEBUG[2023-10-14 11:05:08.195][self$getDbsInfo()$define] Define connector expasy.enzyme.
biodb.DEBUG[2023-10-14 11:05:08.197][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-10-14 11:05:08.198][self$setPropertyValue] Setting property "description" to "Write here the description of this database.".
biodb.DEBUG[2023-10-14 11:05:08.199][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-10-14 11:05:08.200][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-10-14 11:05:08.201][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-10-14 11:05:08.202][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-10-14 11:05:08.203][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2023-10-14 11:05:08.204][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-10-14 11:05:08.205][self$setPropertyValue] Setting property "entry.content.type" to "txt".
biodb.DEBUG[2023-10-14 11:05:08.205][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-10-14 11:05:08.206][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-10-14 11:05:08.207][self$setPropertyValue] Setting property "name" to "Expasy ENZYME database.".
biodb.DEBUG[2023-10-14 11:05:08.208][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-10-14 11:05:08.209][self$setPropertyValue] Setting property "parsing.expr" to "^ID\s+([0-9.]+)$".
biodb.DEBUG[2023-10-14 11:05:08.209][self$setPropertyValue] Setting property "parsing.expr" to "^CA\s+(.+?)\.?$".
biodb.DEBUG[2023-10-14 11:05:08.209][self$setPropertyValue] Setting property "parsing.expr" to "^CF\s+(.+?)\.?$".
biodb.DEBUG[2023-10-14 11:05:08.209][self$setPropertyValue] Setting property "parsing.expr" to "^DE\s+(.+?)\.?$".
biodb.DEBUG[2023-10-14 11:05:08.210][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2023-10-14 11:05:08.211][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2023-10-14 11:05:08.212][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2023-10-14 11:05:08.213][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-10-14 11:05:08.214][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-10-14 11:05:08.215][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-10-14 11:05:08.216][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-10-14 11:05:08.216][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-10-14 11:05:08.217][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-10-14 11:05:08.218][self$setPropertyValue] Setting property "urls" to "https://enzyme.expasy.org/".
biodb.DEBUG[2023-10-14 11:05:08.219][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-10-14 11:05:08.220][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-10-14 11:05:08.221][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2023-10-14 11:05:08.222][self$setPropertyValue]
biodb.DEBUG[2023-10-14 11:05:08.227][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2023-10-14 11:05:08.250][super$initialize] Initialize connector expasy.enzyme.
biodb.DEBUG[2023-10-14 11:05:08.251][super$initialize] Register connector expasy.enzyme with the request scheduler
biodb.DEBUG[2023-10-14 11:05:08.256][private$bdb$getRequestScheduler()$re ...] Register connector expasy.enzyme.
biodb.DEBUG[2023-10-14 11:05:08.260][private$addConnectorRules] Create new rule for URL "enzyme.expasy.org" of connector "expasy.enzyme".
biodb.DEBUG[2023-10-14 11:05:08.264][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2023-10-14 11:05:08.265][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2023-10-14 11:05:08.266][biodb$getFactory()$createConn] Creating new connector expasy.enzyme for database class expasy.enzyme .
biodb.INFO [2023-10-14 11:05:08.276][biodb::testThat]
biodb.INFO [2023-10-14 11:05:08.277][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2023-10-14 11:05:08.278][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-10-14 11:05:08.279][biodb::testThat]
biodb.TRACE[2023-10-14 11:05:08.282][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/bbs-3.17-bioc-longtests/meat/biodbExpasy.Rcheck/biodbExpasy/testref/entry-expasy.enzyme-1.1.1.1-content.txt".
biodb.DEBUG[2023-10-14 11:05:08.284][biodb$getFactory()$createEntryFromCo ...] Creating Expasy ENZYME database. entries from 1 content(s).
biodb.DEBUG[2023-10-14 11:05:08.294][biodb$getFactory()$createEntryFromCo ...] Parsing 1 Expasy ENZYME database. entries.
biodb.DEBUG[2023-10-14 11:05:08.302][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-10-14 11:05:08.303][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-14 11:05:08.304][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-14 11:05:08.317][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:05:08.317][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-14 11:05:08.318][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:05:08.319][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-10-14 11:05:08.329][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-14 11:05:08.330][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-14 11:05:08.331][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:05:08.332][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:05:08.356][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2023-10-14 11:05:08.367][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2023-10-14 11:05:08.368][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:05:08.369][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:05:08.370][self$getBiodb()$getEntryFields()$get] Asked field names are: cofactor.
biodb.TRACE[2023-10-14 11:05:08.371][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2023-10-14 11:05:08.372][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:05:08.373][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:05:08.374][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-10-14 11:05:08.375][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-14 11:05:08.376][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:05:08.377][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:05:08.378][self$getBiodb()$getEntryFields()$get] Asked field names are: COFACTOR.
biodb.TRACE[2023-10-14 11:05:08.379][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2023-10-14 11:05:08.380][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:05:08.380][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:05:08.381][self$getBiodb()$getEntryFields()$get] Asked field names are: cofactor.
biodb.TRACE[2023-10-14 11:05:08.382][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2023-10-14 11:05:08.383][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:05:08.384][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:05:08.385][self$getBiodb()$getEntryFields()$get] Asked field names are: cofactor.
biodb.TRACE[2023-10-14 11:05:08.386][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2023-10-14 11:05:08.387][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:05:08.388][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:05:08.389][self$getBiodb()$getEntryFields()$get] Asked field names are: cofactor.
biodb.TRACE[2023-10-14 11:05:08.390][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2023-10-14 11:05:08.391][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:05:08.391][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:05:08.392][self$getBiodb()$getEntryFields()$get] Asked field names are: COFACTOR.
biodb.TRACE[2023-10-14 11:05:08.393][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2023-10-14 11:05:08.394][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:05:08.395][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:05:08.411][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-10-14 11:05:08.412][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-14 11:05:08.413][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:05:08.414][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:05:08.415][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-10-14 11:05:08.416][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-14 11:05:08.417][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:05:08.418][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:05:08.447][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-10-14 11:05:08.448][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-14 11:05:08.449][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:05:08.450][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:05:08.451][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-10-14 11:05:08.452][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-14 11:05:08.453][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:05:08.454][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:05:08.455][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-10-14 11:05:08.456][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-14 11:05:08.456][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:05:08.457][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:05:08.458][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2023-10-14 11:05:08.459][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2023-10-14 11:05:08.460][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:05:08.461][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:05:08.462][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2023-10-14 11:05:08.463][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2023-10-14 11:05:08.464][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:05:08.465][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:05:08.466][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-14 11:05:08.467][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-14 11:05:08.468][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:05:08.468][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:05:08.469][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2023-10-14 11:05:08.470][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2023-10-14 11:05:08.471][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:05:08.472][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:05:08.473][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-14 11:05:08.474][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-14 11:05:08.475][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:05:08.476][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:05:08.477][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-14 11:05:08.478][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-14 11:05:08.479][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:05:08.480][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:05:08.481][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-14 11:05:08.482][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-14 11:05:08.482][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:05:08.483][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:05:08.484][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-14 11:05:08.485][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-14 11:05:08.486][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:05:08.487][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:05:08.488][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-14 11:05:08.489][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-14 11:05:08.490][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:05:08.491][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:05:08.492][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-14 11:05:08.493][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-14 11:05:08.494][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:05:08.495][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-10-14 11:05:08.496][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 1.1.1.1.
