Back to Long Tests report for BioC 3.19

This page was generated on 2024-10-12 23:55 -0400 (Sat, 12 Oct 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.1 (2024-06-14) -- "Race for Your Life" 4763
palomino7Windows Server 2022 Datacenterx644.4.1 (2024-06-14 ucrt) -- "Race for Your Life" 4500
merida1macOS 12.7.5 Montereyx86_644.4.1 (2024-06-14) -- "Race for Your Life" 4529
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 7/33HostnameOS / ArchCHECK
biodbExpasy 1.8.1  (landing page)
Pierrick Roger
Snapshot Date: 2024-10-12 09:55 -0400 (Sat, 12 Oct 2024)
git_url: https://git.bioconductor.org/packages/biodbExpasy
git_branch: RELEASE_3_19
git_last_commit: 8918846
git_last_commit_date: 2024-08-03 12:10:16 -0400 (Sat, 03 Aug 2024)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  ERROR  
palomino7Windows Server 2022 Datacenter / x64  ERROR  
merida1macOS 12.7.5 Monterey / x86_64  ERROR  

CHECK results for biodbExpasy on merida1

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: 1.8.1
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --test-dir=longtests --no-stop-on-test-error --no-codoc --no-examples --no-manual --ignore-vignettes --check-subdirs=no biodbExpasy_1.8.1.tar.gz
StartedAt: 2024-10-12 16:01:31 -0400 (Sat, 12 Oct 2024)
EndedAt: 2024-10-12 16:02:40 -0400 (Sat, 12 Oct 2024)
EllapsedTime: 69.1 seconds
RetCode: 1
Status:   ERROR  
CheckDir: biodbExpasy.Rcheck
Warnings: NA

Tests output

biodbExpasy.Rcheck/tests/testthat.Rout.fail


R version 4.4.1 (2024-06-14) -- "Race for Your Life"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
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 [2024-10-12 16:02:27.544][biodb::testContext]
biodb.INFO [2024-10-12 16:02:27.549][biodb::testContext] ********************************************************************************
biodb.INFO [2024-10-12 16:02:27.550][biodb::testContext] Test context - Generic long tests
biodb.INFO [2024-10-12 16:02:27.552][biodb::testContext] ********************************************************************************
biodb.INFO [2024-10-12 16:02:27.553][biodb::testContext]
biodb.INFO [2024-10-12 16:02:27.561][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.12.0.
biodb.DEBUG[2024-10-12 16:02:27.564][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2024-10-12 16:02:27.573][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-10-12 16:02:27.575][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-10-12 16:02:27.576][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-10-12 16:02:27.578][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:02:27.579][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:02:27.581][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:02:27.582][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-10-12 16:02:27.614][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-10-12 16:02:27.616][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:02:27.630][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:02:27.631][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[2024-10-12 16:02:27.633][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-10-12 16:02:27.634][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-10-12 16:02:27.635][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:02:27.636][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:02:27.637][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:02:27.638][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-10-12 16:02:27.640][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-10-12 16:02:27.641][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-10-12 16:02:27.642][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:02:27.643][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:02:27.644][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:02:27.646][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-10-12 16:02:27.647][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-10-12 16:02:27.648][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-10-12 16:02:27.649][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:02:27.650][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:02:27.651][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:02:27.653][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-10-12 16:02:27.654][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-10-12 16:02:27.655][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:02:27.656][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:02:27.657][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:02:27.658][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-10-12 16:02:27.660][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-10-12 16:02:27.661][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-10-12 16:02:27.662][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:02:27.663][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:02:27.664][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:02:27.666][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-10-12 16:02:27.667][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-10-12 16:02:27.668][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:02:27.669][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:02:27.670][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:02:27.672][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-10-12 16:02:27.673][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-10-12 16:02:27.674][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-10-12 16:02:27.675][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:02:27.676][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:02:27.678][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:02:27.679][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-10-12 16:02:27.680][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-10-12 16:02:27.681][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-10-12 16:02:27.683][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-10-12 16:02:27.684][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-10-12 16:02:27.685][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-10-12 16:02:27.686][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:02:27.688][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:02:27.689][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:02:27.690][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-10-12 16:02:27.691][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-10-12 16:02:27.692][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:02:27.693][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:02:27.695][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:02:27.696][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-10-12 16:02:27.697][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-10-12 16:02:27.698][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:02:27.699][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:02:27.700][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:02:27.702][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-10-12 16:02:27.703][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-10-12 16:02:27.704][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:02:27.705][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:02:27.707][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:02:27.708][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-10-12 16:02:27.709][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-10-12 16:02:27.710][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:02:27.712][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:02:27.713][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:02:27.714][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-10-12 16:02:27.715][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-10-12 16:02:27.717][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:02:27.718][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:02:27.719][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:02:27.720][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-10-12 16:02:27.721][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-10-12 16:02:27.733][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-10-12 16:02:27.734][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:02:27.735][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:02:27.736][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:02:27.738][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-10-12 16:02:27.739][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-10-12 16:02:27.740][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-10-12 16:02:27.741][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:02:27.743][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:02:27.744][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:02:27.748][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-10-12 16:02:27.793][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-10-12 16:02:27.815][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2024-10-12 16:02:27.817][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-10-12 16:02:27.818][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-10-12 16:02:27.819][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-10-12 16:02:27.821][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-10-12 16:02:27.822][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-10-12 16:02:27.823][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-10-12 16:02:27.824][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-10-12 16:02:27.826][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-10-12 16:02:27.827][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-10-12 16:02:27.828][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-10-12 16:02:27.829][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-10-12 16:02:27.831][self$setPropertyValue]
biodb.DEBUG[2024-10-12 16:02:27.832][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-10-12 16:02:27.833][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-10-12 16:02:27.833][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-10-12 16:02:27.833][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-10-12 16:02:27.833][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-10-12 16:02:27.833][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-10-12 16:02:27.835][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-10-12 16:02:27.836][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-12 16:02:27.837][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-12 16:02:27.838][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-10-12 16:02:27.839][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-12 16:02:27.840][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-12 16:02:27.842][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-10-12 16:02:27.843][self$setPropertyValue]
biodb.DEBUG[2024-10-12 16:02:27.844][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-10-12 16:02:27.845][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-10-12 16:02:27.847][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-10-12 16:02:27.848][self$setPropertyValue]
biodb.DEBUG[2024-10-12 16:02:27.849][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-10-12 16:02:27.851][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-10-12 16:02:27.853][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-10-12 16:02:27.854][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-10-12 16:02:27.855][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-10-12 16:02:27.856][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-10-12 16:02:27.858][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-10-12 16:02:27.859][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-10-12 16:02:27.860][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-10-12 16:02:27.862][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-10-12 16:02:27.863][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-10-12 16:02:27.864][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-10-12 16:02:27.866][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-10-12 16:02:27.867][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-10-12 16:02:27.868][self$setPropertyValue]
biodb.DEBUG[2024-10-12 16:02:27.869][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-10-12 16:02:27.871][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-10-12 16:02:27.871][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-10-12 16:02:27.871][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-10-12 16:02:27.871][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-10-12 16:02:27.871][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-10-12 16:02:27.872][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-10-12 16:02:27.873][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-12 16:02:27.874][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-12 16:02:27.876][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-10-12 16:02:27.877][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-12 16:02:27.878][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-12 16:02:27.879][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-10-12 16:02:27.886][self$setPropertyValue]
biodb.DEBUG[2024-10-12 16:02:27.887][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-10-12 16:02:27.888][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-10-12 16:02:27.889][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-10-12 16:02:27.891][self$setPropertyValue]
biodb.DEBUG[2024-10-12 16:02:27.892][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-10-12 16:02:27.894][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-10-12 16:02:27.896][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2024-10-12 16:02:27.897][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-10-12 16:02:27.898][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-10-12 16:02:27.899][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-10-12 16:02:27.901][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-10-12 16:02:27.902][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-10-12 16:02:27.903][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-10-12 16:02:27.904][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-10-12 16:02:27.906][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-10-12 16:02:27.907][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-10-12 16:02:27.908][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-10-12 16:02:27.909][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-10-12 16:02:27.911][self$setPropertyValue]
biodb.DEBUG[2024-10-12 16:02:27.912][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-10-12 16:02:27.913][self$setPropertyValue]
biodb.DEBUG[2024-10-12 16:02:27.914][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-10-12 16:02:27.916][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-12 16:02:27.917][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-12 16:02:27.918][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-10-12 16:02:27.920][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-12 16:02:27.921][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-12 16:02:27.922][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-10-12 16:02:27.923][self$setPropertyValue]
biodb.DEBUG[2024-10-12 16:02:27.924][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-10-12 16:02:27.925][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-10-12 16:02:27.927][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-10-12 16:02:27.928][self$setPropertyValue]
biodb.DEBUG[2024-10-12 16:02:27.929][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-10-12 16:02:27.932][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-10-12 16:02:27.933][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-10-12 16:02:27.934][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-10-12 16:02:27.936][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-10-12 16:02:27.937][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-10-12 16:02:27.938][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-10-12 16:02:27.940][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-10-12 16:02:27.941][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-10-12 16:02:27.942][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-10-12 16:02:27.943][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-10-12 16:02:27.945][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-10-12 16:02:27.946][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-10-12 16:02:27.947][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-10-12 16:02:27.949][self$setPropertyValue]
biodb.DEBUG[2024-10-12 16:02:27.950][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-10-12 16:02:27.951][self$setPropertyValue]
biodb.DEBUG[2024-10-12 16:02:27.952][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-10-12 16:02:27.954][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-12 16:02:27.955][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-12 16:02:27.956][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-10-12 16:02:27.957][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-12 16:02:27.958][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-12 16:02:27.960][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-10-12 16:02:27.961][self$setPropertyValue]
biodb.DEBUG[2024-10-12 16:02:27.962][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-10-12 16:02:27.963][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-10-12 16:02:27.965][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-10-12 16:02:27.966][self$setPropertyValue]
