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 palomino7

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: E:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --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 16:02:39 -0400 (Sat, 12 Oct 2024)
EndedAt: 2024-10-12 16:03:29 -0400 (Sat, 12 Oct 2024)
EllapsedTime: 50.1 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 ucrt) -- "Race for Your Life"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64

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> # 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 16:03:21.388][biodb::testContext]
biodb.INFO [2024-10-12 16:03:21.391][biodb::testContext] ********************************************************************************
biodb.INFO [2024-10-12 16:03:21.392][biodb::testContext] Test context - Generic long tests
biodb.INFO [2024-10-12 16:03:21.394][biodb::testContext] ********************************************************************************
biodb.INFO [2024-10-12 16:03:21.395][biodb::testContext]
biodb.INFO [2024-10-12 16:03:21.402][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.12.0.
biodb.DEBUG[2024-10-12 16:03:21.404][self$loadDefinitions] Load definitions from file "E:/biocbuild/bbs-3.19-bioc/R/library/biodb/definitions.yml".
biodb.DEBUG[2024-10-12 16:03:21.439][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-10-12 16:03:21.441][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-10-12 16:03:21.442][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-10-12 16:03:21.444][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:03:21.445][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:03:21.446][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:03:21.447][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-10-12 16:03:21.479][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-10-12 16:03:21.480][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:03:21.481][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:03:21.482][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:03:21.483][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-10-12 16:03:21.484][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-10-12 16:03:21.485][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:03:21.486][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:03:21.487][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:03:21.489][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-10-12 16:03:21.490][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-10-12 16:03:21.491][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-10-12 16:03:21.492][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:03:21.493][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:03:21.494][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:03:21.495][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-10-12 16:03:21.496][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-10-12 16:03:21.498][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-10-12 16:03:21.499][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:03:21.500][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:03:21.501][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:03:21.502][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-10-12 16:03:21.503][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-10-12 16:03:21.504][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:03:21.505][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:03:21.506][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:03:21.507][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-10-12 16:03:21.508][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-10-12 16:03:21.510][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-10-12 16:03:21.511][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:03:21.512][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:03:21.513][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:03:21.514][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-10-12 16:03:21.515][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-10-12 16:03:21.516][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:03:21.517][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:03:21.518][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:03:21.519][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-10-12 16:03:21.521][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-10-12 16:03:21.522][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-10-12 16:03:21.523][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:03:21.524][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:03:21.525][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:03:21.526][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-10-12 16:03:21.527][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-10-12 16:03:21.528][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-10-12 16:03:21.530][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-10-12 16:03:21.531][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-10-12 16:03:21.532][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-10-12 16:03:21.533][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:03:21.534][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:03:21.535][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:03:21.536][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-10-12 16:03:21.537][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-10-12 16:03:21.538][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:03:21.539][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:03:21.541][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:03:21.542][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-10-12 16:03:21.543][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-10-12 16:03:21.544][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:03:21.545][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:03:21.546][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:03:21.547][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-10-12 16:03:21.548][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-10-12 16:03:21.549][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:03:21.550][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:03:21.552][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:03:21.553][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-10-12 16:03:21.554][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-10-12 16:03:21.555][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:03:21.556][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:03:21.557][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:03:21.558][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-10-12 16:03:21.559][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-10-12 16:03:21.560][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:03:21.561][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:03:21.562][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:03:21.564][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-10-12 16:03:21.565][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-10-12 16:03:21.568][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-10-12 16:03:21.569][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:03:21.570][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:03:21.571][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:03:21.573][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-10-12 16:03:21.574][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-10-12 16:03:21.575][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-10-12 16:03:21.576][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:03:21.577][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:03:21.578][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:03:21.581][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-10-12 16:03:21.608][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-10-12 16:03:21.622][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2024-10-12 16:03:21.624][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-10-12 16:03:21.625][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-10-12 16:03:21.626][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-10-12 16:03:21.627][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-10-12 16:03:21.628][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-10-12 16:03:21.630][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-10-12 16:03:21.631][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-10-12 16:03:21.632][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-10-12 16:03:21.633][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-10-12 16:03:21.634][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-10-12 16:03:21.636][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-10-12 16:03:21.637][self$setPropertyValue]
biodb.DEBUG[2024-10-12 16:03:21.638][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-10-12 16:03:21.639][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-10-12 16:03:21.639][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-10-12 16:03:21.639][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-10-12 16:03:21.639][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-10-12 16:03:21.639][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-10-12 16:03:21.640][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-10-12 16:03:21.641][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-12 16:03:21.643][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-12 16:03:21.644][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-10-12 16:03:21.645][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-12 16:03:21.646][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-12 16:03:21.647][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-10-12 16:03:21.648][self$setPropertyValue]
biodb.DEBUG[2024-10-12 16:03:21.649][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-10-12 16:03:21.650][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-10-12 16:03:21.652][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-10-12 16:03:21.653][self$setPropertyValue]
biodb.DEBUG[2024-10-12 16:03:21.654][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-10-12 16:03:21.657][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-10-12 16:03:21.658][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-10-12 16:03:21.664][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-10-12 16:03:21.666][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-10-12 16:03:21.667][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-10-12 16:03:21.668][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-10-12 16:03:21.669][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-10-12 16:03:21.670][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-10-12 16:03:21.671][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-10-12 16:03:21.672][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-10-12 16:03:21.674][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-10-12 16:03:21.675][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-10-12 16:03:21.676][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-10-12 16:03:21.677][self$setPropertyValue]
biodb.DEBUG[2024-10-12 16:03:21.678][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-10-12 16:03:21.679][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-10-12 16:03:21.679][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-10-12 16:03:21.679][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-10-12 16:03:21.679][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-10-12 16:03:21.679][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-10-12 16:03:21.681][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-10-12 16:03:21.682][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-12 16:03:21.683][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-12 16:03:21.684][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-10-12 16:03:21.685][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-12 16:03:21.686][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-12 16:03:21.687][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-10-12 16:03:21.688][self$setPropertyValue]
biodb.DEBUG[2024-10-12 16:03:21.690][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-10-12 16:03:21.691][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-10-12 16:03:21.692][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-10-12 16:03:21.693][self$setPropertyValue]
biodb.DEBUG[2024-10-12 16:03:21.694][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-10-12 16:03:21.696][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-10-12 16:03:21.697][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2024-10-12 16:03:21.699][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-10-12 16:03:21.700][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-10-12 16:03:21.701][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-10-12 16:03:21.702][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-10-12 16:03:21.703][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-10-12 16:03:21.704][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-10-12 16:03:21.705][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-10-12 16:03:21.707][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-10-12 16:03:21.708][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-10-12 16:03:21.709][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-10-12 16:03:21.710][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-10-12 16:03:21.712][self$setPropertyValue]
biodb.DEBUG[2024-10-12 16:03:21.713][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-10-12 16:03:21.714][self$setPropertyValue]
biodb.DEBUG[2024-10-12 16:03:21.715][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-10-12 16:03:21.716][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-12 16:03:21.717][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-12 16:03:21.718][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-10-12 16:03:21.719][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-12 16:03:21.721][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-12 16:03:21.722][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-10-12 16:03:21.723][self$setPropertyValue]
biodb.DEBUG[2024-10-12 16:03:21.724][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-10-12 16:03:21.725][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-10-12 16:03:21.726][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-10-12 16:03:21.727][self$setPropertyValue]
biodb.DEBUG[2024-10-12 16:03:21.729][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-10-12 16:03:21.731][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-10-12 16:03:21.732][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-10-12 16:03:21.733][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-10-12 16:03:21.734][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-10-12 16:03:21.735][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-10-12 16:03:21.736][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-10-12 16:03:21.738][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-10-12 16:03:21.739][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-10-12 16:03:21.740][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-10-12 16:03:21.741][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-10-12 16:03:21.742][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-10-12 16:03:21.743][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-10-12 16:03:21.745][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-10-12 16:03:21.746][self$setPropertyValue]
biodb.DEBUG[2024-10-12 16:03:21.747][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-10-12 16:03:21.748][self$setPropertyValue]
biodb.DEBUG[2024-10-12 16:03:21.749][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-10-12 16:03:21.750][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-12 16:03:21.751][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-12 16:03:21.753][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-10-12 16:03:21.754][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-12 16:03:21.755][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-12 16:03:21.756][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-10-12 16:03:21.757][self$setPropertyValue]
biodb.DEBUG[2024-10-12 16:03:21.758][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-10-12 16:03:21.759][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-10-12 16:03:21.760][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-10-12 16:03:21.762][self$setPropertyValue]