biodb.TRACE[2023-10-14 11:05:08.498][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2023-10-14 11:05:08.504][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2023-10-14 11:05:08.505][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:05:08.506][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:05:08.507][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2023-10-14 11:05:08.508][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2023-10-14 11:05:08.509][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:05:08.510][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:05:08.511][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2023-10-14 11:05:08.512][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2023-10-14 11:05:08.513][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:05:08.513][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:05:08.514][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2023-10-14 11:05:08.515][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2023-10-14 11:05:08.516][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:05:08.517][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:05:08.531][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-14 11:05:08.532][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-14 11:05:08.533][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:05:08.534][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:05:08.547][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2023-10-14 11:05:08.548][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2023-10-14 11:05:08.549][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:05:08.550][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:05:08.555][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-14 11:05:08.556][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-14 11:05:08.557][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:05:08.558][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:05:08.559][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-14 11:05:08.560][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-14 11:05:08.561][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:05:08.562][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:05:08.563][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-14 11:05:08.564][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-14 11:05:08.565][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:05:08.565][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:05:08.568][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-14 11:05:08.569][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-14 11:05:08.570][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:05:08.570][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:05:08.571][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-14 11:05:08.572][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-14 11:05:08.573][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:05:08.574][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:05:08.575][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-14 11:05:08.576][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-14 11:05:08.577][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:05:08.578][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:05:08.579][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2023-10-14 11:05:08.580][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2023-10-14 11:05:08.581][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:05:08.582][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:05:08.583][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2023-10-14 11:05:08.584][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2023-10-14 11:05:08.584][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:05:08.585][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:05:08.586][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2023-10-14 11:05:08.587][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2023-10-14 11:05:08.588][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:05:08.589][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:05:08.597][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-14 11:05:08.598][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-14 11:05:08.599][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:05:08.600][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:05:08.601][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-14 11:05:08.602][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-14 11:05:08.602][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:05:08.603][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:05:08.604][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-14 11:05:08.605][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-14 11:05:08.606][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:05:08.607][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:05:08.608][ef$get] Asked field names are: accession.
biodb.TRACE[2023-10-14 11:05:08.609][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-14 11:05:08.610][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:05:08.611][ef$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:05:08.612][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-14 11:05:08.613][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-14 11:05:08.613][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:05:08.614][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:05:08.623][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-10-14 11:05:08.624][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-14 11:05:08.625][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:05:08.626][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:05:08.627][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-10-14 11:05:08.628][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-14 11:05:08.629][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:05:08.629][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:05:08.630][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-10-14 11:05:08.631][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-14 11:05:08.632][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:05:08.633][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:05:08.634][ef$get] Asked field names are: name.
biodb.TRACE[2023-10-14 11:05:08.635][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-10-14 11:05:08.636][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:05:08.637][ef$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:05:08.638][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-10-14 11:05:08.639][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-14 11:05:08.640][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:05:08.640][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:05:08.649][self$getBiodb()$getEntryFields()$get] Asked field names are: cofactor.
biodb.TRACE[2023-10-14 11:05:08.650][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2023-10-14 11:05:08.651][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:05:08.652][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:05:08.652][self$getBiodb()$getEntryFields()$get] Asked field names are: cofactor.
biodb.TRACE[2023-10-14 11:05:08.653][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2023-10-14 11:05:08.654][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:05:08.655][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:05:08.656][self$getBiodb()$getEntryFields()$get] Asked field names are: cofactor.
biodb.TRACE[2023-10-14 11:05:08.657][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2023-10-14 11:05:08.658][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:05:08.659][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:05:08.660][ef$get] Asked field names are: cofactor.
biodb.TRACE[2023-10-14 11:05:08.661][ef$get] Realnames of fields are: cofactor.
biodb.TRACE[2023-10-14 11:05:08.662][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:05:08.662][ef$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:05:08.663][self$getBiodb()$getEntryFields()$get] Asked field names are: cofactor.
biodb.TRACE[2023-10-14 11:05:08.664][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2023-10-14 11:05:08.665][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:05:08.666][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:05:08.674][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2023-10-14 11:05:08.675][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2023-10-14 11:05:08.676][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:05:08.677][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:05:08.678][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2023-10-14 11:05:08.679][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2023-10-14 11:05:08.680][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:05:08.681][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:05:08.682][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2023-10-14 11:05:08.683][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2023-10-14 11:05:08.684][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:05:08.685][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:05:08.685][ef$get] Asked field names are: catalytic.activity.
biodb.TRACE[2023-10-14 11:05:08.686][ef$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2023-10-14 11:05:08.687][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:05:08.688][ef$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:05:08.689][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2023-10-14 11:05:08.690][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2023-10-14 11:05:08.691][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:05:08.692][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:05:08.700][ef$get] Asked field names are: accession.
biodb.TRACE[2023-10-14 11:05:08.701][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-14 11:05:08.702][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:05:08.703][ef$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:05:08.708][ef$get] Asked field names are: catalytic.activity.
biodb.TRACE[2023-10-14 11:05:08.709][ef$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2023-10-14 11:05:08.710][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:05:08.715][ef$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:05:08.720][ef$get] Asked field names are: cofactor.
biodb.TRACE[2023-10-14 11:05:08.721][ef$get] Realnames of fields are: cofactor.
biodb.TRACE[2023-10-14 11:05:08.722][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:05:08.723][ef$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:05:08.728][ef$get] Asked field names are: name.
biodb.TRACE[2023-10-14 11:05:08.729][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-10-14 11:05:08.730][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:05:08.731][ef$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:05:08.747][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/bbs-3.17-bioc-longtests/meat/biodbExpasy.Rcheck/biodbExpasy/testref/entry-expasy.enzyme-1.1.1.54-content.txt".
biodb.DEBUG[2023-10-14 11:05:08.777][biodb$getFactory()$createEntryFromCo ...] Creating Expasy ENZYME database. entries from 1 content(s).
biodb.DEBUG[2023-10-14 11:05:08.778][biodb$getFactory()$createEntryFromCo ...] Parsing 1 Expasy ENZYME database. entries.
biodb.DEBUG[2023-10-14 11:05:08.780][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-10-14 11:05:08.781][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-14 11:05:08.782][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-14 11:05:08.787][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:05:08.788][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-14 11:05:08.788][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:05:08.789][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-10-14 11:05:08.791][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-14 11:05:08.792][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-14 11:05:08.793][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:05:08.794][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:05:08.795][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2023-10-14 11:05:08.796][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2023-10-14 11:05:08.797][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:05:08.798][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:05:08.799][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-10-14 11:05:08.800][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-14 11:05:08.801][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:05:08.802][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:05:08.803][self$getBiodb()$getEntryFields()$get] Asked field names are: COFACTOR.