biodb.DEBUG[2024-10-12 16:02:27.970][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-10-12 16:02:27.971][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:02:27.973][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:02:27.974][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:02:27.975][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:02:27.976][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-12 16:02:27.978][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:02:27.979][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:02:27.980][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:02:27.981][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:02:27.982][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-12 16:02:27.983][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:02:27.985][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:02:27.986][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:02:27.987][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:02:27.988][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-12 16:02:27.989][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:02:27.990][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:02:27.991][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:02:27.993][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:02:27.994][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-12 16:02:27.995][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:02:27.996][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:02:27.997][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:02:27.998][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:02:27.999][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-12 16:02:28.000][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:02:28.002][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:02:28.003][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:02:28.004][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:02:28.005][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-12 16:02:28.006][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:02:28.007][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:02:28.009][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:02:28.010][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:02:28.011][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-12 16:02:28.012][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:02:28.014][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:02:28.015][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:02:28.016][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:02:28.017][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-12 16:02:28.018][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:02:28.020][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:02:28.021][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:02:28.022][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:02:28.023][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-12 16:02:28.024][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:02:28.026][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:02:28.027][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:02:28.028][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:02:28.029][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-12 16:02:28.030][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:02:28.032][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:02:28.033][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:02:28.034][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:02:28.035][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-12 16:02:28.036][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:02:28.038][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:02:28.039][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:02:28.040][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:02:28.041][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-12 16:02:28.043][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:02:28.044][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:02:28.045][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:02:28.046][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:02:28.047][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-12 16:02:28.049][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:02:28.050][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:02:28.051][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:02:28.052][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:02:28.053][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-12 16:02:28.054][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:02:28.056][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:02:28.057][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:02:28.058][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:02:28.059][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-12 16:02:28.060][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:02:28.061][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:02:28.062][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:02:28.063][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:02:28.064][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-12 16:02:28.065][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:02:28.067][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:02:28.068][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:02:28.069][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:02:28.070][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-12 16:02:28.071][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:02:28.072][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:02:28.073][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-10-12 16:02:28.079][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-10-12 16:02:28.081][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-10-12 16:02:28.082][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-10-12 16:02:28.084][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-10-12 16:02:28.086][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-10-12 16:02:28.087][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-10-12 16:02:28.089][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-10-12 16:02:28.091][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-10-12 16:02:28.093][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-10-12 16:02:28.094][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-10-12 16:02:28.096][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-10-12 16:02:28.098][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-10-12 16:02:28.100][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-10-12 16:02:28.102][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-10-12 16:02:28.103][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-10-12 16:02:28.105][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-10-12 16:02:28.107][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-10-12 16:02:28.109][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-10-12 16:02:28.111][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-10-12 16:02:28.113][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-10-12 16:02:28.114][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-10-12 16:02:28.116][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-10-12 16:02:28.118][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-10-12 16:02:28.120][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-10-12 16:02:28.121][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-10-12 16:02:28.123][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-10-12 16:02:28.125][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-10-12 16:02:28.127][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-10-12 16:02:28.133][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-10-12 16:02:28.135][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-10-12 16:02:28.136][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-10-12 16:02:28.138][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-10-12 16:02:28.140][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-10-12 16:02:28.142][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-10-12 16:02:28.143][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-10-12 16:02:28.145][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-10-12 16:02:28.147][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-10-12 16:02:28.149][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-10-12 16:02:28.150][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-10-12 16:02:28.152][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-10-12 16:02:28.154][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-10-12 16:02:28.155][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-10-12 16:02:28.157][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-10-12 16:02:28.159][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-10-12 16:02:28.161][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-10-12 16:02:28.162][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-10-12 16:02:28.164][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-10-12 16:02:28.166][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-10-12 16:02:28.168][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-10-12 16:02:28.169][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-10-12 16:02:28.171][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-10-12 16:02:28.173][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-10-12 16:02:28.175][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-10-12 16:02:28.176][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-10-12 16:02:28.178][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-10-12 16:02:28.180][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-10-12 16:02:28.182][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-10-12 16:02:28.183][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-10-12 16:02:28.185][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-10-12 16:02:28.187][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-10-12 16:02:28.189][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-10-12 16:02:28.190][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-10-12 16:02:28.192][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-10-12 16:02:28.194][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-10-12 16:02:28.196][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-10-12 16:02:28.197][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-10-12 16:02:28.199][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-10-12 16:02:28.201][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-10-12 16:02:28.203][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-10-12 16:02:28.204][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-10-12 16:02:28.206][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-10-12 16:02:28.208][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-10-12 16:02:28.210][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-10-12 16:02:28.211][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-10-12 16:02:28.213][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-10-12 16:02:28.215][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-10-12 16:02:28.216][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-10-12 16:02:28.218][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-10-12 16:02:28.220][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-10-12 16:02:28.222][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-10-12 16:02:28.223][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-10-12 16:02:28.225][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-10-12 16:02:28.233][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-10-12 16:02:28.235][initialize] This is biodb version 1.12.0.
biodb.DEBUG[2024-10-12 16:02:28.239][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-10-12 16:02:28.240][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:02:28.241][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-12 16:02:28.242][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:02:28.243][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:02:28.250][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:02:28.251][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-12 16:02:28.252][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-12 16:02:28.253][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:02:28.254][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-12 16:02:28.255][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:02:28.256][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:02:28.257][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:02:28.258][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-12 16:02:28.259][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-12 16:02:28.261][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:02:28.262][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-12 16:02:28.263][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:02:28.264][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:02:28.265][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:02:28.266][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-12 16:02:28.267][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-12 16:02:28.268][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:02:28.269][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-12 16:02:28.270][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:02:28.271][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:02:28.273][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:02:28.274][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-12 16:02:28.275][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-12 16:02:28.276][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:02:28.277][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-12 16:02:28.278][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:02:28.279][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:02:28.280][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:02:28.281][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-12 16:02:28.282][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-12 16:02:28.283][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:02:28.284][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-12 16:02:28.285][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:02:28.287][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:02:28.288][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:02:28.289][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-12 16:02:28.290][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-12 16:02:28.291][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:02:28.292][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-12 16:02:28.293][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:02:28.294][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:02:28.295][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:02:28.296][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-12 16:02:28.298][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-12 16:02:28.299][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:02:28.300][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-12 16:02:28.301][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:02:28.302][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:02:28.303][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:02:28.304][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-12 16:02:28.305][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-12 16:02:28.306][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:02:28.307][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-12 16:02:28.308][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:02:28.310][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:02:28.311][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:02:28.312][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-12 16:02:28.313][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-12 16:02:28.314][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:02:28.315][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-12 16:02:28.316][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:02:28.317][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:02:28.318][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:02:28.319][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-12 16:02:28.321][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-12 16:02:28.322][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:02:28.323][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-12 16:02:28.324][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:02:28.325][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:02:28.326][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:02:28.327][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-12 16:02:28.328][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-12 16:02:28.329][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:02:28.330][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-12 16:02:28.331][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:02:28.333][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:02:28.334][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:02:28.335][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-12 16:02:28.336][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-12 16:02:28.337][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:02:28.338][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-12 16:02:28.339][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:02:28.340][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:02:28.341][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:02:28.342][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-12 16:02:28.343][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-12 16:02:28.345][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:02:28.346][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-12 16:02:28.347][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:02:28.348][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:02:28.349][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:02:28.350][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-12 16:02:28.351][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-12 16:02:28.352][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:02:28.353][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-12 16:02:28.354][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:02:28.355][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:02:28.357][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:02:28.362][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-12 16:02:28.363][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-12 16:02:28.364][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:02:28.365][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-12 16:02:28.366][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:02:28.368][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:02:28.369][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:02:28.370][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-12 16:02:28.371][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-12 16:02:28.372][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:02:28.373][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-12 16:02:28.374][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:02:28.375][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:02:28.376][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:02:28.377][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-12 16:02:28.378][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-12 16:02:28.380][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:02:28.381][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-12 16:02:28.382][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:02:28.383][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:02:28.385][biodb$loadDefinitions] Load definitions from file "/Users/biocbuild/bbs-3.19-bioc-longtests/meat/biodbExpasy.Rcheck/biodbExpasy/definitions.yml".
biodb.DEBUG[2024-10-12 16:02:28.398][self$getDbsInfo()$define] Define connector expasy.enzyme.
biodb.DEBUG[2024-10-12 16:02:28.401][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-10-12 16:02:28.402][self$setPropertyValue] Setting property "description" to "Write here the description of this database.".