biodb.DEBUG[2024-10-12 16:03:21.765][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-10-12 16:03:21.766][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:03:21.767][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:03:21.768][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:03:21.769][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:03:21.770][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 16:03:21.772][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:03:21.773][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:03:21.774][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:03:21.775][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:03:21.776][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-12 16:03:21.777][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:03:21.778][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:03:21.779][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:03:21.780][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:03:21.781][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-12 16:03:21.782][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:03:21.783][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:03:21.784][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:03:21.785][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:03:21.786][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 16:03:21.787][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:03:21.788][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:03:21.790][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:03:21.791][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:03:21.792][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 16:03:21.793][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:03:21.794][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:03:21.795][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:03:21.796][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:03:21.797][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-12 16:03:21.798][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:03:21.799][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:03:21.800][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:03:21.801][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:03:21.802][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-12 16:03:21.803][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:03:21.804][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:03:21.806][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:03:21.807][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:03:21.808][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-12 16:03:21.809][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:03:21.810][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:03:21.811][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:03:21.812][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:03:21.813][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-12 16:03:21.814][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:03:21.815][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:03:21.816][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:03:21.817][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:03:21.818][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 16:03:21.819][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:03:21.820][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:03:21.821][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:03:21.822][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:03:21.823][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 16:03:21.824][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:03:21.826][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:03:21.827][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:03:21.828][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:03:21.829][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 16:03:21.830][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:03:21.831][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:03:21.832][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:03:21.833][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:03:21.834][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 16:03:21.835][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:03:21.836][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:03:21.837][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:03:21.838][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:03:21.839][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 16:03:21.840][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:03:21.841][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:03:21.842][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:03:21.843][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:03:21.845][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 16:03:21.846][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:03:21.847][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:03:21.848][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:03:21.849][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:03:21.850][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 16:03:21.851][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:03:21.852][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:03:21.853][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:03:21.854][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:03:21.855][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-12 16:03:21.856][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:03:21.857][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:03:21.858][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-10-12 16:03:21.862][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-10-12 16:03:21.864][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-10-12 16:03:21.866][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-10-12 16:03:21.867][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-10-12 16:03:21.869][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-10-12 16:03:21.870][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-10-12 16:03:21.872][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-10-12 16:03:21.879][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-10-12 16:03:21.880][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-10-12 16:03:21.882][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-10-12 16:03:21.883][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-10-12 16:03:21.885][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-10-12 16:03:21.886][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-10-12 16:03:21.888][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-10-12 16:03:21.889][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-10-12 16:03:21.891][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-10-12 16:03:21.892][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-10-12 16:03:21.894][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-10-12 16:03:21.895][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-10-12 16:03:21.897][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-10-12 16:03:21.898][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-10-12 16:03:21.900][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-10-12 16:03:21.902][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-10-12 16:03:21.903][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-10-12 16:03:21.905][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-10-12 16:03:21.906][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-10-12 16:03:21.908][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-10-12 16:03:21.909][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-10-12 16:03:21.911][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-10-12 16:03:21.912][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-10-12 16:03:21.914][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-10-12 16:03:21.915][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-10-12 16:03:21.917][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-10-12 16:03:21.918][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-10-12 16:03:21.920][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-10-12 16:03:21.921][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-10-12 16:03:21.923][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-10-12 16:03:21.924][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-10-12 16:03:21.926][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-10-12 16:03:21.927][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-10-12 16:03:21.929][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-10-12 16:03:21.931][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-10-12 16:03:21.932][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-10-12 16:03:21.934][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-10-12 16:03:21.935][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-10-12 16:03:21.937][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-10-12 16:03:21.938][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-10-12 16:03:21.940][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-10-12 16:03:21.941][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-10-12 16:03:21.943][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-10-12 16:03:21.944][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-10-12 16:03:21.946][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-10-12 16:03:21.947][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-10-12 16:03:21.949][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-10-12 16:03:21.950][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-10-12 16:03:21.952][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-10-12 16:03:21.953][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-10-12 16:03:21.955][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-10-12 16:03:21.956][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-10-12 16:03:21.958][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-10-12 16:03:21.960][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-10-12 16:03:21.961][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-10-12 16:03:21.963][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-10-12 16:03:21.964][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-10-12 16:03:21.966][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-10-12 16:03:21.967][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-10-12 16:03:21.969][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-10-12 16:03:21.970][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-10-12 16:03:21.972][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-10-12 16:03:21.974][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-10-12 16:03:21.976][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-10-12 16:03:21.978][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-10-12 16:03:21.979][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-10-12 16:03:21.981][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-10-12 16:03:21.982][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-10-12 16:03:21.984][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-10-12 16:03:21.985][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-10-12 16:03:21.987][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-10-12 16:03:21.988][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-10-12 16:03:21.990][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-10-12 16:03:21.991][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-10-12 16:03:21.993][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-10-12 16:03:22.023][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-10-12 16:03:22.026][initialize] This is biodb version 1.12.0.
biodb.DEBUG[2024-10-12 16:03:22.028][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-10-12 16:03:22.030][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:03:22.031][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 16:03:22.032][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:03:22.033][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:03:22.037][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:03:22.038][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-12 16:03:22.039][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-12 16:03:22.040][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:03:22.041][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 16:03:22.042][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:03:22.043][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:03:22.044][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:03:22.045][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-12 16:03:22.047][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-12 16:03:22.048][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:03:22.049][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-12 16:03:22.050][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:03:22.051][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:03:22.052][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:03:22.053][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-12 16:03:22.054][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-12 16:03:22.055][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:03:22.056][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 16:03:22.057][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:03:22.058][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:03:22.059][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:03:22.060][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-12 16:03:22.061][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-12 16:03:22.062][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:03:22.063][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 16:03:22.064][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:03:22.065][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:03:22.066][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:03:22.068][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-12 16:03:22.069][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-12 16:03:22.070][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:03:22.071][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 16:03:22.072][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:03:22.073][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:03:22.074][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:03:22.075][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-12 16:03:22.076][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-12 16:03:22.077][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:03:22.078][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 16:03:22.079][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:03:22.080][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:03:22.081][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:03:22.082][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-12 16:03:22.083][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-12 16:03:22.084][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:03:22.085][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 16:03:22.086][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:03:22.087][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:03:22.088][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:03:22.089][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-12 16:03:22.090][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-12 16:03:22.092][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:03:22.093][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 16:03:22.099][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:03:22.100][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:03:22.101][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:03:22.102][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-12 16:03:22.103][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-12 16:03:22.104][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:03:22.105][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 16:03:22.106][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:03:22.108][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:03:22.109][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:03:22.110][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-12 16:03:22.111][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-12 16:03:22.112][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:03:22.113][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 16:03:22.114][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:03:22.115][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:03:22.116][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:03:22.117][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-12 16:03:22.118][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-12 16:03:22.119][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:03:22.120][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 16:03:22.121][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:03:22.122][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:03:22.123][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:03:22.124][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-12 16:03:22.125][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-12 16:03:22.126][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:03:22.127][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-12 16:03:22.128][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:03:22.129][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:03:22.131][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:03:22.132][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-12 16:03:22.133][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-12 16:03:22.134][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:03:22.135][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 16:03:22.136][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:03:22.137][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:03:22.138][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:03:22.139][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-12 16:03:22.140][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-12 16:03:22.141][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:03:22.142][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 16:03:22.143][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:03:22.144][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:03:22.145][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:03:22.146][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-12 16:03:22.147][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-12 16:03:22.148][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:03:22.150][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 16:03:22.151][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:03:22.152][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:03:22.153][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:03:22.154][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-12 16:03:22.155][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-12 16:03:22.156][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:03:22.157][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 16:03:22.158][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:03:22.159][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 16:03:22.160][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:03:22.161][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-12 16:03:22.162][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-12 16:03:22.163][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:03:22.164][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 16:03:22.165][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:03:22.166][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:03:22.170][biodb$loadDefinitions] Load definitions from file "E:/biocbuild/bbs-3.19-bioc-longtests/meat/biodbExpasy.Rcheck/biodbExpasy/definitions.yml".
biodb.DEBUG[2024-10-12 16:03:22.179][self$getDbsInfo()$define] Define connector expasy.enzyme.
biodb.DEBUG[2024-10-12 16:03:22.181][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-10-12 16:03:22.182][self$setPropertyValue] Setting property "description" to "Write here the description of this database.".
biodb.DEBUG[2024-10-12 16:03:22.183][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-10-12 16:03:22.184][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-10-12 16:03:22.185][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-10-12 16:03:22.187][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-10-12 16:03:22.188][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-10-12 16:03:22.189][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-10-12 16:03:22.190][self$setPropertyValue] Setting property "entry.content.type" to "txt".
biodb.DEBUG[2024-10-12 16:03:22.191][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-10-12 16:03:22.192][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-10-12 16:03:22.194][self$setPropertyValue] Setting property "name" to "Expasy ENZYME database.".
biodb.DEBUG[2024-10-12 16:03:22.195][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-10-12 16:03:22.196][self$setPropertyValue] Setting property "parsing.expr" to "^ID\s+([0-9.]+)$".
biodb.DEBUG[2024-10-12 16:03:22.196][self$setPropertyValue] Setting property "parsing.expr" to "^CA\s+(.+?)\.?$".