biodb.TRACE[2023-10-14 11:05:08.804][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2023-10-14 11:05:08.805][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:05:08.805][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:05:08.806][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2023-10-14 11:05:08.807][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2023-10-14 11:05:08.808][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:05:08.809][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:05:08.810][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2023-10-14 11:05:08.811][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2023-10-14 11:05:08.812][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:05:08.813][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:05:08.814][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-14 11:05:08.815][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-14 11:05:08.816][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:05:08.816][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:05:08.817][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2023-10-14 11:05:08.818][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2023-10-14 11:05:08.819][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:05:08.820][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:05:08.821][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-14 11:05:08.822][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-14 11:05:08.823][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:05:08.824][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:05:08.825][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-14 11:05:08.826][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-14 11:05:08.827][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:05:08.827][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:05:08.828][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-14 11:05:08.829][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-14 11:05:08.830][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:05:08.831][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:05:08.832][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-14 11:05:08.833][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-14 11:05:08.834][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:05:08.835][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:05:08.836][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-14 11:05:08.837][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-14 11:05:08.838][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:05:08.839][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:05:08.839][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-14 11:05:08.840][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-14 11:05:08.841][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:05:08.842][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-10-14 11:05:08.843][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 1.1.1.54.
biodb.TRACE[2023-10-14 11:05:08.861][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2023-10-14 11:05:08.862][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2023-10-14 11:05:08.863][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:05:08.864][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:05:08.865][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2023-10-14 11:05:08.866][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2023-10-14 11:05:08.867][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:05:08.867][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:05:08.868][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2023-10-14 11:05:08.869][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2023-10-14 11:05:08.870][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:05:08.871][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:05:08.872][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2023-10-14 11:05:08.873][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2023-10-14 11:05:08.874][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:05:08.875][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:05:08.876][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-14 11:05:08.877][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-14 11:05:08.878][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:05:08.879][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:05:08.884][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2023-10-14 11:05:08.885][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2023-10-14 11:05:08.886][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:05:08.887][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:05:08.892][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-14 11:05:08.893][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-14 11:05:08.894][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:05:08.895][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:05:08.896][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-14 11:05:08.897][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-14 11:05:08.898][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:05:08.899][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:05:08.900][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-14 11:05:08.901][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-14 11:05:08.920][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:05:08.921][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:05:08.923][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-14 11:05:08.924][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-14 11:05:08.925][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:05:08.926][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:05:08.927][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-14 11:05:08.928][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-14 11:05:08.929][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:05:08.930][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:05:08.931][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-14 11:05:08.931][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-14 11:05:08.932][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:05:08.933][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:05:08.934][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2023-10-14 11:05:08.935][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2023-10-14 11:05:08.936][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:05:08.937][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:05:08.938][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2023-10-14 11:05:08.939][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2023-10-14 11:05:08.940][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:05:08.941][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:05:08.942][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2023-10-14 11:05:08.943][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2023-10-14 11:05:08.943][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:05:08.944][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:05:08.961][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-14 11:05:08.962][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-14 11:05:08.962][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:05:08.963][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:05:08.964][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-14 11:05:08.965][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-14 11:05:08.966][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:05:08.967][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:05:08.968][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-14 11:05:08.969][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-14 11:05:08.970][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:05:08.971][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:05:08.972][ef$get] Asked field names are: accession.
biodb.TRACE[2023-10-14 11:05:08.973][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-14 11:05:08.974][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:05:08.974][ef$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:05:08.975][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-14 11:05:08.976][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-14 11:05:08.977][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:05:08.978][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:05:08.987][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-10-14 11:05:08.988][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-14 11:05:08.989][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:05:08.989][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:05:08.990][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-10-14 11:05:08.991][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-14 11:05:08.992][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:05:08.993][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:05:08.994][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-10-14 11:05:08.995][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-14 11:05:08.996][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:05:08.997][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:05:08.998][ef$get] Asked field names are: name.
biodb.TRACE[2023-10-14 11:05:08.999][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-10-14 11:05:09.000][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:05:09.000][ef$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:05:09.001][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-10-14 11:05:09.002][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-14 11:05:09.003][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:05:09.004][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:05:09.013][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2023-10-14 11:05:09.014][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2023-10-14 11:05:09.014][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:05:09.015][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:05:09.016][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2023-10-14 11:05:09.017][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2023-10-14 11:05:09.018][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:05:09.019][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:05:09.020][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2023-10-14 11:05:09.021][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2023-10-14 11:05:09.022][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:05:09.023][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:05:09.024][ef$get] Asked field names are: catalytic.activity.
biodb.TRACE[2023-10-14 11:05:09.025][ef$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2023-10-14 11:05:09.025][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:05:09.026][ef$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:05:09.027][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2023-10-14 11:05:09.028][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2023-10-14 11:05:09.029][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:05:09.030][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:05:09.038][ef$get] Asked field names are: accession.
biodb.TRACE[2023-10-14 11:05:09.039][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-14 11:05:09.040][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:05:09.041][ef$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:05:09.046][ef$get] Asked field names are: catalytic.activity.
biodb.TRACE[2023-10-14 11:05:09.047][ef$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2023-10-14 11:05:09.048][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:05:09.049][ef$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:05:09.054][ef$get] Asked field names are: name.
biodb.TRACE[2023-10-14 11:05:09.055][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-10-14 11:05:09.056][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:05:09.057][ef$get] fields variable is a list.
biodb.INFO [2023-10-14 11:05:09.065][biodb::testThat]
biodb.INFO [2023-10-14 11:05:09.066][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2023-10-14 11:05:09.067][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-10-14 11:05:09.068][biodb::testThat]
biodb.DEBUG[2023-10-14 11:05:09.070][private$loadEntries] Creating entries from ids [2]: "1.1.1.1, 1.1.1.54".
biodb.DEBUG[2023-10-14 11:05:09.077][conn$getEntryContent] Get Expasy ENZYME database. entry content(s) for 2 id(s)...
biodb.TRACE[2023-10-14 11:05:09.081][cch$loadFileContent] Trying to load 2 files from cache: [2]: "1.1.1.1, 1.1.1.54".
biodb.INFO [2023-10-14 11:05:09.082][self$getFolderPath] Create cache folder "/home/biocbuild/.cache/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280" for "expasy.enzyme-b59b84d962b6741050ba8f70ff4db280".
biodb.TRACE[2023-10-14 11:05:09.084][cch$loadFileContent] file.exist = [2]: "FALSE, FALSE".
biodb.TRACE[2023-10-14 11:05:09.085][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2023-10-14 11:05:09.086][conn$getEntryContent] 0 Expasy ENZYME database. entry content(s) loaded from cache.
biodb.DEBUG[2023-10-14 11:05:09.087][conn$getEntryContent] 2 entry content(s) need to be fetched from Expasy ENZYME database. database "https://enzyme.expasy.org/".
biodb.DEBUG[2023-10-14 11:05:09.087][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2023-10-14 11:05:09.088][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2023-10-14 11:05:09.093][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-10-14 11:05:09.094][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-14 11:05:09.095][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-14 11:05:09.100][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:05:09.101][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-14 11:05:09.102][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:05:09.103][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:05:09.104][scheduler$sendRequest] Getting content of get URL request "https://enzyme.expasy.org/EC/1.1.1.1.txt".
biodb.DEBUG[2023-10-14 11:05:09.127][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-10-14 11:05:09.128][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-10-14 11:05:09.129][private$doSendRequestOnce] Sent URL is "https://enzyme.expasy.org/EC/1.1.1.1.txt".