biodb.DEBUG[2024-10-12 16:02:28.403][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-10-12 16:02:28.405][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-10-12 16:02:28.406][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-10-12 16:02:28.407][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-10-12 16:02:28.408][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-10-12 16:02:28.410][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-10-12 16:02:28.411][self$setPropertyValue] Setting property "entry.content.type" to "txt".
biodb.DEBUG[2024-10-12 16:02:28.412][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-10-12 16:02:28.413][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-10-12 16:02:28.414][self$setPropertyValue] Setting property "name" to "Expasy ENZYME database.".
biodb.DEBUG[2024-10-12 16:02:28.416][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-10-12 16:02:28.417][self$setPropertyValue] Setting property "parsing.expr" to "^ID\s+([0-9.]+)$".
biodb.DEBUG[2024-10-12 16:02:28.417][self$setPropertyValue] Setting property "parsing.expr" to "^CA\s+(.+?)\.?$".
biodb.DEBUG[2024-10-12 16:02:28.417][self$setPropertyValue] Setting property "parsing.expr" to "^CF\s+(.+?)\.?$".
biodb.DEBUG[2024-10-12 16:02:28.417][self$setPropertyValue] Setting property "parsing.expr" to "^DE\s+(.+?)\.?$".
biodb.DEBUG[2024-10-12 16:02:28.418][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-10-12 16:02:28.420][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-10-12 16:02:28.421][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2024-10-12 16:02:28.422][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-12 16:02:28.423][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-12 16:02:28.424][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-10-12 16:02:28.425][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-12 16:02:28.427][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-12 16:02:28.428][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-10-12 16:02:28.429][self$setPropertyValue] Setting property "urls" to "https://enzyme.expasy.org/".
biodb.DEBUG[2024-10-12 16:02:28.430][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-10-12 16:02:28.431][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-10-12 16:02:28.433][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-10-12 16:02:28.434][self$setPropertyValue]
biodb.DEBUG[2024-10-12 16:02:28.442][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-10-12 16:02:28.466][super$initialize] Initialize connector expasy.enzyme.
biodb.DEBUG[2024-10-12 16:02:28.467][super$initialize] Register connector expasy.enzyme with the request scheduler
biodb.DEBUG[2024-10-12 16:02:28.472][private$bdb$getRequestScheduler()$re ...] Register connector expasy.enzyme.
biodb.DEBUG[2024-10-12 16:02:28.476][private$addConnectorRules] Create new rule for URL "enzyme.expasy.org" of connector "expasy.enzyme".
biodb.DEBUG[2024-10-12 16:02:28.481][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-10-12 16:02:28.482][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-10-12 16:02:28.484][biodb$getFactory()$createConn] Creating new connector expasy.enzyme for database class expasy.enzyme .
biodb.INFO [2024-10-12 16:02:28.494][biodb::testThat]
biodb.INFO [2024-10-12 16:02:28.495][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2024-10-12 16:02:28.497][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-10-12 16:02:28.498][biodb::testThat]
biodb.TRACE[2024-10-12 16:02:28.502][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/bbs-3.19-bioc-longtests/meat/biodbExpasy.Rcheck/biodbExpasy/testref/entry-expasy.enzyme-1.1.1.1-content.txt".
biodb.DEBUG[2024-10-12 16:02:28.504][biodb$getFactory()$createEntryFromCo ...] Creating Expasy ENZYME database. entries from 1 content(s).
biodb.DEBUG[2024-10-12 16:02:28.508][biodb$getFactory()$createEntryFromCo ...] Parsing 1 Expasy ENZYME database. entries.
biodb.DEBUG[2024-10-12 16:02:28.519][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-12 16:02:28.520][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-12 16:02:28.521][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-12 16:02:28.539][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:02:28.540][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-12 16:02:28.542][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:02:28.543][FUN] Functions in observer BiodbConfig: [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[2024-10-12 16:02:28.554][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-12 16:02:28.556][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-12 16:02:28.557][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:02:28.558][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:02:28.596][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-10-12 16:02:28.623][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-10-12 16:02:28.624][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:02:28.626][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:02:28.627][self$getBiodb()$getEntryFields()$get] Asked field names are: cofactor.
biodb.TRACE[2024-10-12 16:02:28.629][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-10-12 16:02:28.630][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:02:28.631][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:02:28.632][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-12 16:02:28.634][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-12 16:02:28.635][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:02:28.636][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:02:28.638][self$getBiodb()$getEntryFields()$get] Asked field names are: COFACTOR.
biodb.TRACE[2024-10-12 16:02:28.639][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-10-12 16:02:28.640][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:02:28.641][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:02:28.643][self$getBiodb()$getEntryFields()$get] Asked field names are: cofactor.
biodb.TRACE[2024-10-12 16:02:28.644][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-10-12 16:02:28.645][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:02:28.646][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:02:28.648][self$getBiodb()$getEntryFields()$get] Asked field names are: cofactor.
biodb.TRACE[2024-10-12 16:02:28.649][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-10-12 16:02:28.650][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:02:28.651][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:02:28.653][self$getBiodb()$getEntryFields()$get] Asked field names are: cofactor.
biodb.TRACE[2024-10-12 16:02:28.654][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-10-12 16:02:28.655][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:02:28.656][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:02:28.658][self$getBiodb()$getEntryFields()$get] Asked field names are: COFACTOR.
biodb.TRACE[2024-10-12 16:02:28.659][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-10-12 16:02:28.661][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:02:28.662][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:02:28.688][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-12 16:02:28.689][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-12 16:02:28.691][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:02:28.692][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:02:28.693][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-12 16:02:28.694][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-12 16:02:28.696][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:02:28.697][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:02:28.744][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-12 16:02:28.746][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-12 16:02:28.747][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:02:28.748][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:02:28.749][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-12 16:02:28.751][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-12 16:02:28.752][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:02:28.753][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:02:28.754][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-12 16:02:28.756][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-12 16:02:28.757][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:02:28.758][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:02:28.759][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-10-12 16:02:28.761][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-10-12 16:02:28.762][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:02:28.763][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:02:28.764][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-10-12 16:02:28.765][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-10-12 16:02:28.767][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:02:28.768][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:02:28.769][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-12 16:02:28.770][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-12 16:02:28.772][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:02:28.773][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:02:28.774][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-10-12 16:02:28.775][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-10-12 16:02:28.776][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:02:28.778][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:02:28.779][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-12 16:02:28.780][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-12 16:02:28.781][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:02:28.783][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:02:28.784][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-12 16:02:28.785][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-12 16:02:28.786][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:02:28.788][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:02:28.789][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-12 16:02:28.790][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-12 16:02:28.792][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:02:28.793][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:02:28.794][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-12 16:02:28.796][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-12 16:02:28.797][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:02:28.798][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:02:28.799][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-12 16:02:28.801][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-12 16:02:28.802][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:02:28.803][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:02:28.834][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-12 16:02:28.836][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-12 16:02:28.837][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:02:28.838][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-12 16:02:28.839][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 1.1.1.1.
biodb.TRACE[2024-10-12 16:02:28.842][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-10-12 16:02:28.844][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-10-12 16:02:28.845][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:02:28.846][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:02:28.847][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-10-12 16:02:28.849][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-10-12 16:02:28.850][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:02:28.851][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:02:28.852][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-10-12 16:02:28.854][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-10-12 16:02:28.855][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:02:28.856][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:02:28.857][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-10-12 16:02:28.859][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-10-12 16:02:28.860][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:02:28.861][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:02:28.881][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-12 16:02:28.882][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-12 16:02:28.883][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:02:28.885][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:02:28.904][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-10-12 16:02:28.906][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-10-12 16:02:28.907][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:02:28.908][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:02:28.916][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-12 16:02:28.917][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-12 16:02:28.919][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:02:28.920][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:02:28.921][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-12 16:02:28.922][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-12 16:02:28.924][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:02:28.926][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:02:28.927][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-12 16:02:28.929][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-12 16:02:28.930][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:02:28.932][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:02:28.936][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-12 16:02:28.937][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-12 16:02:28.939][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:02:28.940][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:02:28.942][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-12 16:02:28.944][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-12 16:02:28.945][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:02:28.946][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:02:28.948][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-12 16:02:28.949][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-12 16:02:28.951][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:02:28.952][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:02:28.954][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-10-12 16:02:28.955][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-10-12 16:02:28.956][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:02:28.957][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:02:28.959][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-10-12 16:02:28.960][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-10-12 16:02:28.961][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:02:28.962][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:02:28.964][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-10-12 16:02:28.965][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-10-12 16:02:28.966][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:02:28.968][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:02:28.978][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-12 16:02:28.980][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-12 16:02:28.981][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:02:28.983][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:02:28.984][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-12 16:02:28.985][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-12 16:02:28.986][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:02:28.988][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:02:28.989][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-12 16:02:28.990][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-12 16:02:28.991][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:02:28.993][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:02:28.994][ef$get] Asked field names are: accession.
biodb.TRACE[2024-10-12 16:02:28.995][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-12 16:02:28.997][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:02:28.998][ef$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:02:28.999][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-12 16:02:29.001][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-12 16:02:29.002][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:02:29.003][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:02:29.015][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-12 16:02:29.017][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-12 16:02:29.018][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:02:29.019][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:02:29.021][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-12 16:02:29.022][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-12 16:02:29.023][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:02:29.025][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:02:29.026][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-12 16:02:29.027][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-12 16:02:29.028][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:02:29.030][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:02:29.031][ef$get] Asked field names are: name.