biodb.DEBUG[2024-10-12 16:03:22.196][self$setPropertyValue] Setting property "parsing.expr" to "^CF\s+(.+?)\.?$".
biodb.DEBUG[2024-10-12 16:03:22.196][self$setPropertyValue] Setting property "parsing.expr" to "^DE\s+(.+?)\.?$".
biodb.DEBUG[2024-10-12 16:03:22.197][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-10-12 16:03:22.198][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-10-12 16:03:22.199][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2024-10-12 16:03:22.201][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-12 16:03:22.202][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-12 16:03:22.203][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-10-12 16:03:22.204][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-12 16:03:22.205][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-12 16:03:22.206][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-10-12 16:03:22.207][self$setPropertyValue] Setting property "urls" to "https://enzyme.expasy.org/".
biodb.DEBUG[2024-10-12 16:03:22.208][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-10-12 16:03:22.209][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-10-12 16:03:22.210][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-10-12 16:03:22.212][self$setPropertyValue]
biodb.DEBUG[2024-10-12 16:03:22.217][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-10-12 16:03:22.238][super$initialize] Initialize connector expasy.enzyme.
biodb.DEBUG[2024-10-12 16:03:22.239][super$initialize] Register connector expasy.enzyme with the request scheduler
biodb.DEBUG[2024-10-12 16:03:22.243][private$bdb$getRequestScheduler()$re ...] Register connector expasy.enzyme.
biodb.DEBUG[2024-10-12 16:03:22.247][private$addConnectorRules] Create new rule for URL "enzyme.expasy.org" of connector "expasy.enzyme".
biodb.DEBUG[2024-10-12 16:03:22.250][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-10-12 16:03:22.252][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-10-12 16:03:22.253][biodb$getFactory()$createConn] Creating new connector expasy.enzyme for database class expasy.enzyme .
biodb.INFO [2024-10-12 16:03:22.263][biodb::testThat]
biodb.INFO [2024-10-12 16:03:22.264][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2024-10-12 16:03:22.265][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-10-12 16:03:22.266][biodb::testThat]
biodb.TRACE[2024-10-12 16:03:22.271][loadFileContents] Loaded 1 files from cache: [1]: "E:/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 16:03:22.273][biodb$getFactory()$createEntryFromCo ...] Creating Expasy ENZYME database. entries from 1 content(s).
biodb.DEBUG[2024-10-12 16:03:22.276][biodb$getFactory()$createEntryFromCo ...] Parsing 1 Expasy ENZYME database. entries.
biodb.DEBUG[2024-10-12 16:03:22.296][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-12 16:03:22.298][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-12 16:03:22.299][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-12 16:03:22.344][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:03:22.345][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 16:03:22.347][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:03:22.348][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.TRACE[2024-10-12 16:03:22.368][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-12 16:03:22.370][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-12 16:03:22.371][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:03:22.372][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:03:22.395][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-10-12 16:03:22.405][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-10-12 16:03:22.407][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:03:22.408][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:03:22.410][self$getBiodb()$getEntryFields()$get] Asked field names are: cofactor.
biodb.TRACE[2024-10-12 16:03:22.411][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-10-12 16:03:22.412][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:03:22.413][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:03:22.415][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-12 16:03:22.416][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-12 16:03:22.417][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:03:22.418][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:03:22.420][self$getBiodb()$getEntryFields()$get] Asked field names are: COFACTOR.
biodb.TRACE[2024-10-12 16:03:22.421][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-10-12 16:03:22.422][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:03:22.423][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:03:22.424][self$getBiodb()$getEntryFields()$get] Asked field names are: cofactor.
biodb.TRACE[2024-10-12 16:03:22.426][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-10-12 16:03:22.427][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:03:22.428][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:03:22.429][self$getBiodb()$getEntryFields()$get] Asked field names are: cofactor.
biodb.TRACE[2024-10-12 16:03:22.430][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-10-12 16:03:22.431][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:03:22.433][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:03:22.434][self$getBiodb()$getEntryFields()$get] Asked field names are: cofactor.
biodb.TRACE[2024-10-12 16:03:22.435][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-10-12 16:03:22.436][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:03:22.437][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:03:22.438][self$getBiodb()$getEntryFields()$get] Asked field names are: COFACTOR.
biodb.TRACE[2024-10-12 16:03:22.440][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-10-12 16:03:22.441][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:03:22.442][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:03:22.457][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-12 16:03:22.459][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-12 16:03:22.460][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:03:22.461][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:03:22.462][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-12 16:03:22.463][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-12 16:03:22.464][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:03:22.466][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:03:22.529][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-12 16:03:22.530][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-12 16:03:22.532][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:03:22.533][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:03:22.534][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-12 16:03:22.535][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-12 16:03:22.536][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:03:22.537][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:03:22.539][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-12 16:03:22.540][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-12 16:03:22.541][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:03:22.542][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:03:22.543][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-10-12 16:03:22.545][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-10-12 16:03:22.546][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:03:22.547][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:03:22.548][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-10-12 16:03:22.549][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-10-12 16:03:22.550][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:03:22.552][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:03:22.553][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-12 16:03:22.554][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-12 16:03:22.555][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:03:22.556][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:03:22.557][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-10-12 16:03:22.559][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-10-12 16:03:22.560][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:03:22.561][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:03:22.562][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-12 16:03:22.563][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-12 16:03:22.565][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:03:22.566][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:03:22.567][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-12 16:03:22.568][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-12 16:03:22.569][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:03:22.570][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:03:22.572][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-12 16:03:22.573][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-12 16:03:22.574][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:03:22.575][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:03:22.576][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-12 16:03:22.578][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-12 16:03:22.579][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:03:22.580][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:03:22.581][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-12 16:03:22.582][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-12 16:03:22.583][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:03:22.585][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:03:22.586][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-12 16:03:22.587][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-12 16:03:22.588][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:03:22.589][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-12 16:03:22.590][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 1.1.1.1.
biodb.TRACE[2024-10-12 16:03:22.594][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-10-12 16:03:22.595][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-10-12 16:03:22.596][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:03:22.597][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:03:22.598][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-10-12 16:03:22.600][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-10-12 16:03:22.601][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:03:22.602][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:03:22.603][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-10-12 16:03:22.604][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-10-12 16:03:22.606][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:03:22.607][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:03:22.608][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-10-12 16:03:22.609][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-10-12 16:03:22.610][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:03:22.611][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:03:22.632][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-12 16:03:22.634][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-12 16:03:22.635][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:03:22.636][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:03:22.650][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-10-12 16:03:22.652][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-10-12 16:03:22.653][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:03:22.654][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:03:22.661][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-12 16:03:22.662][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-12 16:03:22.664][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:03:22.665][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:03:22.666][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-12 16:03:22.667][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-12 16:03:22.668][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:03:22.669][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:03:22.671][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-12 16:03:22.672][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-12 16:03:22.673][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:03:22.674][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:03:22.677][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-12 16:03:22.678][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-12 16:03:22.679][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:03:22.680][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:03:22.682][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-12 16:03:22.683][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-12 16:03:22.684][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:03:22.685][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:03:22.686][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-12 16:03:22.688][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-12 16:03:22.689][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:03:22.690][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:03:22.697][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-10-12 16:03:22.698][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-10-12 16:03:22.699][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:03:22.700][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:03:22.701][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-10-12 16:03:22.703][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-10-12 16:03:22.704][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:03:22.705][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:03:22.706][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-10-12 16:03:22.707][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-10-12 16:03:22.708][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:03:22.710][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:03:22.720][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-12 16:03:22.721][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-12 16:03:22.722][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:03:22.723][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:03:22.725][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-12 16:03:22.726][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-12 16:03:22.727][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:03:22.728][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:03:22.729][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-12 16:03:22.731][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-12 16:03:22.732][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:03:22.733][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:03:22.734][ef$get] Asked field names are: accession.
biodb.TRACE[2024-10-12 16:03:22.735][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-12 16:03:22.736][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:03:22.737][ef$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:03:22.739][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-12 16:03:22.740][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-12 16:03:22.741][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:03:22.742][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:03:22.753][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-12 16:03:22.754][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-12 16:03:22.756][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:03:22.757][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:03:22.758][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-12 16:03:22.759][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-12 16:03:22.760][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:03:22.761][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:03:22.763][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-12 16:03:22.764][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-12 16:03:22.765][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:03:22.766][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:03:22.767][ef$get] Asked field names are: name.
biodb.TRACE[2024-10-12 16:03:22.768][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-10-12 16:03:22.770][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:03:22.771][ef$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:03:22.772][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-12 16:03:22.773][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-12 16:03:22.774][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:03:22.775][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:03:22.786][self$getBiodb()$getEntryFields()$get] Asked field names are: cofactor.