biodb.TRACE[2023-10-14 11:05:10.664][getRCurlRequestResult] Using RCurl package for sending request (https://enzyme.expasy.org/EC/1.1.1.1.txt).
biodb.DEBUG[2023-10-14 11:05:11.745][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2023-10-14 11:05:11.750][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280/a52675cfd2f0c2b41556caa64d9341e3.content"
biodb.TRACE[2023-10-14 11:05:11.781][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280/a52675cfd2f0c2b41556caa64d9341e3.request"
biodb.DEBUG[2023-10-14 11:05:11.785][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-10-14 11:05:11.787][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-14 11:05:11.788][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-14 11:05:11.798][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:05:11.799][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-14 11:05:11.801][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:05:11.802][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:05:11.826][scheduler$sendRequest] Getting content of get URL request "https://enzyme.expasy.org/EC/1.1.1.54.txt".
biodb.DEBUG[2023-10-14 11:05:11.841][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-10-14 11:05:11.842][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-10-14 11:05:11.855][private$doSendRequestOnce] Sent URL is "https://enzyme.expasy.org/EC/1.1.1.54.txt".
biodb.TRACE[2023-10-14 11:05:12.879][getRCurlRequestResult] Using RCurl package for sending request (https://enzyme.expasy.org/EC/1.1.1.54.txt).
biodb.DEBUG[2023-10-14 11:05:13.711][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2023-10-14 11:05:13.716][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280/a9b93566a091cbe35a06e4b3871f95c9.content"
biodb.TRACE[2023-10-14 11:05:13.724][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280/a9b93566a091cbe35a06e4b3871f95c9.request"
biodb.TRACE[2023-10-14 11:05:13.729][private$doSaveContentToFile] Saving to cache [2]: "/home/biocbuild/.cache/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280/1.1.1.1.txt, /home/biocbuild/.cache/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280/1.1.1.54.txt"
biodb.DEBUG[2023-10-14 11:05:13.732][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2023-10-14 11:05:13.735][self$createEntryFromContent] Creating Expasy ENZYME database. entries from 2 content(s).
biodb.DEBUG[2023-10-14 11:05:13.737][self$createEntryFromContent] Parsing 2 Expasy ENZYME database. entries.
biodb.DEBUG[2023-10-14 11:05:13.740][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-10-14 11:05:13.741][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-14 11:05:13.743][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-14 11:05:13.752][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:05:13.753][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-14 11:05:13.755][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:05:13.756][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-10-14 11:05:13.759][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-14 11:05:13.761][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-14 11:05:13.762][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:05:13.763][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:05:13.765][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2023-10-14 11:05:13.766][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2023-10-14 11:05:13.767][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:05:13.768][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:05:13.770][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-10-14 11:05:13.771][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-14 11:05:13.772][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:05:13.773][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:05:13.774][self$getBiodb()$getEntryFields()$get] Asked field names are: COFACTOR.
biodb.TRACE[2023-10-14 11:05:13.775][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2023-10-14 11:05:13.776][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:05:13.777][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:05:13.779][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-10-14 11:05:13.780][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-14 11:05:13.781][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:05:13.781][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:05:13.782][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-10-14 11:05:13.783][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-14 11:05:13.784][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:05:13.785][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:05:13.789][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-10-14 11:05:13.792][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-14 11:05:13.793][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:05:13.794][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:05:13.795][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-10-14 11:05:13.796][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-14 11:05:13.797][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:05:13.798][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:05:13.799][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-10-14 11:05:13.800][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-14 11:05:13.801][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:05:13.802][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:05:13.803][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2023-10-14 11:05:13.804][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2023-10-14 11:05:13.805][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:05:13.806][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:05:13.807][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2023-10-14 11:05:13.808][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2023-10-14 11:05:13.809][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:05:13.810][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:05:13.811][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-14 11:05:13.812][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-14 11:05:13.813][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:05:13.814][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:05:13.815][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2023-10-14 11:05:13.816][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2023-10-14 11:05:13.817][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:05:13.818][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:05:13.819][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-14 11:05:13.820][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-14 11:05:13.821][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:05:13.822][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:05:13.823][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-14 11:05:13.825][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-14 11:05:13.826][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:05:13.827][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:05:13.828][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-14 11:05:13.829][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-14 11:05:13.830][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:05:13.831][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-10-14 11:05:13.832][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-10-14 11:05:13.833][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-14 11:05:13.834][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-14 11:05:13.841][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:05:13.842][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-14 11:05:13.843][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:05:13.844][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-10-14 11:05:13.847][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-14 11:05:13.848][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-14 11:05:13.849][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:05:13.850][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:05:13.851][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2023-10-14 11:05:13.852][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2023-10-14 11:05:13.853][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:05:13.854][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:05:13.855][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-10-14 11:05:13.856][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-14 11:05:13.857][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:05:13.858][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:05:13.859][self$getBiodb()$getEntryFields()$get] Asked field names are: COFACTOR.
biodb.TRACE[2023-10-14 11:05:13.861][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2023-10-14 11:05:13.861][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:05:13.862][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:05:13.864][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2023-10-14 11:05:13.865][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2023-10-14 11:05:13.866][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:05:13.867][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:05:13.868][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2023-10-14 11:05:13.869][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2023-10-14 11:05:13.870][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:05:13.871][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:05:13.872][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-14 11:05:13.873][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-14 11:05:13.874][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:05:13.875][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:05:13.876][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2023-10-14 11:05:13.877][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2023-10-14 11:05:13.878][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:05:13.879][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:05:13.880][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-14 11:05:13.881][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-14 11:05:13.882][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:05:13.883][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:05:13.884][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-14 11:05:13.885][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-14 11:05:13.886][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:05:13.887][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:05:13.888][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-14 11:05:13.889][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-14 11:05:13.890][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:05:13.891][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:05:13.892][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-14 11:05:13.893][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-14 11:05:13.894][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:05:13.895][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:05:13.896][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-14 11:05:13.897][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-14 11:05:13.898][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:05:13.899][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:05:13.900][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-14 11:05:13.901][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-14 11:05:13.902][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:05:13.903][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:05:13.904][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-14 11:05:13.905][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-14 11:05:13.906][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:05:13.907][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:05:13.908][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-14 11:05:13.909][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-14 11:05:13.910][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:05:13.911][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:05:13.912][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-14 11:05:13.913][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-14 11:05:13.914][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:05:13.915][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-10-14 11:05:13.916][self$createEntryFromContent] Accession numbers: 1.1.1.1, 1.1.1.54.
biodb.TRACE[2023-10-14 11:05:13.917][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2023-10-14 11:05:13.918][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2023-10-14 11:05:13.919][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:05:13.920][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:05:13.921][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2023-10-14 11:05:13.922][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2023-10-14 11:05:13.923][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:05:13.924][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:05:13.925][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2023-10-14 11:05:13.926][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2023-10-14 11:05:13.927][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:05:13.928][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:05:13.934][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2023-10-14 11:05:13.935][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2023-10-14 11:05:13.936][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:05:13.937][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:05:13.938][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2023-10-14 11:05:13.939][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2023-10-14 11:05:13.952][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:05:13.953][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:05:13.954][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2023-10-14 11:05:13.955][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2023-10-14 11:05:13.956][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:05:13.957][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2023-10-14 11:05:13.968][biodb::testThat]
biodb.INFO [2023-10-14 11:05:13.969][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2023-10-14 11:05:13.970][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-10-14 11:05:13.971][biodb::testThat]
biodb.TRACE[2023-10-14 11:05:13.974][ef$get] Asked field names are: name.