biodb.TRACE[2024-10-12 16:02:29.032][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-10-12 16:02:29.034][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:02:29.035][ef$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:02:29.036][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-12 16:02:29.038][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-12 16:02:29.039][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:02:29.040][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:02:29.056][self$getBiodb()$getEntryFields()$get] Asked field names are: cofactor.
biodb.TRACE[2024-10-12 16:02:29.058][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-10-12 16:02:29.059][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:02:29.060][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:02:29.062][self$getBiodb()$getEntryFields()$get] Asked field names are: cofactor.
biodb.TRACE[2024-10-12 16:02:29.063][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-10-12 16:02:29.064][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:02:29.065][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:02:29.067][self$getBiodb()$getEntryFields()$get] Asked field names are: cofactor.
biodb.TRACE[2024-10-12 16:02:29.068][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-10-12 16:02:29.069][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:02:29.070][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:02:29.072][ef$get] Asked field names are: cofactor.
biodb.TRACE[2024-10-12 16:02:29.073][ef$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-10-12 16:02:29.074][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:02:29.076][ef$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:02:29.077][self$getBiodb()$getEntryFields()$get] Asked field names are: cofactor.
biodb.TRACE[2024-10-12 16:02:29.078][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-10-12 16:02:29.080][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:02:29.081][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:02:29.093][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-10-12 16:02:29.094][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-10-12 16:02:29.095][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:02:29.097][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:02:29.098][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-10-12 16:02:29.099][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-10-12 16:02:29.100][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:02:29.102][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:02:29.103][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-10-12 16:02:29.104][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-10-12 16:02:29.105][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:02:29.107][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:02:29.108][ef$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-10-12 16:02:29.110][ef$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-10-12 16:02:29.111][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:02:29.113][ef$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:02:29.114][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-10-12 16:02:29.116][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-10-12 16:02:29.117][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:02:29.118][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:02:29.130][ef$get] Asked field names are: accession.
biodb.TRACE[2024-10-12 16:02:29.132][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-12 16:02:29.133][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:02:29.134][ef$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:02:29.141][ef$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-10-12 16:02:29.142][ef$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-10-12 16:02:29.144][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:02:29.145][ef$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:02:29.153][ef$get] Asked field names are: cofactor.
biodb.TRACE[2024-10-12 16:02:29.155][ef$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-10-12 16:02:29.157][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:02:29.158][ef$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:02:29.165][ef$get] Asked field names are: name.
biodb.TRACE[2024-10-12 16:02:29.166][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-10-12 16:02:29.167][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:02:29.168][ef$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:02:29.193][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/bbs-3.19-bioc-longtests/meat/biodbExpasy.Rcheck/biodbExpasy/testref/entry-expasy.enzyme-1.1.1.54-content.txt".
biodb.DEBUG[2024-10-12 16:02:29.244][biodb$getFactory()$createEntryFromCo ...] Creating Expasy ENZYME database. entries from 1 content(s).
biodb.DEBUG[2024-10-12 16:02:29.246][biodb$getFactory()$createEntryFromCo ...] Parsing 1 Expasy ENZYME database. entries.
biodb.DEBUG[2024-10-12 16:02:29.248][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-12 16:02:29.249][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-12 16:02:29.250][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-12 16:02:29.261][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:02:29.262][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-12 16:02:29.263][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:02:29.264][FUN] Functions in observer BiodbConfig: [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[2024-10-12 16:02:29.267][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-12 16:02:29.268][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-12 16:02:29.270][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:02:29.271][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:02:29.272][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-10-12 16:02:29.274][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-10-12 16:02:29.275][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:02:29.276][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:02:29.278][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-12 16:02:29.279][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-12 16:02:29.281][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:02:29.282][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:02:29.283][self$getBiodb()$getEntryFields()$get] Asked field names are: COFACTOR.
biodb.TRACE[2024-10-12 16:02:29.285][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-10-12 16:02:29.286][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:02:29.287][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:02:29.289][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-10-12 16:02:29.290][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-10-12 16:02:29.291][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:02:29.293][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:02:29.294][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-10-12 16:02:29.295][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-10-12 16:02:29.297][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:02:29.298][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:02:29.299][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-12 16:02:29.301][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-12 16:02:29.302][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:02:29.303][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:02:29.305][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-10-12 16:02:29.306][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-10-12 16:02:29.307][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:02:29.309][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:02:29.310][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-12 16:02:29.311][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-12 16:02:29.313][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:02:29.314][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:02:29.315][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-12 16:02:29.317][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-12 16:02:29.318][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:02:29.319][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:02:29.320][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-12 16:02:29.322][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-12 16:02:29.323][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:02:29.324][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:02:29.326][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-12 16:02:29.327][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-12 16:02:29.328][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:02:29.329][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:02:29.331][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-12 16:02:29.332][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-12 16:02:29.333][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:02:29.335][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:02:29.337][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-12 16:02:29.339][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-12 16:02:29.341][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:02:29.342][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-12 16:02:29.343][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 1.1.1.54.
biodb.TRACE[2024-10-12 16:02:29.374][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-10-12 16:02:29.376][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-10-12 16:02:29.377][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:02:29.378][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:02:29.379][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-10-12 16:02:29.381][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-10-12 16:02:29.382][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:02:29.383][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:02:29.385][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-10-12 16:02:29.386][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-10-12 16:02:29.387][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:02:29.388][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:02:29.390][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-10-12 16:02:29.391][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-10-12 16:02:29.392][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:02:29.394][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:02:29.396][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-12 16:02:29.397][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-12 16:02:29.399][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:02:29.400][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:02:29.407][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-10-12 16:02:29.408][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-10-12 16:02:29.410][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:02:29.411][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:02:29.418][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-12 16:02:29.419][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-12 16:02:29.420][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:02:29.422][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:02:29.423][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-12 16:02:29.425][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-12 16:02:29.426][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:02:29.427][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:02:29.428][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-12 16:02:29.430][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-12 16:02:29.431][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:02:29.432][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:02:29.435][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-12 16:02:29.437][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-12 16:02:29.438][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:02:29.439][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:02:29.440][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-12 16:02:29.442][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-12 16:02:29.443][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:02:29.444][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:02:29.445][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-12 16:02:29.447][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-12 16:02:29.448][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:02:29.449][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:02:29.451][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-10-12 16:02:29.452][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-10-12 16:02:29.453][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:02:29.454][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:02:29.456][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-10-12 16:02:29.457][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-10-12 16:02:29.458][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:02:29.459][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:02:29.465][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-10-12 16:02:29.466][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-10-12 16:02:29.467][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:02:29.468][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:02:29.491][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-12 16:02:29.492][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-12 16:02:29.493][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:02:29.494][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:02:29.496][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-12 16:02:29.497][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-12 16:02:29.498][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:02:29.499][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:02:29.501][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-12 16:02:29.502][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-12 16:02:29.503][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:02:29.504][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:02:29.505][ef$get] Asked field names are: accession.
biodb.TRACE[2024-10-12 16:02:29.507][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-12 16:02:29.508][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:02:29.509][ef$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:02:29.510][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-12 16:02:29.512][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-12 16:02:29.513][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:02:29.514][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:02:29.527][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-12 16:02:29.529][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-12 16:02:29.530][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:02:29.531][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:02:29.532][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-12 16:02:29.534][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-12 16:02:29.535][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:02:29.536][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:02:29.537][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-12 16:02:29.539][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-12 16:02:29.540][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:02:29.541][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:02:29.542][ef$get] Asked field names are: name.
biodb.TRACE[2024-10-12 16:02:29.544][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-10-12 16:02:29.545][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:02:29.546][ef$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:02:29.547][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-12 16:02:29.549][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-12 16:02:29.550][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:02:29.551][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:02:29.563][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-10-12 16:02:29.565][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-10-12 16:02:29.566][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:02:29.567][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:02:29.569][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-10-12 16:02:29.570][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-10-12 16:02:29.571][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:02:29.572][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:02:29.574][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-10-12 16:02:29.575][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-10-12 16:02:29.577][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:02:29.578][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:02:29.579][ef$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-10-12 16:02:29.581][ef$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-10-12 16:02:29.582][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:02:29.583][ef$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:02:29.585][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-10-12 16:02:29.586][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-10-12 16:02:29.587][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:02:29.588][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:02:29.600][ef$get] Asked field names are: accession.
biodb.TRACE[2024-10-12 16:02:29.601][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-12 16:02:29.602][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:02:29.603][ef$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:02:29.610][ef$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-10-12 16:02:29.612][ef$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-10-12 16:02:29.613][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:02:29.614][ef$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:02:29.621][ef$get] Asked field names are: name.
biodb.TRACE[2024-10-12 16:02:29.622][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-10-12 16:02:29.623][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:02:29.624][ef$get] fields variable is a list.
biodb.INFO [2024-10-12 16:02:29.636][biodb::testThat]
biodb.INFO [2024-10-12 16:02:29.637][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2024-10-12 16:02:29.638][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-10-12 16:02:29.640][biodb::testThat]
biodb.DEBUG[2024-10-12 16:02:29.642][private$loadEntries] Creating entries from ids [2]: "1.1.1.1, 1.1.1.54".