biodb.TRACE[2024-10-12 16:03:22.787][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-10-12 16:03:22.789][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:03:22.790][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:03:22.791][self$getBiodb()$getEntryFields()$get] Asked field names are: cofactor.
biodb.TRACE[2024-10-12 16:03:22.792][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-10-12 16:03:22.793][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:03:22.794][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:03:22.796][self$getBiodb()$getEntryFields()$get] Asked field names are: cofactor.
biodb.TRACE[2024-10-12 16:03:22.797][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-10-12 16:03:22.798][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:03:22.799][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:03:22.800][ef$get] Asked field names are: cofactor.
biodb.TRACE[2024-10-12 16:03:22.802][ef$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-10-12 16:03:22.803][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:03:22.804][ef$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:03:22.805][self$getBiodb()$getEntryFields()$get] Asked field names are: cofactor.
biodb.TRACE[2024-10-12 16:03:22.806][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-10-12 16:03:22.807][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:03:22.809][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:03:22.820][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-10-12 16:03:22.821][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-10-12 16:03:22.822][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:03:22.823][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:03:22.824][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-10-12 16:03:22.826][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-10-12 16:03:22.827][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:03:22.828][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:03:22.829][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-10-12 16:03:22.831][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-10-12 16:03:22.832][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:03:22.833][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:03:22.834][ef$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-10-12 16:03:22.835][ef$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-10-12 16:03:22.836][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:03:22.838][ef$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:03:22.839][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-10-12 16:03:22.840][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-10-12 16:03:22.841][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:03:22.842][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:03:22.853][ef$get] Asked field names are: accession.
biodb.TRACE[2024-10-12 16:03:22.855][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-12 16:03:22.856][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:03:22.857][ef$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:03:22.864][ef$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-10-12 16:03:22.865][ef$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-10-12 16:03:22.866][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:03:22.867][ef$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:03:22.874][ef$get] Asked field names are: cofactor.
biodb.TRACE[2024-10-12 16:03:22.876][ef$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-10-12 16:03:22.882][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:03:22.883][ef$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:03:22.890][ef$get] Asked field names are: name.
biodb.TRACE[2024-10-12 16:03:22.891][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-10-12 16:03:22.893][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:03:22.894][ef$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:03:22.912][loadFileContents] Loaded 1 files from cache: [1]: "E:/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 16:03:22.942][biodb$getFactory()$createEntryFromCo ...] Creating Expasy ENZYME database. entries from 1 content(s).
biodb.DEBUG[2024-10-12 16:03:22.944][biodb$getFactory()$createEntryFromCo ...] Parsing 1 Expasy ENZYME database. entries.
biodb.DEBUG[2024-10-12 16:03:22.945][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-12 16:03:22.947][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-12 16:03:22.948][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-12 16:03:22.954][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:03:22.956][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 16:03:22.957][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:03:22.958][FUN] Functions in observer BiodbConfig: [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 16:03:22.960][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-12 16:03:22.961][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-12 16:03:22.963][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:03:22.964][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:03:22.965][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-10-12 16:03:22.967][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-10-12 16:03:22.968][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:03:22.969][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:03:22.970][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-12 16:03:22.972][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-12 16:03:22.973][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:03:22.975][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:03:22.977][self$getBiodb()$getEntryFields()$get] Asked field names are: COFACTOR.
biodb.TRACE[2024-10-12 16:03:22.979][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-10-12 16:03:22.980][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:03:22.981][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:03:22.982][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-10-12 16:03:22.984][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-10-12 16:03:22.985][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:03:22.986][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:03:22.987][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-10-12 16:03:22.988][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-10-12 16:03:22.990][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:03:22.991][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:03:22.992][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-12 16:03:22.993][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-12 16:03:22.994][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:03:22.996][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:03:22.997][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-10-12 16:03:22.998][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-10-12 16:03:22.999][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:03:23.000][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:03:23.002][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-12 16:03:23.003][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-12 16:03:23.004][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:03:23.005][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:03:23.006][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-12 16:03:23.008][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-12 16:03:23.009][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:03:23.010][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:03:23.011][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-12 16:03:23.012][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-12 16:03:23.014][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:03:23.015][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:03:23.016][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-12 16:03:23.018][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-12 16:03:23.019][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:03:23.020][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:03:23.021][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-12 16:03:23.022][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-12 16:03:23.023][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:03:23.024][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:03:23.026][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-12 16:03:23.027][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-12 16:03:23.033][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:03:23.035][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-12 16:03:23.036][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 1.1.1.54.
biodb.TRACE[2024-10-12 16:03:23.054][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-10-12 16:03:23.056][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-10-12 16:03:23.057][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:03:23.058][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:03:23.060][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-10-12 16:03:23.061][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-10-12 16:03:23.062][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:03:23.063][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:03:23.064][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-10-12 16:03:23.066][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-10-12 16:03:23.067][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:03:23.068][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:03:23.069][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-10-12 16:03:23.071][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-10-12 16:03:23.072][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:03:23.073][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:03:23.075][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-12 16:03:23.076][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-12 16:03:23.077][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:03:23.079][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:03:23.086][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-10-12 16:03:23.087][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-10-12 16:03:23.088][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:03:23.089][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:03:23.096][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-12 16:03:23.098][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-12 16:03:23.099][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:03:23.100][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:03:23.101][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-12 16:03:23.102][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-12 16:03:23.103][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:03:23.105][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:03:23.106][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-12 16:03:23.107][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-12 16:03:23.108][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:03:23.109][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:03:23.112][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-12 16:03:23.113][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-12 16:03:23.115][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:03:23.116][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:03:23.117][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-12 16:03:23.118][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-12 16:03:23.119][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:03:23.120][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:03:23.122][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-12 16:03:23.123][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-12 16:03:23.124][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:03:23.125][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:03:23.126][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-10-12 16:03:23.128][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-10-12 16:03:23.129][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:03:23.130][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:03:23.131][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-10-12 16:03:23.132][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-10-12 16:03:23.134][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:03:23.135][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:03:23.136][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-10-12 16:03:23.137][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-10-12 16:03:23.138][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:03:23.139][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:03:23.157][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-12 16:03:23.159][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-12 16:03:23.160][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:03:23.161][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:03:23.162][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-12 16:03:23.164][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-12 16:03:23.165][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:03:23.166][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:03:23.167][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-12 16:03:23.168][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-12 16:03:23.169][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:03:23.171][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:03:23.172][ef$get] Asked field names are: accession.
biodb.TRACE[2024-10-12 16:03:23.173][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-12 16:03:23.174][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:03:23.175][ef$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:03:23.177][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-12 16:03:23.178][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-12 16:03:23.179][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:03:23.180][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:03:23.191][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-12 16:03:23.198][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-12 16:03:23.199][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:03:23.200][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:03:23.201][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-12 16:03:23.203][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-12 16:03:23.204][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:03:23.205][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:03:23.206][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-12 16:03:23.207][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-12 16:03:23.209][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:03:23.210][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:03:23.211][ef$get] Asked field names are: name.
biodb.TRACE[2024-10-12 16:03:23.212][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-10-12 16:03:23.213][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:03:23.214][ef$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:03:23.216][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-12 16:03:23.217][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-12 16:03:23.218][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:03:23.219][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:03:23.230][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-10-12 16:03:23.232][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-10-12 16:03:23.233][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:03:23.234][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:03:23.235][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-10-12 16:03:23.236][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-10-12 16:03:23.237][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:03:23.239][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:03:23.240][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-10-12 16:03:23.241][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-10-12 16:03:23.242][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:03:23.243][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:03:23.245][ef$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-10-12 16:03:23.246][ef$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-10-12 16:03:23.247][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:03:23.248][ef$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:03:23.249][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-10-12 16:03:23.251][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-10-12 16:03:23.252][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:03:23.253][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:03:23.264][ef$get] Asked field names are: accession.
biodb.TRACE[2024-10-12 16:03:23.265][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-12 16:03:23.266][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:03:23.268][ef$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:03:23.274][ef$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-10-12 16:03:23.275][ef$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-10-12 16:03:23.277][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:03:23.278][ef$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:03:23.284][ef$get] Asked field names are: name.
biodb.TRACE[2024-10-12 16:03:23.286][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-10-12 16:03:23.287][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:03:23.288][ef$get] fields variable is a list.
biodb.INFO [2024-10-12 16:03:23.300][biodb::testThat]
biodb.INFO [2024-10-12 16:03:23.302][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2024-10-12 16:03:23.303][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-10-12 16:03:23.304][biodb::testThat]
biodb.DEBUG[2024-10-12 16:03:23.307][private$loadEntries] Creating entries from ids [2]: "1.1.1.1, 1.1.1.54".
biodb.DEBUG[2024-10-12 16:03:23.313][conn$getEntryContent] Get Expasy ENZYME database. entry content(s) for 2 id(s)...
biodb.TRACE[2024-10-12 16:03:23.334][cch$loadFileContent] Trying to load 2 files from cache: [2]: "1.1.1.1, 1.1.1.54".