biodb.TRACE[2023-10-14 11:05:13.975][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-10-14 11:05:13.976][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:05:13.977][ef$get] fields variable is a list.
biodb.DEBUG[2023-10-14 11:05:13.978][function(conn, opt)] Testing searchForEntries() with entry "1.1.1.1" and field "name".
biodb.TRACE[2023-10-14 11:05:14.006][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-10-14 11:05:14.007][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-14 11:05:14.008][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:05:14.009][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:05:14.010][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-10-14 11:05:14.011][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-14 11:05:14.011][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:05:14.012][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:05:14.013][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-10-14 11:05:14.014][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-14 11:05:14.015][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:05:14.016][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-10-14 11:05:14.019][function(conn, opt)] With value "alcohol dehydrogenase".
biodb.DEBUG[2023-10-14 11:05:14.021][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://enzyme.expasy.org/enzyme-byname.html?alcohol dehydrogenase".
biodb.DEBUG[2023-10-14 11:05:14.024][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-10-14 11:05:14.025][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-10-14 11:05:14.026][private$doSendRequestOnce] Sent URL is "https://enzyme.expasy.org/enzyme-byname.html?alcohol%20dehydrogenase".
biodb.TRACE[2023-10-14 11:05:14.835][getRCurlRequestResult] Using RCurl package for sending request (https://enzyme.expasy.org/enzyme-byname.html?alcohol%20dehydrogenase).
biodb.DEBUG[2023-10-14 11:05:15.732][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2023-10-14 11:05:15.736][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280/f603fa2a57aec59588edc37541c6f6d5.content"
biodb.TRACE[2023-10-14 11:05:15.744][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280/f603fa2a57aec59588edc37541c6f6d5.request"
biodb.DEBUG[2023-10-14 11:05:15.757][function(conn, opt)] With found IDs [1]: "1.1.1.1".
biodb.INFO [2023-10-14 11:05:15.792][biodb::testThat]
biodb.INFO [2023-10-14 11:05:15.794][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2023-10-14 11:05:15.795][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-10-14 11:05:15.796][biodb::testThat]
biodb.TRACE[2023-10-14 11:05:15.825][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-10-14 11:05:15.826][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-14 11:05:15.827][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:05:15.828][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:05:15.829][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-10-14 11:05:15.830][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-14 11:05:15.831][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:05:15.832][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:05:15.832][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-10-14 11:05:15.833][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-14 11:05:15.834][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:05:15.835][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-10-14 11:05:15.865][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://enzyme.expasy.org/enzyme-byname.html?alcohol dehydrogenase".
biodb.DEBUG[2023-10-14 11:05:15.875][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-10-14 11:05:15.889][cch$loadFileContent] Trying to load 1 files from cache: [1]: "f603fa2a57aec59588edc37541c6f6d5".
biodb.TRACE[2023-10-14 11:05:15.890][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-10-14 11:05:15.891][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280/f603fa2a57aec59588edc37541c6f6d5.content".
biodb.INFO [2023-10-14 11:05:15.910][biodb::testThat]
biodb.INFO [2023-10-14 11:05:15.911][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2023-10-14 11:05:15.912][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-10-14 11:05:15.913][biodb::testThat]
biodb.TRACE[2023-10-14 11:05:15.923][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2023-10-14 11:05:15.924][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2023-10-14 11:05:15.925][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:05:15.925][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:05:15.926][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2023-10-14 11:05:15.927][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2023-10-14 11:05:15.928][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:05:15.929][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:05:15.930][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2023-10-14 11:05:15.931][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2023-10-14 11:05:15.932][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:05:15.933][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:05:15.934][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2023-10-14 11:05:15.935][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2023-10-14 11:05:15.936][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:05:15.937][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:05:15.966][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2023-10-14 11:05:15.967][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2023-10-14 11:05:15.968][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:05:15.968][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:05:15.969][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2023-10-14 11:05:15.970][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2023-10-14 11:05:15.971][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:05:15.972][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:05:15.973][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2023-10-14 11:05:15.974][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2023-10-14 11:05:15.975][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:05:15.976][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:05:15.977][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2023-10-14 11:05:15.978][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2023-10-14 11:05:15.979][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:05:15.980][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2023-10-14 11:05:15.986][biodb::testThat]
biodb.INFO [2023-10-14 11:05:15.987][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2023-10-14 11:05:15.988][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-10-14 11:05:15.989][biodb::testThat]
biodb.INFO [2023-10-14 11:05:15.998][biodb::testThat]
biodb.INFO [2023-10-14 11:05:15.999][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2023-10-14 11:05:15.999][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-10-14 11:05:16.000][biodb::testThat]
biodb.INFO [2023-10-14 11:05:16.008][biodb::testThat]
biodb.INFO [2023-10-14 11:05:16.009][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2023-10-14 11:05:16.010][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-10-14 11:05:16.011][biodb::testThat]
biodb.DEBUG[2023-10-14 11:05:16.024][function(conn, opt)] Trying to download "https://enzyme.expasy.org/cgi-bin/enzyme/enzyme-search-ec?field1=1&field2=1&field3=1&field4=1".
biodb.DEBUG[2023-10-14 11:05:16.831][getUrlContent] Use RCurl for downloading content of URL https://enzyme.expasy.org/cgi-bin/enzyme/enzyme-search-ec?field1=1&field2=1&field3=1&field4=1.
biodb.INFO [2023-10-14 11:05:17.726][biodb::testThat]
biodb.INFO [2023-10-14 11:05:17.728][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2023-10-14 11:05:17.730][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-10-14 11:05:17.732][biodb::testThat]
biodb.DEBUG[2023-10-14 11:05:19.573][getUrlContent] Use RCurl for downloading content of URL https://enzyme.expasy.org/images/1.1.1.1/image.png.
biodb.TRACE[2023-10-14 11:05:20.090][ef$get] Asked field names are: name.
biodb.TRACE[2023-10-14 11:05:20.093][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-10-14 11:05:20.095][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:05:20.097][ef$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:05:20.100][ef$get] Asked field names are: name.
biodb.TRACE[2023-10-14 11:05:20.102][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-10-14 11:05:20.104][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:05:20.106][ef$get] fields variable is a list.
biodb.INFO [2023-10-14 11:05:20.109][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2023-10-14 11:05:20.111][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector expasy.enzyme from the request scheduler
biodb.INFO [2023-10-14 11:05:20.113][self$deleteConn] Connector "expasy.enzyme" deleted.
biodb.DEBUG[2023-10-14 11:05:20.115][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2023-10-14 11:05:20.117][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-14 11:05:20.119][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-14 11:05:20.121][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:05:20.123][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-14 11:05:20.125][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:05:20.127][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2023-10-14 11:05:20.143][biodb::testContext]
biodb.INFO [2023-10-14 11:05:20.144][biodb::testContext] ********************************************************************************
biodb.INFO [2023-10-14 11:05:20.145][biodb::testContext] Test context - Example long tests
biodb.INFO [2023-10-14 11:05:20.147][biodb::testContext] ********************************************************************************
biodb.INFO [2023-10-14 11:05:20.148][biodb::testContext]
biodb.INFO [2023-10-14 11:05:20.151][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.8.1.