biodb.DEBUG[2024-10-12 16:02:29.650][conn$getEntryContent] Get Expasy ENZYME database. entry content(s) for 2 id(s)...
biodb.TRACE[2024-10-12 16:02:29.656][cch$loadFileContent] Trying to load 2 files from cache: [2]: "1.1.1.1, 1.1.1.54".
biodb.INFO [2024-10-12 16:02:29.658][self$getFolderPath] Create cache folder "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280" for "expasy.enzyme-b59b84d962b6741050ba8f70ff4db280".
biodb.TRACE[2024-10-12 16:02:29.659][cch$loadFileContent] file.exist = [2]: "FALSE, FALSE".
biodb.TRACE[2024-10-12 16:02:29.661][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-10-12 16:02:29.662][conn$getEntryContent] 0 Expasy ENZYME database. entry content(s) loaded from cache.
biodb.DEBUG[2024-10-12 16:02:29.663][conn$getEntryContent] 2 entry content(s) need to be fetched from Expasy ENZYME database. database "https://enzyme.expasy.org/".
biodb.DEBUG[2024-10-12 16:02:29.665][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-10-12 16:02:29.666][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-10-12 16:02:29.678][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-12 16:02:29.679][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-12 16:02:29.680][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-12 16:02:29.686][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:02:29.688][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-12 16:02:29.689][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:02:29.690][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:02:29.691][scheduler$sendRequest] Getting content of get URL request "https://enzyme.expasy.org/EC/1.1.1.1.txt".
biodb.DEBUG[2024-10-12 16:02:29.721][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-12 16:02:29.722][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-10-12 16:02:29.724][private$doSendRequestOnce] Sent URL is "https://enzyme.expasy.org/EC/1.1.1.1.txt".
biodb.TRACE[2024-10-12 16:02:33.382][getRCurlRequestResult] Using RCurl package for sending request (https://enzyme.expasy.org/EC/1.1.1.1.txt).
biodb.DEBUG[2024-10-12 16:02:33.846][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-10-12 16:02:33.848][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280/a52675cfd2f0c2b41556caa64d9341e3.content"
biodb.TRACE[2024-10-12 16:02:33.867][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280/a52675cfd2f0c2b41556caa64d9341e3.request"
biodb.DEBUG[2024-10-12 16:02:33.870][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-12 16:02:33.871][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-12 16:02:33.872][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-12 16:02:33.878][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:02:33.879][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-12 16:02:33.881][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:02:33.882][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:02:33.912][scheduler$sendRequest] Getting content of get URL request "https://enzyme.expasy.org/EC/1.1.1.54.txt".
biodb.DEBUG[2024-10-12 16:02:33.933][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-12 16:02:33.934][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-10-12 16:02:33.955][private$doSendRequestOnce] Sent URL is "https://enzyme.expasy.org/EC/1.1.1.54.txt".
biodb.TRACE[2024-10-12 16:02:34.395][getRCurlRequestResult] Using RCurl package for sending request (https://enzyme.expasy.org/EC/1.1.1.54.txt).
biodb.DEBUG[2024-10-12 16:02:34.839][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-10-12 16:02:34.842][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280/a9b93566a091cbe35a06e4b3871f95c9.content"
biodb.TRACE[2024-10-12 16:02:34.846][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280/a9b93566a091cbe35a06e4b3871f95c9.request"
biodb.TRACE[2024-10-12 16:02:34.910][private$doSaveContentToFile] Saving to cache [2]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280/1.1.1.1.txt, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280/1.1.1.54.txt"
biodb.DEBUG[2024-10-12 16:02:34.913][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-10-12 16:02:34.914][self$createEntryFromContent] Creating Expasy ENZYME database. entries from 2 content(s).
biodb.DEBUG[2024-10-12 16:02:34.915][self$createEntryFromContent] Parsing 2 Expasy ENZYME database. entries.
biodb.DEBUG[2024-10-12 16:02:34.917][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-12 16:02:34.928][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-12 16:02:34.929][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-12 16:02:34.935][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:02:34.936][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-12 16:02:34.937][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:02:34.938][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-12 16:02:34.941][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-12 16:02:34.943][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-12 16:02:34.944][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:02:34.945][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:02:34.947][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-10-12 16:02:34.948][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-10-12 16:02:34.949][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:02:34.950][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:02:34.952][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-12 16:02:34.953][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-12 16:02:34.954][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:02:34.955][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:02:34.957][self$getBiodb()$getEntryFields()$get] Asked field names are: COFACTOR.
biodb.TRACE[2024-10-12 16:02:34.958][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-10-12 16:02:34.959][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:02:34.960][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:02:34.961][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-12 16:02:34.963][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-12 16:02:34.964][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:02:34.965][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:02:34.966][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-12 16:02:34.968][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-12 16:02:34.969][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:02:34.970][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:02:34.971][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-12 16:02:34.972][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-12 16:02:34.974][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:02:34.975][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:02:34.976][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-12 16:02:34.977][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-12 16:02:34.978][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:02:34.980][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:02:34.981][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-12 16:02:34.982][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-12 16:02:34.983][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:02:34.984][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:02:34.986][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-10-12 16:02:34.987][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-10-12 16:02:34.988][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:02:34.989][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:02:34.991][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-10-12 16:02:34.992][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-10-12 16:02:34.993][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:02:34.994][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:02:34.995][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-12 16:02:34.997][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-12 16:02:34.998][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:02:34.999][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:02:35.000][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-10-12 16:02:35.001][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-10-12 16:02:35.003][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:02:35.004][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:02:35.005][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-12 16:02:35.006][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-12 16:02:35.008][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:02:35.009][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:02:35.010][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-12 16:02:35.011][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-12 16:02:35.012][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:02:35.013][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:02:35.015][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-12 16:02:35.016][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-12 16:02:35.017][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:02:35.018][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-12 16:02:35.020][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-12 16:02:35.021][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-12 16:02:35.022][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-12 16:02:35.028][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:02:35.029][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-12 16:02:35.030][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:02:35.031][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-12 16:02:35.033][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-12 16:02:35.035][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-12 16:02:35.036][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:02:35.037][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:02:35.039][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-10-12 16:02:35.040][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-10-12 16:02:35.041][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:02:35.042][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:02:35.044][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-12 16:02:35.045][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-12 16:02:35.046][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:02:35.047][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:02:35.049][self$getBiodb()$getEntryFields()$get] Asked field names are: COFACTOR.
biodb.TRACE[2024-10-12 16:02:35.050][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-10-12 16:02:35.051][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:02:35.052][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:02:35.054][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-10-12 16:02:35.055][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-10-12 16:02:35.056][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:02:35.057][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:02:35.058][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-10-12 16:02:35.060][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-10-12 16:02:35.061][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:02:35.062][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:02:35.063][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-12 16:02:35.065][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-12 16:02:35.066][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:02:35.067][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:02:35.068][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-10-12 16:02:35.069][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-10-12 16:02:35.070][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:02:35.072][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:02:35.073][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-12 16:02:35.078][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-12 16:02:35.079][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:02:35.080][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:02:35.082][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-12 16:02:35.083][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-12 16:02:35.084][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:02:35.085][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:02:35.086][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-12 16:02:35.088][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-12 16:02:35.089][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:02:35.090][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:02:35.091][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-12 16:02:35.093][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-12 16:02:35.094][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:02:35.095][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:02:35.096][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-12 16:02:35.098][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-12 16:02:35.099][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:02:35.100][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:02:35.101][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-12 16:02:35.102][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-12 16:02:35.103][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:02:35.105][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:02:35.106][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-12 16:02:35.107][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-12 16:02:35.108][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:02:35.109][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:02:35.111][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-12 16:02:35.112][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-12 16:02:35.113][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:02:35.114][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:02:35.115][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-12 16:02:35.117][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-12 16:02:35.118][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:02:35.119][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-12 16:02:35.120][self$createEntryFromContent] Accession numbers: 1.1.1.1, 1.1.1.54.
biodb.TRACE[2024-10-12 16:02:35.122][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2024-10-12 16:02:35.123][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2024-10-12 16:02:35.124][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:02:35.125][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:02:35.126][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2024-10-12 16:02:35.128][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2024-10-12 16:02:35.129][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:02:35.130][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:02:35.131][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2024-10-12 16:02:35.133][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2024-10-12 16:02:35.134][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:02:35.135][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:02:35.142][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2024-10-12 16:02:35.143][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2024-10-12 16:02:35.144][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:02:35.145][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:02:35.147][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2024-10-12 16:02:35.148][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2024-10-12 16:02:35.149][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:02:35.150][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:02:35.152][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2024-10-12 16:02:35.153][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2024-10-12 16:02:35.154][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:02:35.155][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-10-12 16:02:35.166][biodb::testThat]
biodb.INFO [2024-10-12 16:02:35.168][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2024-10-12 16:02:35.169][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-10-12 16:02:35.170][biodb::testThat]
biodb.TRACE[2024-10-12 16:02:35.174][ef$get] Asked field names are: name.
biodb.TRACE[2024-10-12 16:02:35.175][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-10-12 16:02:35.176][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:02:35.178][ef$get] fields variable is a list.
biodb.DEBUG[2024-10-12 16:02:35.179][function(conn, opt)] Testing searchForEntries() with entry "1.1.1.1" and field "name".