biodb.INFO [2024-10-12 16:03:23.335][self$getFolderPath] Create cache folder "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280" for "expasy.enzyme-b59b84d962b6741050ba8f70ff4db280".
biodb.TRACE[2024-10-12 16:03:23.337][cch$loadFileContent] file.exist = [2]: "FALSE, FALSE".
biodb.TRACE[2024-10-12 16:03:23.339][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-10-12 16:03:23.340][conn$getEntryContent] 0 Expasy ENZYME database. entry content(s) loaded from cache.
biodb.DEBUG[2024-10-12 16:03:23.341][conn$getEntryContent] 2 entry content(s) need to be fetched from Expasy ENZYME database. database "https://enzyme.expasy.org/".
biodb.DEBUG[2024-10-12 16:03:23.343][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-10-12 16:03:23.344][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-10-12 16:03:23.349][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-12 16:03:23.350][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-12 16:03:23.351][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-12 16:03:23.358][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:03:23.359][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-12 16:03:23.360][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:03:23.361][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:03:23.362][scheduler$sendRequest] Getting content of get URL request "https://enzyme.expasy.org/EC/1.1.1.1.txt".
biodb.DEBUG[2024-10-12 16:03:23.380][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-12 16:03:23.382][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-10-12 16:03:23.383][private$doSendRequestOnce] Sent URL is "https://enzyme.expasy.org/EC/1.1.1.1.txt".
biodb.TRACE[2024-10-12 16:03:24.110][doesRCurlRequestUrlExist] According to RCurl, URL https://enzyme.expasy.org/EC/1.1.1.1.txt does not exist.
biodb.TRACE[2024-10-12 16:03:24.111][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-10-12 16:03:24.113][getUrlRequestResult] URL "https://enzyme.expasy.org/EC/1.1.1.1.txt" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-10-12 16:03:24.114][getBaseUrlRequestResult] Using base::url() for sending request (https://enzyme.expasy.org/EC/1.1.1.1.txt).
biodb.DEBUG[2024-10-12 16:03:24.549][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-10-12 16:03:24.552][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280/a52675cfd2f0c2b41556caa64d9341e3.content"
biodb.TRACE[2024-10-12 16:03:24.566][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280/a52675cfd2f0c2b41556caa64d9341e3.request"
biodb.DEBUG[2024-10-12 16:03:24.580][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-12 16:03:24.581][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-12 16:03:24.583][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-12 16:03:24.589][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:03:24.591][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 16:03:24.592][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:03:24.593][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:03:24.611][scheduler$sendRequest] Getting content of get URL request "https://enzyme.expasy.org/EC/1.1.1.54.txt".
biodb.DEBUG[2024-10-12 16:03:24.625][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-12 16:03:24.626][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-10-12 16:03:24.639][private$doSendRequestOnce] Sent URL is "https://enzyme.expasy.org/EC/1.1.1.54.txt".
biodb.TRACE[2024-10-12 16:03:24.866][doesRCurlRequestUrlExist] According to RCurl, URL https://enzyme.expasy.org/EC/1.1.1.54.txt does not exist.
biodb.TRACE[2024-10-12 16:03:24.867][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-10-12 16:03:24.868][getUrlRequestResult] URL "https://enzyme.expasy.org/EC/1.1.1.54.txt" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-10-12 16:03:24.869][getBaseUrlRequestResult] Using base::url() for sending request (https://enzyme.expasy.org/EC/1.1.1.54.txt).
biodb.DEBUG[2024-10-12 16:03:25.295][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-10-12 16:03:25.297][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280/a9b93566a091cbe35a06e4b3871f95c9.content"
biodb.TRACE[2024-10-12 16:03:25.302][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280/a9b93566a091cbe35a06e4b3871f95c9.request"
biodb.TRACE[2024-10-12 16:03:25.305][private$doSaveContentToFile] Saving to cache [2]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280/1.1.1.1.txt, C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280/1.1.1.54.txt"
biodb.DEBUG[2024-10-12 16:03:25.308][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-10-12 16:03:25.310][self$createEntryFromContent] Creating Expasy ENZYME database. entries from 2 content(s).
biodb.DEBUG[2024-10-12 16:03:25.311][self$createEntryFromContent] Parsing 2 Expasy ENZYME database. entries.
biodb.DEBUG[2024-10-12 16:03:25.313][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-12 16:03:25.314][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-12 16:03:25.315][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-12 16:03:25.322][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:03:25.323][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-12 16:03:25.324][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:03:25.325][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-12 16:03:25.328][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-12 16:03:25.329][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-12 16:03:25.336][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:03:25.337][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:03:25.338][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-10-12 16:03:25.340][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-10-12 16:03:25.341][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:03:25.342][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:03:25.343][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-12 16:03:25.345][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-12 16:03:25.346][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:03:25.347][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:03:25.348][self$getBiodb()$getEntryFields()$get] Asked field names are: COFACTOR.
biodb.TRACE[2024-10-12 16:03:25.350][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-10-12 16:03:25.351][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:03:25.352][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:03:25.353][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-12 16:03:25.355][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-12 16:03:25.356][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:03:25.357][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:03:25.358][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-12 16:03:25.359][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-12 16:03:25.360][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:03:25.362][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:03:25.363][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-12 16:03:25.364][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-12 16:03:25.365][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:03:25.366][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:03:25.368][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-12 16:03:25.369][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-12 16:03:25.370][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:03:25.371][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:03:25.372][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-12 16:03:25.374][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-12 16:03:25.375][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:03:25.376][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:03:25.377][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-10-12 16:03:25.379][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-10-12 16:03:25.380][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:03:25.381][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:03:25.382][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-10-12 16:03:25.383][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-10-12 16:03:25.384][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:03:25.386][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:03:25.387][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-12 16:03:25.388][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-12 16:03:25.389][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:03:25.390][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:03:25.391][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-10-12 16:03:25.393][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-10-12 16:03:25.394][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:03:25.395][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:03:25.396][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-12 16:03:25.398][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-12 16:03:25.399][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:03:25.400][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:03:25.401][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-12 16:03:25.402][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-12 16:03:25.403][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:03:25.405][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:03:25.406][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-12 16:03:25.407][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-12 16:03:25.408][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:03:25.409][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-12 16:03:25.411][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-12 16:03:25.412][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-12 16:03:25.413][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-12 16:03:25.420][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:03:25.421][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-12 16:03:25.422][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:03:25.423][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-12 16:03:25.426][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-12 16:03:25.427][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-12 16:03:25.428][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:03:25.429][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:03:25.431][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-10-12 16:03:25.432][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-10-12 16:03:25.433][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:03:25.434][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:03:25.436][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-12 16:03:25.437][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-12 16:03:25.438][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:03:25.440][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:03:25.441][self$getBiodb()$getEntryFields()$get] Asked field names are: COFACTOR.
biodb.TRACE[2024-10-12 16:03:25.442][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-10-12 16:03:25.443][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:03:25.444][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:03:25.446][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-10-12 16:03:25.447][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-10-12 16:03:25.448][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:03:25.449][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:03:25.451][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-10-12 16:03:25.452][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-10-12 16:03:25.453][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:03:25.454][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:03:25.455][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-12 16:03:25.456][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-12 16:03:25.458][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:03:25.459][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:03:25.460][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-10-12 16:03:25.461][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-10-12 16:03:25.462][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:03:25.463][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:03:25.465][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-12 16:03:25.466][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-12 16:03:25.472][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:03:25.473][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:03:25.474][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-12 16:03:25.475][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-12 16:03:25.477][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:03:25.478][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:03:25.479][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-12 16:03:25.480][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-12 16:03:25.481][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:03:25.482][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:03:25.484][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-12 16:03:25.485][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-12 16:03:25.486][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:03:25.487][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:03:25.488][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-12 16:03:25.490][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-12 16:03:25.491][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:03:25.492][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:03:25.493][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-12 16:03:25.494][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-12 16:03:25.496][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:03:25.497][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:03:25.498][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-12 16:03:25.499][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-12 16:03:25.500][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:03:25.501][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:03:25.503][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-12 16:03:25.504][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-12 16:03:25.505][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:03:25.506][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:03:25.507][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-12 16:03:25.509][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-12 16:03:25.510][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:03:25.511][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-12 16:03:25.512][self$createEntryFromContent] Accession numbers: 1.1.1.1, 1.1.1.54.
biodb.TRACE[2024-10-12 16:03:25.513][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2024-10-12 16:03:25.515][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2024-10-12 16:03:25.516][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:03:25.517][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:03:25.518][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2024-10-12 16:03:25.519][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2024-10-12 16:03:25.521][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:03:25.522][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:03:25.523][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2024-10-12 16:03:25.524][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2024-10-12 16:03:25.525][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:03:25.526][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:03:25.534][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2024-10-12 16:03:25.535][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2024-10-12 16:03:25.536][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:03:25.537][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:03:25.538][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2024-10-12 16:03:25.540][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2024-10-12 16:03:25.541][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:03:25.542][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:03:25.543][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2024-10-12 16:03:25.544][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2024-10-12 16:03:25.546][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:03:25.547][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-10-12 16:03:25.559][biodb::testThat]
biodb.INFO [2024-10-12 16:03:25.560][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2024-10-12 16:03:25.561][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-10-12 16:03:25.563][biodb::testThat]
biodb.TRACE[2024-10-12 16:03:25.566][ef$get] Asked field names are: name.