biodb.DEBUG[2023-10-14 11:05:20.153][self$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.17-bioc/R/site-library/biodb/definitions.yml".
biodb.DEBUG[2023-10-14 11:05:20.158][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-10-14 11:05:20.159][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2023-10-14 11:05:20.160][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2023-10-14 11:05:20.161][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:05:20.162][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:05:20.163][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[2023-10-14 11:05:20.164][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2023-10-14 11:05:20.165][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2023-10-14 11:05:20.166][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:05:20.167][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:05:20.168][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:05:20.169][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2023-10-14 11:05:20.170][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2023-10-14 11:05:20.171][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:05:20.172][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:05:20.173][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:05:20.174][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2023-10-14 11:05:20.175][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2023-10-14 11:05:20.176][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2023-10-14 11:05:20.176][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:05:20.177][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:05:20.178][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:05:20.179][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2023-10-14 11:05:20.180][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2023-10-14 11:05:20.181][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2023-10-14 11:05:20.182][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:05:20.183][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:05:20.183][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:05:20.184][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2023-10-14 11:05:20.185][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2023-10-14 11:05:20.186][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:05:20.187][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:05:20.188][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:05:20.189][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2023-10-14 11:05:20.189][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2023-10-14 11:05:20.190][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2023-10-14 11:05:20.191][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:05:20.192][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:05:20.193][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:05:20.194][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2023-10-14 11:05:20.195][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2023-10-14 11:05:20.196][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:05:20.196][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:05:20.197][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:05:20.198][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2023-10-14 11:05:20.199][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2023-10-14 11:05:20.200][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2023-10-14 11:05:20.201][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:05:20.202][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:05:20.202][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:05:20.203][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2023-10-14 11:05:20.204][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2023-10-14 11:05:20.205][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2023-10-14 11:05:20.206][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2023-10-14 11:05:20.207][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2023-10-14 11:05:20.208][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2023-10-14 11:05:20.209][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:05:20.210][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:05:20.210][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:05:20.211][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2023-10-14 11:05:20.212][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2023-10-14 11:05:20.213][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:05:20.214][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:05:20.215][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:05:20.216][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2023-10-14 11:05:20.217][self$set] Set key entries.sep to "|".
biodb.DEBUG[2023-10-14 11:05:20.217][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:05:20.218][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:05:20.219][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:05:20.220][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2023-10-14 11:05:20.221][self$set] Set key offline to FALSE.
biodb.DEBUG[2023-10-14 11:05:20.222][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:05:20.222][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:05:20.223][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:05:20.224][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2023-10-14 11:05:20.225][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2023-10-14 11:05:20.226][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:05:20.227][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:05:20.228][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:05:20.229][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2023-10-14 11:05:20.229][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2023-10-14 11:05:20.230][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:05:20.231][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:05:20.232][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:05:20.233][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2023-10-14 11:05:20.234][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2023-10-14 11:05:20.238][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2023-10-14 11:05:20.238][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:05:20.239][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:05:20.240][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:05:20.241][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2023-10-14 11:05:20.242][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2023-10-14 11:05:20.243][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2023-10-14 11:05:20.244][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:05:20.245][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:05:20.245][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:05:20.246][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2023-10-14 11:05:20.248][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-10-14 11:05:20.249][self$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[2023-10-14 11:05:20.250][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-10-14 11:05:20.251][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-10-14 11:05:20.252][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-10-14 11:05:20.253][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-10-14 11:05:20.254][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-10-14 11:05:20.255][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-10-14 11:05:20.256][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2023-10-14 11:05:20.257][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-10-14 11:05:20.257][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-10-14 11:05:20.258][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2023-10-14 11:05:20.259][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-10-14 11:05:20.260][self$setPropertyValue]
biodb.DEBUG[2023-10-14 11:05:20.261][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-10-14 11:05:20.262][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2023-10-14 11:05:20.262][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2023-10-14 11:05:20.262][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2023-10-14 11:05:20.262][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2023-10-14 11:05:20.262][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2023-10-14 11:05:20.263][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-10-14 11:05:20.264][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-10-14 11:05:20.265][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-10-14 11:05:20.266][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-10-14 11:05:20.267][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-10-14 11:05:20.267][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-10-14 11:05:20.268][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-10-14 11:05:20.269][self$setPropertyValue]
biodb.DEBUG[2023-10-14 11:05:20.270][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-10-14 11:05:20.271][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-10-14 11:05:20.272][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-10-14 11:05:20.273][self$setPropertyValue]
biodb.DEBUG[2023-10-14 11:05:20.274][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2023-10-14 11:05:20.275][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-10-14 11:05:20.276][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2023-10-14 11:05:20.281][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-10-14 11:05:20.286][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-10-14 11:05:20.287][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-10-14 11:05:20.288][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-10-14 11:05:20.289][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-10-14 11:05:20.290][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-10-14 11:05:20.291][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2023-10-14 11:05:20.291][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-10-14 11:05:20.292][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-10-14 11:05:20.293][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2023-10-14 11:05:20.294][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-10-14 11:05:20.295][self$setPropertyValue]
biodb.DEBUG[2023-10-14 11:05:20.296][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-10-14 11:05:20.297][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2023-10-14 11:05:20.297][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2023-10-14 11:05:20.297][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2023-10-14 11:05:20.297][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2023-10-14 11:05:20.297][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2023-10-14 11:05:20.298][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-10-14 11:05:20.299][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-10-14 11:05:20.300][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-10-14 11:05:20.301][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-10-14 11:05:20.301][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-10-14 11:05:20.302][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-10-14 11:05:20.303][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-10-14 11:05:20.304][self$setPropertyValue]
biodb.DEBUG[2023-10-14 11:05:20.305][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-10-14 11:05:20.306][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-10-14 11:05:20.307][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-10-14 11:05:20.308][self$setPropertyValue]
biodb.DEBUG[2023-10-14 11:05:20.309][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2023-10-14 11:05:20.310][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2023-10-14 11:05:20.311][self$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[2023-10-14 11:05:20.312][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-10-14 11:05:20.313][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-10-14 11:05:20.314][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-10-14 11:05:20.315][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-10-14 11:05:20.316][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-10-14 11:05:20.317][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-10-14 11:05:20.318][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2023-10-14 11:05:20.319][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-10-14 11:05:20.320][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2023-10-14 11:05:20.321][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2023-10-14 11:05:20.321][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-10-14 11:05:20.322][self$setPropertyValue]
biodb.DEBUG[2023-10-14 11:05:20.323][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-10-14 11:05:20.324][self$setPropertyValue]
biodb.DEBUG[2023-10-14 11:05:20.325][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-10-14 11:05:20.326][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-10-14 11:05:20.327][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-10-14 11:05:20.328][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-10-14 11:05:20.329][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-10-14 11:05:20.330][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-10-14 11:05:20.330][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-10-14 11:05:20.331][self$setPropertyValue]
biodb.DEBUG[2023-10-14 11:05:20.332][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-10-14 11:05:20.333][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-10-14 11:05:20.334][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-10-14 11:05:20.335][self$setPropertyValue]