biodb.TRACE[2024-10-12 16:02:35.214][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-12 16:02:35.215][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-12 16:02:35.216][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:02:35.217][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:02:35.219][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-12 16:02:35.220][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-12 16:02:35.221][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:02:35.222][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:02:35.223][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-12 16:02:35.225][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-12 16:02:35.230][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:02:35.231][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-12 16:02:35.235][function(conn, opt)] With value "alcohol dehydrogenase".
biodb.DEBUG[2024-10-12 16:02:35.237][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://enzyme.expasy.org/enzyme-byname.html?alcohol dehydrogenase".
biodb.DEBUG[2024-10-12 16:02:35.241][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-12 16:02:35.242][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-10-12 16:02:35.243][private$doSendRequestOnce] Sent URL is "https://enzyme.expasy.org/enzyme-byname.html?alcohol%20dehydrogenase".
biodb.TRACE[2024-10-12 16:02:35.716][getRCurlRequestResult] Using RCurl package for sending request (https://enzyme.expasy.org/enzyme-byname.html?alcohol%20dehydrogenase).
biodb.DEBUG[2024-10-12 16:02:36.189][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-10-12 16:02:36.192][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280/f603fa2a57aec59588edc37541c6f6d5.content"
biodb.TRACE[2024-10-12 16:02:36.254][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280/f603fa2a57aec59588edc37541c6f6d5.request"
biodb.DEBUG[2024-10-12 16:02:36.261][function(conn, opt)] With found IDs [1]: "1.1.1.1".
biodb.INFO [2024-10-12 16:02:36.280][biodb::testThat]
biodb.INFO [2024-10-12 16:02:36.282][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2024-10-12 16:02:36.283][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-10-12 16:02:36.284][biodb::testThat]
biodb.TRACE[2024-10-12 16:02:36.316][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-12 16:02:36.318][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-12 16:02:36.319][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:02:36.320][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:02:36.321][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-12 16:02:36.323][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-12 16:02:36.324][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:02:36.325][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:02:36.326][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-12 16:02:36.328][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-12 16:02:36.329][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:02:36.330][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-12 16:02:36.367][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://enzyme.expasy.org/enzyme-byname.html?alcohol dehydrogenase".
biodb.DEBUG[2024-10-12 16:02:36.370][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-10-12 16:02:36.399][cch$loadFileContent] Trying to load 1 files from cache: [1]: "f603fa2a57aec59588edc37541c6f6d5".
biodb.TRACE[2024-10-12 16:02:36.401][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-10-12 16:02:36.402][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280/f603fa2a57aec59588edc37541c6f6d5.content".
biodb.INFO [2024-10-12 16:02:36.424][biodb::testThat]
biodb.INFO [2024-10-12 16:02:36.426][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2024-10-12 16:02:36.427][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-10-12 16:02:36.428][biodb::testThat]
biodb.TRACE[2024-10-12 16:02:36.440][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-10-12 16:02:36.442][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-10-12 16:02:36.443][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:02:36.444][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:02:36.446][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-10-12 16:02:36.447][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-10-12 16:02:36.448][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:02:36.449][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:02:36.451][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-10-12 16:02:36.452][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-10-12 16:02:36.453][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:02:36.454][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:02:36.455][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-10-12 16:02:36.457][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-10-12 16:02:36.458][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:02:36.459][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:02:36.505][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-10-12 16:02:36.507][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-10-12 16:02:36.508][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:02:36.509][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:02:36.511][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-10-12 16:02:36.512][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-10-12 16:02:36.513][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:02:36.514][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:02:36.515][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-10-12 16:02:36.517][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-10-12 16:02:36.518][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:02:36.519][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:02:36.520][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-10-12 16:02:36.522][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-10-12 16:02:36.523][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:02:36.524][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-10-12 16:02:36.536][biodb::testThat]
biodb.INFO [2024-10-12 16:02:36.537][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2024-10-12 16:02:36.538][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-10-12 16:02:36.539][biodb::testThat]
biodb.INFO [2024-10-12 16:02:36.551][biodb::testThat]
biodb.INFO [2024-10-12 16:02:36.552][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2024-10-12 16:02:36.553][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-10-12 16:02:36.554][biodb::testThat]
biodb.INFO [2024-10-12 16:02:36.565][biodb::testThat]
biodb.INFO [2024-10-12 16:02:36.566][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2024-10-12 16:02:36.567][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-10-12 16:02:36.568][biodb::testThat]
biodb.DEBUG[2024-10-12 16:02:36.587][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[2024-10-12 16:02:37.070][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 [2024-10-12 16:02:37.563][biodb::testThat]
biodb.INFO [2024-10-12 16:02:37.564][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2024-10-12 16:02:37.565][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-10-12 16:02:37.567][biodb::testThat]
biodb.DEBUG[2024-10-12 16:02:38.051][getUrlContent] Use base::url() for downloading content of URL https://enzyme.expasy.org/images/1.1.1.1/image.png.
biodb.TRACE[2024-10-12 16:02:38.542][ef$get] Asked field names are: name.
biodb.TRACE[2024-10-12 16:02:38.544][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-10-12 16:02:38.545][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:02:38.546][ef$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:02:38.547][ef$get] Asked field names are: name.
biodb.TRACE[2024-10-12 16:02:38.549][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-10-12 16:02:38.550][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:02:38.551][ef$get] fields variable is a list.
biodb.INFO [2024-10-12 16:02:38.552][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-10-12 16:02:38.554][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector expasy.enzyme from the request scheduler
biodb.INFO [2024-10-12 16:02:38.555][self$deleteConn] Connector "expasy.enzyme" deleted.
biodb.DEBUG[2024-10-12 16:02:38.556][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-10-12 16:02:38.557][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-12 16:02:38.558][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-12 16:02:38.559][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:02:38.560][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-12 16:02:38.562][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:02:38.563][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2024-10-12 16:02:38.575][biodb::testContext]
biodb.INFO [2024-10-12 16:02:38.577][biodb::testContext] ********************************************************************************
biodb.INFO [2024-10-12 16:02:38.578][biodb::testContext] Test context - Example long tests
biodb.INFO [2024-10-12 16:02:38.579][biodb::testContext] ********************************************************************************
biodb.INFO [2024-10-12 16:02:38.580][biodb::testContext]
biodb.INFO [2024-10-12 16:02:38.583][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.12.0.
biodb.DEBUG[2024-10-12 16:02:38.593][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2024-10-12 16:02:38.598][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-10-12 16:02:38.599][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-10-12 16:02:38.600][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-10-12 16:02:38.601][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:02:38.602][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:02:38.604][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[2024-10-12 16:02:38.605][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-10-12 16:02:38.606][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-10-12 16:02:38.607][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:02:38.608][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:02:38.609][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:02:38.610][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-10-12 16:02:38.612][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-10-12 16:02:38.613][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:02:38.614][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:02:38.615][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[2024-10-12 16:02:38.616][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-10-12 16:02:38.617][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-10-12 16:02:38.619][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-10-12 16:02:38.620][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:02:38.622][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:02:38.623][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:02:38.624][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-10-12 16:02:38.626][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-10-12 16:02:38.627][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-10-12 16:02:38.628][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:02:38.629][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:02:38.630][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:02:38.632][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-10-12 16:02:38.633][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-10-12 16:02:38.634][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:02:38.635][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:02:38.636][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:02:38.637][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-10-12 16:02:38.638][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-10-12 16:02:38.640][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-10-12 16:02:38.641][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:02:38.642][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:02:38.643][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:02:38.644][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-10-12 16:02:38.645][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-10-12 16:02:38.646][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:02:38.647][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:02:38.648][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:02:38.650][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-10-12 16:02:38.651][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-10-12 16:02:38.652][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-10-12 16:02:38.653][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:02:38.654][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:02:38.655][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[2024-10-12 16:02:38.656][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-10-12 16:02:38.658][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-10-12 16:02:38.659][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-10-12 16:02:38.660][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-10-12 16:02:38.661][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-10-12 16:02:38.663][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-10-12 16:02:38.664][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:02:38.665][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:02:38.666][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:02:38.667][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-10-12 16:02:38.668][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-10-12 16:02:38.669][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:02:38.670][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:02:38.671][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:02:38.673][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-10-12 16:02:38.674][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-10-12 16:02:38.675][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:02:38.676][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:02:38.677][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:02:38.678][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-10-12 16:02:38.679][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-10-12 16:02:38.681][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:02:38.682][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:02:38.683][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:02:38.684][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-10-12 16:02:38.685][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-10-12 16:02:38.686][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:02:38.687][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:02:38.688][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:02:38.690][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-10-12 16:02:38.691][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-10-12 16:02:38.692][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:02:38.693][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:02:38.694][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:02:38.695][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-10-12 16:02:38.697][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-10-12 16:02:38.707][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-10-12 16:02:38.708][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:02:38.709][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:02:38.710][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:02:38.711][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-10-12 16:02:38.713][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-10-12 16:02:38.714][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-10-12 16:02:38.715][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:02:38.716][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:02:38.717][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:02:38.719][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-10-12 16:02:38.721][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-10-12 16:02:38.722][self$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[2024-10-12 16:02:38.723][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-10-12 16:02:38.724][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-10-12 16:02:38.726][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-10-12 16:02:38.727][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-10-12 16:02:38.728][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-10-12 16:02:38.729][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-10-12 16:02:38.731][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-10-12 16:02:38.732][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-10-12 16:02:38.733][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-10-12 16:02:38.734][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-10-12 16:02:38.735][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-10-12 16:02:38.737][self$setPropertyValue]
biodb.DEBUG[2024-10-12 16:02:38.738][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-10-12 16:02:38.743][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-10-12 16:02:38.743][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-10-12 16:02:38.743][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-10-12 16:02:38.743][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-10-12 16:02:38.743][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-10-12 16:02:38.745][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-10-12 16:02:38.746][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-12 16:02:38.747][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-12 16:02:38.748][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-10-12 16:02:38.750][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-12 16:02:38.751][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-12 16:02:38.752][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-10-12 16:02:38.753][self$setPropertyValue]
biodb.DEBUG[2024-10-12 16:02:38.754][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-10-12 16:02:38.755][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-10-12 16:02:38.756][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-10-12 16:02:38.758][self$setPropertyValue]