biodb.TRACE[2024-10-12 16:03:25.567][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-10-12 16:03:25.569][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:03:25.570][ef$get] fields variable is a list.
biodb.DEBUG[2024-10-12 16:03:25.572][function(conn, opt)] Testing searchForEntries() with entry "1.1.1.1" and field "name".
biodb.TRACE[2024-10-12 16:03:25.601][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-12 16:03:25.602][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-12 16:03:25.608][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:03:25.609][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:03:25.611][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-12 16:03:25.612][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-12 16:03:25.613][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:03:25.614][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:03:25.616][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-12 16:03:25.617][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-12 16:03:25.618][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:03:25.619][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-12 16:03:25.623][function(conn, opt)] With value "alcohol dehydrogenase".
biodb.DEBUG[2024-10-12 16:03:25.625][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://enzyme.expasy.org/enzyme-byname.html?alcohol dehydrogenase".
biodb.DEBUG[2024-10-12 16:03:25.629][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-12 16:03:25.630][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-10-12 16:03:25.631][private$doSendRequestOnce] Sent URL is "https://enzyme.expasy.org/enzyme-byname.html?alcohol%20dehydrogenase".
biodb.TRACE[2024-10-12 16:03:25.863][doesRCurlRequestUrlExist] According to RCurl, URL https://enzyme.expasy.org/enzyme-byname.html?alcohol%20dehydrogenase does not exist.
biodb.TRACE[2024-10-12 16:03:25.864][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-10-12 16:03:25.865][getUrlRequestResult] URL "https://enzyme.expasy.org/enzyme-byname.html?alcohol%20dehydrogenase" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-10-12 16:03:25.867][getBaseUrlRequestResult] Using base::url() for sending request (https://enzyme.expasy.org/enzyme-byname.html?alcohol%20dehydrogenase).
biodb.DEBUG[2024-10-12 16:03:26.321][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-10-12 16:03:26.324][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280/f603fa2a57aec59588edc37541c6f6d5.content"
biodb.TRACE[2024-10-12 16:03:26.329][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280/f603fa2a57aec59588edc37541c6f6d5.request"
biodb.DEBUG[2024-10-12 16:03:26.336][function(conn, opt)] With found IDs [1]: "1.1.1.1".
biodb.INFO [2024-10-12 16:03:26.364][biodb::testThat]
biodb.INFO [2024-10-12 16:03:26.365][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2024-10-12 16:03:26.366][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-10-12 16:03:26.368][biodb::testThat]
biodb.TRACE[2024-10-12 16:03:26.394][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-12 16:03:26.395][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-12 16:03:26.397][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:03:26.398][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:03:26.399][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-12 16:03:26.400][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-12 16:03:26.401][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:03:26.403][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:03:26.404][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-12 16:03:26.405][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-12 16:03:26.406][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:03:26.407][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-12 16:03:26.441][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://enzyme.expasy.org/enzyme-byname.html?alcohol dehydrogenase".
biodb.DEBUG[2024-10-12 16:03:26.444][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-10-12 16:03:26.458][cch$loadFileContent] Trying to load 1 files from cache: [1]: "f603fa2a57aec59588edc37541c6f6d5".
biodb.TRACE[2024-10-12 16:03:26.460][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-10-12 16:03:26.463][loadFileContents] Loaded 1 files from cache: [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280/f603fa2a57aec59588edc37541c6f6d5.content".
biodb.INFO [2024-10-12 16:03:26.488][biodb::testThat]
biodb.INFO [2024-10-12 16:03:26.489][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2024-10-12 16:03:26.490][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-10-12 16:03:26.491][biodb::testThat]
biodb.TRACE[2024-10-12 16:03:26.504][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-10-12 16:03:26.506][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-10-12 16:03:26.509][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:03:26.511][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:03:26.512][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-10-12 16:03:26.513][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-10-12 16:03:26.515][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:03:26.516][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:03:26.517][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-10-12 16:03:26.518][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-10-12 16:03:26.519][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:03:26.521][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:03:26.522][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-10-12 16:03:26.523][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-10-12 16:03:26.524][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:03:26.525][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:03:26.560][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-10-12 16:03:26.562][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-10-12 16:03:26.563][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:03:26.564][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:03:26.565][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-10-12 16:03:26.567][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-10-12 16:03:26.568][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:03:26.569][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:03:26.570][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-10-12 16:03:26.571][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-10-12 16:03:26.573][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:03:26.574][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:03:26.575][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-10-12 16:03:26.576][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-10-12 16:03:26.577][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:03:26.578][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-10-12 16:03:26.588][biodb::testThat]
biodb.INFO [2024-10-12 16:03:26.589][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2024-10-12 16:03:26.590][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-10-12 16:03:26.591][biodb::testThat]
biodb.INFO [2024-10-12 16:03:26.604][biodb::testThat]
biodb.INFO [2024-10-12 16:03:26.605][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2024-10-12 16:03:26.606][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-10-12 16:03:26.607][biodb::testThat]
biodb.INFO [2024-10-12 16:03:26.619][biodb::testThat]
biodb.INFO [2024-10-12 16:03:26.620][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2024-10-12 16:03:26.621][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-10-12 16:03:26.622][biodb::testThat]
biodb.DEBUG[2024-10-12 16:03:26.636][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 16:03:26.861][getUrlContent] Use base::url() 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 16:03:27.430][biodb::testThat]
biodb.INFO [2024-10-12 16:03:27.431][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2024-10-12 16:03:27.433][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-10-12 16:03:27.434][biodb::testThat]
biodb.DEBUG[2024-10-12 16:03:27.667][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 16:03:28.129][ef$get] Asked field names are: name.
biodb.TRACE[2024-10-12 16:03:28.130][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-10-12 16:03:28.131][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:03:28.132][ef$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:03:28.134][ef$get] Asked field names are: name.
biodb.TRACE[2024-10-12 16:03:28.135][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-10-12 16:03:28.136][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:03:28.137][ef$get] fields variable is a list.
biodb.INFO [2024-10-12 16:03:28.139][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-10-12 16:03:28.140][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector expasy.enzyme from the request scheduler
biodb.INFO [2024-10-12 16:03:28.141][self$deleteConn] Connector "expasy.enzyme" deleted.
biodb.DEBUG[2024-10-12 16:03:28.142][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-10-12 16:03:28.144][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-12 16:03:28.145][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-12 16:03:28.146][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:03:28.147][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-12 16:03:28.148][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:03:28.149][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2024-10-12 16:03:28.159][biodb::testContext]
biodb.INFO [2024-10-12 16:03:28.161][biodb::testContext] ********************************************************************************
biodb.INFO [2024-10-12 16:03:28.162][biodb::testContext] Test context - Example long tests
biodb.INFO [2024-10-12 16:03:28.163][biodb::testContext] ********************************************************************************
biodb.INFO [2024-10-12 16:03:28.164][biodb::testContext]
biodb.INFO [2024-10-12 16:03:28.167][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.12.0.
biodb.DEBUG[2024-10-12 16:03:28.169][self$loadDefinitions] Load definitions from file "E:/biocbuild/bbs-3.19-bioc/R/library/biodb/definitions.yml".