biodb.DEBUG[2023-10-14 11:05:20.336][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2023-10-14 11:05:20.338][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2023-10-14 11:05:20.338][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2023-10-14 11:05:20.339][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-10-14 11:05:20.340][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-10-14 11:05:20.341][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-10-14 11:05:20.342][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-10-14 11:05:20.343][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-10-14 11:05:20.344][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-10-14 11:05:20.345][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2023-10-14 11:05:20.346][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-10-14 11:05:20.347][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2023-10-14 11:05:20.348][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2023-10-14 11:05:20.349][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-10-14 11:05:20.350][self$setPropertyValue]
biodb.DEBUG[2023-10-14 11:05:20.350][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-10-14 11:05:20.351][self$setPropertyValue]
biodb.DEBUG[2023-10-14 11:05:20.352][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-10-14 11:05:20.353][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-10-14 11:05:20.354][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-10-14 11:05:20.355][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-10-14 11:05:20.356][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-10-14 11:05:20.357][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-10-14 11:05:20.358][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-10-14 11:05:20.358][self$setPropertyValue]
biodb.DEBUG[2023-10-14 11:05:20.359][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-10-14 11:05:20.360][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-10-14 11:05:20.361][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-10-14 11:05:20.362][self$setPropertyValue]
biodb.DEBUG[2023-10-14 11:05:20.363][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-10-14 11:05:20.364][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:05:20.365][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:05:20.366][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:05:20.367][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:05:20.367][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-14 11:05:20.368][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:05:20.369][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:05:20.370][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:05:20.371][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:05:20.371][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-14 11:05:20.372][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:05:20.373][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:05:20.374][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:05:20.375][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:05:20.376][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-14 11:05:20.376][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:05:20.377][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:05:20.378][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:05:20.379][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:05:20.380][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-14 11:05:20.381][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:05:20.381][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:05:20.382][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:05:20.383][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:05:20.384][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-14 11:05:20.385][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:05:20.385][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:05:20.386][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:05:20.387][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:05:20.388][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-14 11:05:20.389][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:05:20.390][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:05:20.390][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:05:20.391][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:05:20.392][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-14 11:05:20.393][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:05:20.394][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:05:20.395][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:05:20.395][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:05:20.396][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-14 11:05:20.397][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:05:20.398][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:05:20.399][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:05:20.399][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:05:20.400][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-14 11:05:20.401][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:05:20.402][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:05:20.403][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:05:20.404][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:05:20.404][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-14 11:05:20.405][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:05:20.406][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:05:20.407][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:05:20.408][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:05:20.409][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-14 11:05:20.409][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:05:20.410][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:05:20.411][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:05:20.412][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:05:20.413][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-14 11:05:20.413][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:05:20.414][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:05:20.415][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:05:20.416][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:05:20.417][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-14 11:05:20.418][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:05:20.418][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:05:20.419][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:05:20.420][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:05:20.421][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-14 11:05:20.422][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:05:20.423][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:05:20.423][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:05:20.424][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:05:20.425][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-14 11:05:20.426][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:05:20.427][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:05:20.428][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:05:20.428][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:05:20.429][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-14 11:05:20.430][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:05:20.431][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:05:20.432][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:05:20.432][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:05:20.433][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-14 11:05:20.434][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:05:20.435][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:05:20.436][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2023-10-14 11:05:20.437][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2023-10-14 11:05:20.439][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2023-10-14 11:05:20.440][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2023-10-14 11:05:20.441][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2023-10-14 11:05:20.442][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2023-10-14 11:05:20.444][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2023-10-14 11:05:20.445][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2023-10-14 11:05:20.446][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2023-10-14 11:05:20.448][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2023-10-14 11:05:20.449][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2023-10-14 11:05:20.450][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2023-10-14 11:05:20.451][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2023-10-14 11:05:20.453][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2023-10-14 11:05:20.454][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2023-10-14 11:05:20.455][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2023-10-14 11:05:20.460][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2023-10-14 11:05:20.462][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2023-10-14 11:05:20.463][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2023-10-14 11:05:20.464][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2023-10-14 11:05:20.466][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2023-10-14 11:05:20.467][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2023-10-14 11:05:20.468][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2023-10-14 11:05:20.469][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2023-10-14 11:05:20.471][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2023-10-14 11:05:20.472][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2023-10-14 11:05:20.473][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2023-10-14 11:05:20.474][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2023-10-14 11:05:20.476][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2023-10-14 11:05:20.477][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2023-10-14 11:05:20.478][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2023-10-14 11:05:20.480][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2023-10-14 11:05:20.481][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2023-10-14 11:05:20.482][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2023-10-14 11:05:20.483][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2023-10-14 11:05:20.485][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2023-10-14 11:05:20.486][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2023-10-14 11:05:20.487][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2023-10-14 11:05:20.489][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2023-10-14 11:05:20.490][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2023-10-14 11:05:20.491][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2023-10-14 11:05:20.492][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2023-10-14 11:05:20.494][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2023-10-14 11:05:20.495][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2023-10-14 11:05:20.496][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2023-10-14 11:05:20.498][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2023-10-14 11:05:20.499][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2023-10-14 11:05:20.500][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2023-10-14 11:05:20.501][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2023-10-14 11:05:20.503][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2023-10-14 11:05:20.504][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2023-10-14 11:05:20.505][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2023-10-14 11:05:20.507][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2023-10-14 11:05:20.508][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2023-10-14 11:05:20.509][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2023-10-14 11:05:20.510][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2023-10-14 11:05:20.512][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2023-10-14 11:05:20.513][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2023-10-14 11:05:20.514][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2023-10-14 11:05:20.516][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2023-10-14 11:05:20.517][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2023-10-14 11:05:20.518][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2023-10-14 11:05:20.519][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2023-10-14 11:05:20.521][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2023-10-14 11:05:20.522][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2023-10-14 11:05:20.523][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2023-10-14 11:05:20.524][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2023-10-14 11:05:20.526][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2023-10-14 11:05:20.527][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2023-10-14 11:05:20.528][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2023-10-14 11:05:20.530][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2023-10-14 11:05:20.531][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2023-10-14 11:05:20.532][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2023-10-14 11:05:20.533][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2023-10-14 11:05:20.535][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2023-10-14 11:05:20.536][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2023-10-14 11:05:20.537][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2023-10-14 11:05:20.539][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2023-10-14 11:05:20.540][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2023-10-14 11:05:20.541][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2023-10-14 11:05:20.542][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2023-10-14 11:05:20.544][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2023-10-14 11:05:20.545][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2023-10-14 11:05:20.546][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2023-10-14 11:05:20.548][initialize] This is biodb version 1.8.1.