biodb.DEBUG[2024-10-12 16:02:38.759][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-10-12 16:02:38.761][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-10-12 16:02:38.762][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-10-12 16:02:38.764][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-10-12 16:02:38.765][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-10-12 16:02:38.766][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-10-12 16:02:38.767][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-10-12 16:02:38.769][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-10-12 16:02:38.770][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-10-12 16:02:38.771][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-10-12 16:02:38.772][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-10-12 16:02:38.773][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-10-12 16:02:38.775][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-10-12 16:02:38.776][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-10-12 16:02:38.777][self$setPropertyValue]
biodb.DEBUG[2024-10-12 16:02:38.778][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-10-12 16:02:38.780][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-10-12 16:02:38.780][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-10-12 16:02:38.780][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-10-12 16:02:38.780][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-10-12 16:02:38.780][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-10-12 16:02:38.781][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-10-12 16:02:38.782][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-12 16:02:38.783][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-12 16:02:38.784][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-10-12 16:02:38.785][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-12 16:02:38.787][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-12 16:02:38.788][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-10-12 16:02:38.789][self$setPropertyValue]
biodb.DEBUG[2024-10-12 16:02:38.790][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-10-12 16:02:38.791][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-10-12 16:02:38.792][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-10-12 16:02:38.794][self$setPropertyValue]
biodb.DEBUG[2024-10-12 16:02:38.795][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-10-12 16:02:38.797][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-10-12 16:02:38.798][self$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[2024-10-12 16:02:38.800][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-10-12 16:02:38.801][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-10-12 16:02:38.802][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-10-12 16:02:38.803][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-10-12 16:02:38.805][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-10-12 16:02:38.806][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-10-12 16:02:38.807][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-10-12 16:02:38.808][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-10-12 16:02:38.810][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-10-12 16:02:38.811][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-10-12 16:02:38.812][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-10-12 16:02:38.813][self$setPropertyValue]
biodb.DEBUG[2024-10-12 16:02:38.815][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-10-12 16:02:38.816][self$setPropertyValue]
biodb.DEBUG[2024-10-12 16:02:38.817][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-10-12 16:02:38.818][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-12 16:02:38.819][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-12 16:02:38.821][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-10-12 16:02:38.822][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-12 16:02:38.823][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-12 16:02:38.824][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-10-12 16:02:38.826][self$setPropertyValue]
biodb.DEBUG[2024-10-12 16:02:38.827][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-10-12 16:02:38.828][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-10-12 16:02:38.829][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-10-12 16:02:38.830][self$setPropertyValue]
biodb.DEBUG[2024-10-12 16:02:38.832][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-10-12 16:02:38.834][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-10-12 16:02:38.835][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-10-12 16:02:38.836][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-10-12 16:02:38.838][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-10-12 16:02:38.839][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-10-12 16:02:38.840][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-10-12 16:02:38.841][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-10-12 16:02:38.843][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-10-12 16:02:38.844][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-10-12 16:02:38.845][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-10-12 16:02:38.846][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-10-12 16:02:38.848][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-10-12 16:02:38.849][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-10-12 16:02:38.850][self$setPropertyValue]
biodb.DEBUG[2024-10-12 16:02:38.851][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-10-12 16:02:38.852][self$setPropertyValue]
biodb.DEBUG[2024-10-12 16:02:38.854][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-10-12 16:02:38.855][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-12 16:02:38.856][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-12 16:02:38.857][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-10-12 16:02:38.858][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-12 16:02:38.859][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-12 16:02:38.861][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-10-12 16:02:38.862][self$setPropertyValue]
biodb.DEBUG[2024-10-12 16:02:38.863][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-10-12 16:02:38.864][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-10-12 16:02:38.865][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-10-12 16:02:38.866][self$setPropertyValue]
biodb.DEBUG[2024-10-12 16:02:38.868][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-10-12 16:02:38.869][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:02:38.870][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:02:38.871][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:02:38.873][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:02:38.874][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-12 16:02:38.875][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:02:38.876][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:02:38.877][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:02:38.878][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:02:38.883][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-12 16:02:38.884][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:02:38.885][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[2024-10-12 16:02:38.887][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:02:38.888][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:02:38.889][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-12 16:02:38.890][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:02:38.891][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:02:38.892][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:02:38.893][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:02:38.894][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-12 16:02:38.895][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:02:38.896][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:02:38.897][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:02:38.898][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:02:38.900][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-12 16:02:38.901][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:02:38.902][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[2024-10-12 16:02:38.903][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:02:38.904][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:02:38.905][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-12 16:02:38.906][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:02:38.907][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:02:38.908][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:02:38.909][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:02:38.910][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-12 16:02:38.911][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:02:38.913][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:02:38.914][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:02:38.915][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:02:38.916][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-12 16:02:38.917][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:02:38.918][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[2024-10-12 16:02:38.919][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:02:38.920][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:02:38.921][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-12 16:02:38.922][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:02:38.923][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:02:38.925][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:02:38.926][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:02:38.927][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-12 16:02:38.928][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:02:38.929][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:02:38.930][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:02:38.931][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:02:38.932][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-12 16:02:38.933][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:02:38.934][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:02:38.936][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:02:38.937][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:02:38.938][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-12 16:02:38.939][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:02:38.940][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:02:38.941][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:02:38.942][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:02:38.943][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-12 16:02:38.944][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:02:38.945][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:02:38.947][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:02:38.948][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:02:38.949][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-12 16:02:38.950][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:02:38.951][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:02:38.952][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:02:38.953][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:02:38.954][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-12 16:02:38.955][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:02:38.957][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:02:38.958][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:02:38.959][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:02:38.960][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-12 16:02:38.961][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:02:38.962][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:02:38.963][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:02:38.965][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:02:38.966][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-12 16:02:38.967][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:02:38.968][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:02:38.969][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-10-12 16:02:38.971][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-10-12 16:02:38.973][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-10-12 16:02:38.974][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-10-12 16:02:38.976][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-10-12 16:02:38.978][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-10-12 16:02:38.980][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-10-12 16:02:38.981][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-10-12 16:02:38.983][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-10-12 16:02:38.985][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-10-12 16:02:38.986][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-10-12 16:02:38.988][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-10-12 16:02:38.990][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-10-12 16:02:38.992][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-10-12 16:02:38.993][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-10-12 16:02:38.995][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-10-12 16:02:38.997][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-10-12 16:02:38.998][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-10-12 16:02:39.000][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-10-12 16:02:39.002][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-10-12 16:02:39.004][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-10-12 16:02:39.005][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-10-12 16:02:39.007][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-10-12 16:02:39.009][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-10-12 16:02:39.011][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-10-12 16:02:39.012][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-10-12 16:02:39.014][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-10-12 16:02:39.016][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-10-12 16:02:39.022][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-10-12 16:02:39.024][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-10-12 16:02:39.025][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-10-12 16:02:39.027][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-10-12 16:02:39.029][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-10-12 16:02:39.030][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-10-12 16:02:39.032][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-10-12 16:02:39.034][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-10-12 16:02:39.035][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-10-12 16:02:39.037][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-10-12 16:02:39.039][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-10-12 16:02:39.041][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-10-12 16:02:39.042][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-10-12 16:02:39.044][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-10-12 16:02:39.046][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-10-12 16:02:39.047][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-10-12 16:02:39.049][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-10-12 16:02:39.051][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-10-12 16:02:39.053][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-10-12 16:02:39.054][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-10-12 16:02:39.056][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-10-12 16:02:39.058][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-10-12 16:02:39.059][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-10-12 16:02:39.061][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-10-12 16:02:39.063][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-10-12 16:02:39.064][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-10-12 16:02:39.066][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-10-12 16:02:39.068][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-10-12 16:02:39.070][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-10-12 16:02:39.071][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-10-12 16:02:39.073][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-10-12 16:02:39.075][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-10-12 16:02:39.076][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-10-12 16:02:39.078][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-10-12 16:02:39.080][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-10-12 16:02:39.082][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-10-12 16:02:39.083][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-10-12 16:02:39.085][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-10-12 16:02:39.087][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-10-12 16:02:39.088][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-10-12 16:02:39.090][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-10-12 16:02:39.092][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-10-12 16:02:39.093][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-10-12 16:02:39.095][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-10-12 16:02:39.097][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-10-12 16:02:39.099][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-10-12 16:02:39.100][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-10-12 16:02:39.102][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-10-12 16:02:39.104][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-10-12 16:02:39.105][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-10-12 16:02:39.107][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-10-12 16:02:39.109][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-10-12 16:02:39.111][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-10-12 16:02:39.112][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-10-12 16:02:39.114][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-10-12 16:02:39.116][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-10-12 16:02:39.118][initialize] This is biodb version 1.12.0.