biodb.DEBUG[2024-10-12 16:03:28.175][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-10-12 16:03:28.176][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-10-12 16:03:28.177][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-10-12 16:03:28.178][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:03:28.179][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:03:28.180][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:03:28.182][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-10-12 16:03:28.183][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-10-12 16:03:28.184][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:03:28.185][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:03:28.186][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:03:28.187][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-10-12 16:03:28.189][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-10-12 16:03:28.190][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:03:28.191][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:03:28.192][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:03:28.193][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-10-12 16:03:28.194][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-10-12 16:03:28.195][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-10-12 16:03:28.196][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:03:28.197][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:03:28.198][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:03:28.200][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-10-12 16:03:28.201][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-10-12 16:03:28.202][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-10-12 16:03:28.203][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:03:28.204][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:03:28.205][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 16:03:28.206][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-10-12 16:03:28.208][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-10-12 16:03:28.209][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:03:28.210][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:03:28.211][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:03:28.212][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-10-12 16:03:28.213][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-10-12 16:03:28.214][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-10-12 16:03:28.215][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:03:28.216][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:03:28.218][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:03:28.219][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-10-12 16:03:28.220][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-10-12 16:03:28.221][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:03:28.222][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:03:28.223][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:03:28.224][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-10-12 16:03:28.226][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-10-12 16:03:28.227][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-10-12 16:03:28.228][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:03:28.229][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:03:28.230][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:03:28.231][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-10-12 16:03:28.233][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-10-12 16:03:28.234][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-10-12 16:03:28.235][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-10-12 16:03:28.236][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-10-12 16:03:28.237][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-10-12 16:03:28.238][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:03:28.240][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:03:28.241][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:03:28.242][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-10-12 16:03:28.243][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-10-12 16:03:28.244][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:03:28.245][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:03:28.252][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 16:03:28.253][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-10-12 16:03:28.254][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-10-12 16:03:28.255][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:03:28.256][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:03:28.258][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:03:28.259][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-10-12 16:03:28.260][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-10-12 16:03:28.261][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:03:28.262][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:03:28.263][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:03:28.264][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-10-12 16:03:28.266][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-10-12 16:03:28.267][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:03:28.268][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:03:28.269][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:03:28.270][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-10-12 16:03:28.271][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-10-12 16:03:28.272][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:03:28.273][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:03:28.274][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:03:28.276][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-10-12 16:03:28.277][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-10-12 16:03:28.280][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-10-12 16:03:28.281][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:03:28.282][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:03:28.283][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:03:28.285][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-10-12 16:03:28.286][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-10-12 16:03:28.287][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-10-12 16:03:28.288][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:03:28.289][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:03:28.290][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:03:28.292][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-10-12 16:03:28.294][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-10-12 16:03:28.295][self$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 16:03:28.296][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-10-12 16:03:28.297][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-10-12 16:03:28.299][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-10-12 16:03:28.300][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-10-12 16:03:28.301][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-10-12 16:03:28.302][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-10-12 16:03:28.303][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-10-12 16:03:28.305][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-10-12 16:03:28.306][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-10-12 16:03:28.307][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-10-12 16:03:28.308][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-10-12 16:03:28.309][self$setPropertyValue]
biodb.DEBUG[2024-10-12 16:03:28.311][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-10-12 16:03:28.312][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-10-12 16:03:28.312][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-10-12 16:03:28.312][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-10-12 16:03:28.312][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-10-12 16:03:28.312][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-10-12 16:03:28.313][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-10-12 16:03:28.314][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-12 16:03:28.315][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-12 16:03:28.317][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-10-12 16:03:28.318][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-12 16:03:28.319][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-12 16:03:28.320][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-10-12 16:03:28.321][self$setPropertyValue]
biodb.DEBUG[2024-10-12 16:03:28.322][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-10-12 16:03:28.323][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-10-12 16:03:28.325][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-10-12 16:03:28.326][self$setPropertyValue]
biodb.DEBUG[2024-10-12 16:03:28.327][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-10-12 16:03:28.329][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-10-12 16:03:28.330][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-10-12 16:03:28.332][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-10-12 16:03:28.333][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-10-12 16:03:28.334][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-10-12 16:03:28.335][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-10-12 16:03:28.336][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-10-12 16:03:28.338][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-10-12 16:03:28.339][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-10-12 16:03:28.340][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-10-12 16:03:28.341][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-10-12 16:03:28.342][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-10-12 16:03:28.344][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-10-12 16:03:28.345][self$setPropertyValue]
biodb.DEBUG[2024-10-12 16:03:28.346][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-10-12 16:03:28.347][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-10-12 16:03:28.347][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-10-12 16:03:28.347][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-10-12 16:03:28.347][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-10-12 16:03:28.347][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-10-12 16:03:28.348][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-10-12 16:03:28.350][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-12 16:03:28.351][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-12 16:03:28.352][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-10-12 16:03:28.353][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-12 16:03:28.354][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-12 16:03:28.355][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-10-12 16:03:28.356][self$setPropertyValue]
biodb.DEBUG[2024-10-12 16:03:28.358][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-10-12 16:03:28.359][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-10-12 16:03:28.360][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-10-12 16:03:28.361][self$setPropertyValue]
biodb.DEBUG[2024-10-12 16:03:28.362][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-10-12 16:03:28.364][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-10-12 16:03:28.366][self$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 16:03:28.367][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-10-12 16:03:28.368][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-10-12 16:03:28.369][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-10-12 16:03:28.371][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-10-12 16:03:28.372][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-10-12 16:03:28.373][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-10-12 16:03:28.379][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-10-12 16:03:28.381][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-10-12 16:03:28.382][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-10-12 16:03:28.383][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-10-12 16:03:28.384][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-10-12 16:03:28.385][self$setPropertyValue]
biodb.DEBUG[2024-10-12 16:03:28.387][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-10-12 16:03:28.388][self$setPropertyValue]
biodb.DEBUG[2024-10-12 16:03:28.389][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-10-12 16:03:28.390][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-12 16:03:28.391][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-12 16:03:28.392][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-10-12 16:03:28.394][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-12 16:03:28.395][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-12 16:03:28.396][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-10-12 16:03:28.397][self$setPropertyValue]
biodb.DEBUG[2024-10-12 16:03:28.398][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-10-12 16:03:28.399][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-10-12 16:03:28.400][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-10-12 16:03:28.402][self$setPropertyValue]
biodb.DEBUG[2024-10-12 16:03:28.403][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-10-12 16:03:28.405][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-10-12 16:03:28.406][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-10-12 16:03:28.408][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-10-12 16:03:28.409][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-10-12 16:03:28.410][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-10-12 16:03:28.411][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-10-12 16:03:28.412][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-10-12 16:03:28.414][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-10-12 16:03:28.415][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-10-12 16:03:28.416][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-10-12 16:03:28.417][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-10-12 16:03:28.418][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-10-12 16:03:28.420][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-10-12 16:03:28.421][self$setPropertyValue]
biodb.DEBUG[2024-10-12 16:03:28.422][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-10-12 16:03:28.423][self$setPropertyValue]
biodb.DEBUG[2024-10-12 16:03:28.424][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-10-12 16:03:28.426][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-12 16:03:28.427][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-12 16:03:28.428][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-10-12 16:03:28.429][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-12 16:03:28.430][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-12 16:03:28.431][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-10-12 16:03:28.433][self$setPropertyValue]
biodb.DEBUG[2024-10-12 16:03:28.434][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-10-12 16:03:28.435][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-10-12 16:03:28.436][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-10-12 16:03:28.437][self$setPropertyValue]
biodb.DEBUG[2024-10-12 16:03:28.439][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-10-12 16:03:28.440][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:03:28.441][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:03:28.442][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:03:28.443][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:03:28.444][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 16:03:28.445][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:03:28.446][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:03:28.447][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:03:28.448][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:03:28.449][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 16:03:28.451][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:03:28.452][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:03:28.453][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:03:28.454][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:03:28.455][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 16:03:28.456][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:03:28.457][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:03:28.458][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:03:28.459][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:03:28.460][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 16:03:28.461][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:03:28.463][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:03:28.464][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:03:28.465][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:03:28.466][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 16:03:28.467][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:03:28.468][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:03:28.469][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:03:28.470][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:03:28.471][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 16:03:28.472][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:03:28.473][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:03:28.474][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:03:28.475][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:03:28.477][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 16:03:28.478][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:03:28.479][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:03:28.480][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:03:28.481][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:03:28.482][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 16:03:28.483][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:03:28.484][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:03:28.485][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:03:28.486][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:03:28.487][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 16:03:28.488][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:03:28.490][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:03:28.491][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:03:28.492][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:03:28.493][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 16:03:28.494][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:03:28.495][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:03:28.496][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:03:28.497][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:03:28.498][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 16:03:28.504][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:03:28.505][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:03:28.507][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:03:28.508][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:03:28.509][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 16:03:28.510][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:03:28.511][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:03:28.512][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:03:28.513][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:03:28.514][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 16:03:28.515][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:03:28.516][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:03:28.517][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:03:28.518][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:03:28.519][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 16:03:28.521][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:03:28.522][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:03:28.523][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:03:28.524][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:03:28.525][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 16:03:28.526][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:03:28.527][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:03:28.528][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:03:28.529][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:03:28.530][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 16:03:28.531][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:03:28.532][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:03:28.534][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:03:28.535][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:03:28.536][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 16:03:28.537][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:03:28.538][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:03:28.539][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-10-12 16:03:28.541][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-10-12 16:03:28.542][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-10-12 16:03:28.544][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-10-12 16:03:28.546][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-10-12 16:03:28.547][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-10-12 16:03:28.549][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-10-12 16:03:28.550][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-10-12 16:03:28.552][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-10-12 16:03:28.553][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-10-12 16:03:28.555][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-10-12 16:03:28.556][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-10-12 16:03:28.558][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-10-12 16:03:28.560][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-10-12 16:03:28.561][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-10-12 16:03:28.563][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-10-12 16:03:28.564][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-10-12 16:03:28.566][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-10-12 16:03:28.567][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-10-12 16:03:28.569][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-10-12 16:03:28.570][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-10-12 16:03:28.572][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-10-12 16:03:28.574][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-10-12 16:03:28.575][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-10-12 16:03:28.577][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-10-12 16:03:28.578][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-10-12 16:03:28.580][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-10-12 16:03:28.581][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-10-12 16:03:28.583][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-10-12 16:03:28.584][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-10-12 16:03:28.586][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-10-12 16:03:28.588][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-10-12 16:03:28.589][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-10-12 16:03:28.591][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-10-12 16:03:28.592][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-10-12 16:03:28.594][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-10-12 16:03:28.595][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-10-12 16:03:28.597][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-10-12 16:03:28.598][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-10-12 16:03:28.600][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-10-12 16:03:28.602][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-10-12 16:03:28.603][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-10-12 16:03:28.605][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-10-12 16:03:28.606][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-10-12 16:03:28.608][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-10-12 16:03:28.609][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-10-12 16:03:28.611][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-10-12 16:03:28.613][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-10-12 16:03:28.614][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-10-12 16:03:28.621][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-10-12 16:03:28.623][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-10-12 16:03:28.624][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-10-12 16:03:28.626][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-10-12 16:03:28.628][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-10-12 16:03:28.629][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-10-12 16:03:28.631][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-10-12 16:03:28.632][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-10-12 16:03:28.634][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-10-12 16:03:28.635][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-10-12 16:03:28.637][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-10-12 16:03:28.638][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-10-12 16:03:28.640][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-10-12 16:03:28.642][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-10-12 16:03:28.643][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-10-12 16:03:28.645][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-10-12 16:03:28.646][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-10-12 16:03:28.648][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-10-12 16:03:28.650][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-10-12 16:03:28.651][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-10-12 16:03:28.653][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-10-12 16:03:28.654][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-10-12 16:03:28.656][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-10-12 16:03:28.657][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-10-12 16:03:28.659][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-10-12 16:03:28.661][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-10-12 16:03:28.662][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-10-12 16:03:28.664][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-10-12 16:03:28.665][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-10-12 16:03:28.667][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-10-12 16:03:28.669][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-10-12 16:03:28.670][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-10-12 16:03:28.672][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-10-12 16:03:28.673][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-10-12 16:03:28.675][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-10-12 16:03:28.677][initialize] This is biodb version 1.12.0.