biodb.DEBUG[2023-10-14 11:05:20.549][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-10-14 11:05:20.550][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:05:20.550][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-14 11:05:20.551][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:05:20.552][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:05:20.557][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:05:20.557][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-14 11:05:20.558][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-14 11:05:20.559][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:05:20.560][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-14 11:05:20.561][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:05:20.562][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:05:20.562][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:05:20.563][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-14 11:05:20.564][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-14 11:05:20.565][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:05:20.566][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-14 11:05:20.566][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:05:20.567][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:05:20.568][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:05:20.569][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-14 11:05:20.570][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-14 11:05:20.571][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:05:20.571][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-14 11:05:20.572][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:05:20.573][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:05:20.574][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:05:20.575][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-14 11:05:20.576][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-14 11:05:20.576][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:05:20.577][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-14 11:05:20.578][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:05:20.579][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:05:20.580][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:05:20.580][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-14 11:05:20.581][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-14 11:05:20.582][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:05:20.583][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-14 11:05:20.584][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:05:20.585][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:05:20.585][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:05:20.586][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-14 11:05:20.587][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-14 11:05:20.588][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:05:20.589][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-14 11:05:20.589][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:05:20.590][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:05:20.591][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:05:20.592][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-14 11:05:20.593][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-14 11:05:20.594][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:05:20.594][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-14 11:05:20.595][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:05:20.596][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:05:20.597][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:05:20.598][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-14 11:05:20.599][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-14 11:05:20.599][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:05:20.600][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-14 11:05:20.601][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:05:20.602][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:05:20.603][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:05:20.604][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-14 11:05:20.604][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-14 11:05:20.605][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:05:20.606][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-14 11:05:20.607][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:05:20.608][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:05:20.608][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:05:20.609][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-14 11:05:20.610][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-14 11:05:20.611][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:05:20.612][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-14 11:05:20.613][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:05:20.613][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:05:20.614][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:05:20.615][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-14 11:05:20.616][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-14 11:05:20.617][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:05:20.618][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-14 11:05:20.618][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:05:20.619][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:05:20.620][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:05:20.621][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-14 11:05:20.622][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-14 11:05:20.623][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:05:20.623][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-14 11:05:20.624][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:05:20.625][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:05:20.626][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:05:20.627][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-14 11:05:20.628][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-14 11:05:20.633][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:05:20.633][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-14 11:05:20.634][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:05:20.635][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:05:20.636][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:05:20.637][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-14 11:05:20.638][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-14 11:05:20.638][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:05:20.639][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-14 11:05:20.640][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:05:20.641][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:05:20.642][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:05:20.642][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-14 11:05:20.643][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-14 11:05:20.644][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:05:20.645][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-14 11:05:20.646][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:05:20.647][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:05:20.647][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:05:20.648][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-14 11:05:20.649][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-14 11:05:20.650][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:05:20.651][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-14 11:05:20.652][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:05:20.652][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:05:20.653][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:05:20.654][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-14 11:05:20.655][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-14 11:05:20.656][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:05:20.657][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-14 11:05:20.657][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:05:20.658][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:05:20.660][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.17-bioc-longtests/meat/biodbExpasy.Rcheck/biodbExpasy/definitions.yml".
biodb.DEBUG[2023-10-14 11:05:20.661][self$getDbsInfo()$define] Define connector expasy.enzyme.
biodb.DEBUG[2023-10-14 11:05:20.663][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-10-14 11:05:20.664][self$setPropertyValue] Setting property "description" to "Write here the description of this database.".
biodb.DEBUG[2023-10-14 11:05:20.665][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-10-14 11:05:20.666][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-10-14 11:05:20.666][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-10-14 11:05:20.667][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-10-14 11:05:20.668][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2023-10-14 11:05:20.669][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-10-14 11:05:20.670][self$setPropertyValue] Setting property "entry.content.type" to "txt".
biodb.DEBUG[2023-10-14 11:05:20.671][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-10-14 11:05:20.672][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-10-14 11:05:20.673][self$setPropertyValue] Setting property "name" to "Expasy ENZYME database.".
biodb.DEBUG[2023-10-14 11:05:20.674][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-10-14 11:05:20.675][self$setPropertyValue] Setting property "parsing.expr" to "^ID\s+([0-9.]+)$".
biodb.DEBUG[2023-10-14 11:05:20.675][self$setPropertyValue] Setting property "parsing.expr" to "^CA\s+(.+?)\.?$".
biodb.DEBUG[2023-10-14 11:05:20.675][self$setPropertyValue] Setting property "parsing.expr" to "^CF\s+(.+?)\.?$".
biodb.DEBUG[2023-10-14 11:05:20.675][self$setPropertyValue] Setting property "parsing.expr" to "^DE\s+(.+?)\.?$".
biodb.DEBUG[2023-10-14 11:05:20.676][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2023-10-14 11:05:20.677][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2023-10-14 11:05:20.678][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2023-10-14 11:05:20.679][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-10-14 11:05:20.679][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-10-14 11:05:20.680][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-10-14 11:05:20.681][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-10-14 11:05:20.682][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-10-14 11:05:20.683][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-10-14 11:05:20.684][self$setPropertyValue] Setting property "urls" to "https://enzyme.expasy.org/".
biodb.DEBUG[2023-10-14 11:05:20.685][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-10-14 11:05:20.686][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-10-14 11:05:20.686][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2023-10-14 11:05:20.687][self$setPropertyValue]
biodb.DEBUG[2023-10-14 11:05:20.689][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2023-10-14 11:05:20.692][super$initialize] Initialize connector expasy.enzyme.
biodb.DEBUG[2023-10-14 11:05:20.693][super$initialize] Register connector expasy.enzyme with the request scheduler
biodb.DEBUG[2023-10-14 11:05:20.694][private$bdb$getRequestScheduler()$re ...] Register connector expasy.enzyme.
biodb.DEBUG[2023-10-14 11:05:20.695][private$addConnectorRules] Create new rule for URL "enzyme.expasy.org" of connector "expasy.enzyme".
biodb.DEBUG[2023-10-14 11:05:20.696][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2023-10-14 11:05:20.697][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2023-10-14 11:05:20.698][biodb$getFactory()$createConn] Creating new connector expasy.enzyme for database class expasy.enzyme .
biodb.INFO [2023-10-14 11:05:20.699][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2023-10-14 11:05:20.700][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector expasy.enzyme from the request scheduler
biodb.INFO [2023-10-14 11:05:20.701][self$deleteConn] Connector "expasy.enzyme" deleted.
biodb.DEBUG[2023-10-14 11:05:20.702][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2023-10-14 11:05:20.703][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-14 11:05:20.703][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-14 11:05:20.704][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:05:20.705][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-14 11:05:20.706][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:05:20.707][FUN] Functions in observer 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 86 ]
> 
> proc.time()
   user  system elapsed 
  5.802   0.271  14.822

'R CMD check' output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.17-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 biodbExpasy_1.4.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.17-bioc-longtests/meat/biodbExpasy.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0
    GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0
* running under: Ubuntu 22.04.3 LTS
* using session charset: UTF-8
* using options ‘--no-codoc --no-examples --no-manual --ignore-vignettes --no-stop-on-test-error’
* checking for file ‘biodbExpasy/DESCRIPTION’ ... OK
* this is package ‘biodbExpasy’ version ‘1.4.0’
* 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 ‘biodbExpasy’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Title field: should not end in a period.
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R 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 ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... SKIPPED
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking 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-3.17-bioc-longtests/meat/biodbExpasy.Rcheck/00check.log’
for details.

Installation output

biodbExpasy.Rcheck/00install.out

* installing *source* package ‘biodbExpasy’ ...
** using staged installation
** 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
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (biodbExpasy)