biodb.DEBUG[2024-10-12 16:02:39.119][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-10-12 16:02:39.120][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:02:39.121][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-12 16:02:39.122][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:02:39.123][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[2024-10-12 16:02:39.124][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:02:39.126][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-12 16:02:39.127][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-12 16:02:39.128][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:02:39.129][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-12 16:02:39.130][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:02:39.131][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:02:39.132][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:02:39.133][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-12 16:02:39.134][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-12 16:02:39.135][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:02:39.137][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-12 16:02:39.138][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:02:39.139][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:02:39.140][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:02:39.141][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-12 16:02:39.142][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-12 16:02:39.143][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:02:39.144][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-12 16:02:39.145][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:02:39.147][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[2024-10-12 16:02:39.148][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:02:39.149][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-12 16:02:39.150][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-12 16:02:39.151][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:02:39.156][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-12 16:02:39.158][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:02:39.159][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:02:39.160][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:02:39.161][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-12 16:02:39.162][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-12 16:02:39.163][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:02:39.164][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-12 16:02:39.166][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:02:39.167][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:02:39.168][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:02:39.169][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-12 16:02:39.170][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-12 16:02:39.171][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:02:39.172][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-12 16:02:39.173][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:02:39.174][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:02:39.175][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:02:39.176][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-12 16:02:39.178][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-12 16:02:39.179][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:02:39.180][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-12 16:02:39.181][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:02:39.182][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:02:39.183][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:02:39.184][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-12 16:02:39.185][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-12 16:02:39.186][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:02:39.187][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-12 16:02:39.188][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:02:39.190][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:02:39.191][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:02:39.192][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-12 16:02:39.193][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-12 16:02:39.194][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:02:39.195][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-12 16:02:39.196][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:02:39.197][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[2024-10-12 16:02:39.198][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:02:39.199][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-12 16:02:39.200][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-12 16:02:39.202][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:02:39.203][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-12 16:02:39.204][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:02:39.205][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:02:39.206][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:02:39.207][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-12 16:02:39.208][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-12 16:02:39.209][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:02:39.210][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-12 16:02:39.212][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:02:39.213][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:02:39.214][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:02:39.215][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-12 16:02:39.216][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-12 16:02:39.217][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:02:39.218][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-12 16:02:39.219][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:02:39.221][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:02:39.222][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:02:39.223][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-12 16:02:39.224][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-12 16:02:39.225][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:02:39.226][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-12 16:02:39.227][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:02:39.228][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[2024-10-12 16:02:39.229][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:02:39.231][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-12 16:02:39.232][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-12 16:02:39.233][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:02:39.234][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-12 16:02:39.235][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:02:39.236][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:02:39.237][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:02:39.238][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-12 16:02:39.239][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-12 16:02:39.240][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:02:39.242][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-12 16:02:39.243][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:02:39.244][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:02:39.245][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:02:39.246][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-12 16:02:39.247][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-12 16:02:39.248][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:02:39.249][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-12 16:02:39.250][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:02:39.252][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:02:39.253][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:02:39.254][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-12 16:02:39.255][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-12 16:02:39.256][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:02:39.257][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-12 16:02:39.258][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:02:39.259][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:02:39.262][biodb$loadDefinitions] Load definitions from file "/Users/biocbuild/bbs-3.19-bioc-longtests/meat/biodbExpasy.Rcheck/biodbExpasy/definitions.yml".
biodb.DEBUG[2024-10-12 16:02:39.264][self$getDbsInfo()$define] Define connector expasy.enzyme.
biodb.DEBUG[2024-10-12 16:02:39.266][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-10-12 16:02:39.267][self$setPropertyValue] Setting property "description" to "Write here the description of this database.".
biodb.DEBUG[2024-10-12 16:02:39.269][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-10-12 16:02:39.270][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-10-12 16:02:39.271][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-10-12 16:02:39.272][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-10-12 16:02:39.274][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-10-12 16:02:39.275][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-10-12 16:02:39.276][self$setPropertyValue] Setting property "entry.content.type" to "txt".
biodb.DEBUG[2024-10-12 16:02:39.277][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-10-12 16:02:39.279][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-10-12 16:02:39.280][self$setPropertyValue] Setting property "name" to "Expasy ENZYME database.".
biodb.DEBUG[2024-10-12 16:02:39.281][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-10-12 16:02:39.282][self$setPropertyValue] Setting property "parsing.expr" to "^ID\s+([0-9.]+)$".
biodb.DEBUG[2024-10-12 16:02:39.282][self$setPropertyValue] Setting property "parsing.expr" to "^CA\s+(.+?)\.?$".
biodb.DEBUG[2024-10-12 16:02:39.282][self$setPropertyValue] Setting property "parsing.expr" to "^CF\s+(.+?)\.?$".
biodb.DEBUG[2024-10-12 16:02:39.282][self$setPropertyValue] Setting property "parsing.expr" to "^DE\s+(.+?)\.?$".
biodb.DEBUG[2024-10-12 16:02:39.284][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-10-12 16:02:39.285][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-10-12 16:02:39.286][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2024-10-12 16:02:39.288][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-12 16:02:39.289][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-12 16:02:39.290][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-10-12 16:02:39.291][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-12 16:02:39.297][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-12 16:02:39.298][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-10-12 16:02:39.299][self$setPropertyValue] Setting property "urls" to "https://enzyme.expasy.org/".
biodb.DEBUG[2024-10-12 16:02:39.300][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-10-12 16:02:39.301][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-10-12 16:02:39.303][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-10-12 16:02:39.304][self$setPropertyValue]
biodb.DEBUG[2024-10-12 16:02:39.306][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-10-12 16:02:39.309][super$initialize] Initialize connector expasy.enzyme.
biodb.DEBUG[2024-10-12 16:02:39.311][super$initialize] Register connector expasy.enzyme with the request scheduler
biodb.DEBUG[2024-10-12 16:02:39.312][private$bdb$getRequestScheduler()$re ...] Register connector expasy.enzyme.
biodb.DEBUG[2024-10-12 16:02:39.314][private$addConnectorRules] Create new rule for URL "enzyme.expasy.org" of connector "expasy.enzyme".
biodb.DEBUG[2024-10-12 16:02:39.315][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-10-12 16:02:39.317][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-10-12 16:02:39.318][biodb$getFactory()$createConn] Creating new connector expasy.enzyme for database class expasy.enzyme .
biodb.INFO [2024-10-12 16:02:39.319][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-10-12 16:02:39.321][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector expasy.enzyme from the request scheduler
biodb.INFO [2024-10-12 16:02:39.322][self$deleteConn] Connector "expasy.enzyme" deleted.
biodb.DEBUG[2024-10-12 16:02:39.323][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-10-12 16:02:39.324][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-12 16:02:39.325][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-12 16:02:39.326][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:02:39.327][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-12 16:02:39.328][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:02:39.329][FUN] Functions in observer 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 1 | WARN 0 | SKIP 0 | PASS 85 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test_long_100_generic.R:37:1'): The entry image URL can be downloaded. ──
Error in `charToRaw(content)`: argument must be a character vector of length 1
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb (local) `<fn>`(conn = `<ExpsyEnC>`, opt = `<named list>`)
 3.   └─biodb:::getUrlContent(url, binary = TRUE)
 4.     └─biodb:::getBaseUrlContent(u, binary = binary)
 5.       └─base::charToRaw(content)

[ FAIL 1 | WARN 0 | SKIP 0 | PASS 85 ]
Error: Test failures
Execution halted

'R CMD check' output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --test-dir=longtests --no-stop-on-test-error --no-codoc --no-examples --no-manual --ignore-vignettes --check-subdirs=no biodbExpasy_1.8.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.19-bioc-longtests/meat/biodbExpasy.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using options ‘--no-codoc --no-examples --no-manual --ignore-vignettes --no-stop-on-test-error’
* checking for file ‘biodbExpasy/DESCRIPTION’ ... OK
* this is package ‘biodbExpasy’ version ‘1.8.1’
* 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 code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... SKIPPED
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... SKIPPED
* checking examples ... SKIPPED
* checking for unstated dependencies in ‘longtests’ ... OK
* checking tests in ‘longtests’ ...
  Running ‘testthat.R’
 ERROR
Running the tests in ‘longtests/testthat.R’ failed.
Last 13 lines of output:
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test_long_100_generic.R:37:1'): The entry image URL can be downloaded. ──
  Error in `charToRaw(content)`: argument must be a character vector of length 1
  Backtrace:
      ▆
   1. ├─base::do.call(fct, params)
   2. └─biodb (local) `<fn>`(conn = `<ExpsyEnC>`, opt = `<named list>`)
   3.   └─biodb:::getUrlContent(url, binary = TRUE)
   4.     └─biodb:::getBaseUrlContent(u, binary = binary)
   5.       └─base::charToRaw(content)
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 85 ]
  Error: Test failures
  Execution halted
* DONE

Status: 1 ERROR, 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.19-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)