biodb.DEBUG[2024-10-12 16:03:28.679][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-10-12 16:03:28.680][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:03:28.681][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 16:03:28.682][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:03:28.683][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 16:03:28.684][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:03:28.685][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-12 16:03:28.686][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-12 16:03:28.687][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:03:28.688][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 16:03:28.689][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:03:28.690][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 16:03:28.692][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:03:28.693][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-12 16:03:28.694][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-12 16:03:28.695][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:03:28.696][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 16:03:28.697][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:03:28.698][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:03:28.699][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:03:28.700][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-12 16:03:28.701][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-12 16:03:28.702][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:03:28.703][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 16:03:28.704][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:03:28.705][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:03:28.706][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:03:28.707][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-12 16:03:28.709][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-12 16:03:28.710][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:03:28.711][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 16:03:28.712][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:03:28.713][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 16:03:28.714][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:03:28.715][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-12 16:03:28.716][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-12 16:03:28.717][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:03:28.718][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-12 16:03:28.719][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:03:28.720][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:03:28.721][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:03:28.722][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-12 16:03:28.723][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-12 16:03:28.725][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:03:28.726][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 16:03:28.727][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:03:28.728][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:03:28.729][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:03:28.730][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-12 16:03:28.731][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-12 16:03:28.732][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:03:28.733][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-12 16:03:28.734][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:03:28.741][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:03:28.742][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:03:28.743][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-12 16:03:28.744][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-12 16:03:28.745][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:03:28.746][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-12 16:03:28.748][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:03:28.749][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:03:28.750][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:03:28.751][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-12 16:03:28.752][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-12 16:03:28.753][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:03:28.754][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 16:03:28.755][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:03:28.756][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:03:28.757][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:03:28.758][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-12 16:03:28.759][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-12 16:03:28.760][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:03:28.761][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-12 16:03:28.763][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:03:28.764][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:03:28.765][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:03:28.766][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-12 16:03:28.767][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-12 16:03:28.768][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:03:28.769][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-12 16:03:28.770][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:03:28.771][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:03:28.772][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:03:28.773][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-12 16:03:28.774][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-12 16:03:28.775][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:03:28.777][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 16:03:28.778][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:03:28.779][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:03:28.780][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:03:28.781][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-12 16:03:28.782][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-12 16:03:28.783][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:03:28.784][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-12 16:03:28.785][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:03:28.786][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:03:28.787][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:03:28.788][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-12 16:03:28.789][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-12 16:03:28.790][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:03:28.791][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-12 16:03:28.793][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:03:28.794][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:03:28.795][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:03:28.796][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-12 16:03:28.797][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-12 16:03:28.798][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:03:28.799][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-12 16:03:28.800][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:03:28.801][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:03:28.802][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:03:28.803][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-12 16:03:28.804][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-12 16:03:28.805][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:03:28.806][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 16:03:28.807][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:03:28.808][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:03:28.809][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:03:28.811][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-12 16:03:28.812][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-12 16:03:28.813][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:03:28.814][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 16:03:28.815][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:03:28.816][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:03:28.819][biodb$loadDefinitions] Load definitions from file "E:/biocbuild/bbs-3.19-bioc-longtests/meat/biodbExpasy.Rcheck/biodbExpasy/definitions.yml".
biodb.DEBUG[2024-10-12 16:03:28.821][self$getDbsInfo()$define] Define connector expasy.enzyme.
biodb.DEBUG[2024-10-12 16:03:28.823][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-10-12 16:03:28.824][self$setPropertyValue] Setting property "description" to "Write here the description of this database.".
biodb.DEBUG[2024-10-12 16:03:28.825][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-10-12 16:03:28.826][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-10-12 16:03:28.828][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-10-12 16:03:28.829][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-10-12 16:03:28.830][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-10-12 16:03:28.831][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-10-12 16:03:28.832][self$setPropertyValue] Setting property "entry.content.type" to "txt".
biodb.DEBUG[2024-10-12 16:03:28.833][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-10-12 16:03:28.835][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-10-12 16:03:28.836][self$setPropertyValue] Setting property "name" to "Expasy ENZYME database.".
biodb.DEBUG[2024-10-12 16:03:28.837][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-10-12 16:03:28.838][self$setPropertyValue] Setting property "parsing.expr" to "^ID\s+([0-9.]+)$".
biodb.DEBUG[2024-10-12 16:03:28.838][self$setPropertyValue] Setting property "parsing.expr" to "^CA\s+(.+?)\.?$".
biodb.DEBUG[2024-10-12 16:03:28.838][self$setPropertyValue] Setting property "parsing.expr" to "^CF\s+(.+?)\.?$".
biodb.DEBUG[2024-10-12 16:03:28.838][self$setPropertyValue] Setting property "parsing.expr" to "^DE\s+(.+?)\.?$".
biodb.DEBUG[2024-10-12 16:03:28.839][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-10-12 16:03:28.841][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-10-12 16:03:28.842][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2024-10-12 16:03:28.843][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-12 16:03:28.844][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-12 16:03:28.845][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-10-12 16:03:28.846][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-12 16:03:28.847][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-12 16:03:28.849][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-10-12 16:03:28.850][self$setPropertyValue] Setting property "urls" to "https://enzyme.expasy.org/".
biodb.DEBUG[2024-10-12 16:03:28.851][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-10-12 16:03:28.852][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-10-12 16:03:28.853][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-10-12 16:03:28.854][self$setPropertyValue]
biodb.DEBUG[2024-10-12 16:03:28.856][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-10-12 16:03:28.865][super$initialize] Initialize connector expasy.enzyme.
biodb.DEBUG[2024-10-12 16:03:28.866][super$initialize] Register connector expasy.enzyme with the request scheduler
biodb.DEBUG[2024-10-12 16:03:28.868][private$bdb$getRequestScheduler()$re ...] Register connector expasy.enzyme.
biodb.DEBUG[2024-10-12 16:03:28.869][private$addConnectorRules] Create new rule for URL "enzyme.expasy.org" of connector "expasy.enzyme".
biodb.DEBUG[2024-10-12 16:03:28.871][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-10-12 16:03:28.872][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-10-12 16:03:28.873][biodb$getFactory()$createConn] Creating new connector expasy.enzyme for database class expasy.enzyme .
biodb.INFO [2024-10-12 16:03:28.874][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-10-12 16:03:28.876][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector expasy.enzyme from the request scheduler
biodb.INFO [2024-10-12 16:03:28.877][self$deleteConn] Connector "expasy.enzyme" deleted.
biodb.DEBUG[2024-10-12 16:03:28.878][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-10-12 16:03:28.879][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-12 16:03:28.880][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-12 16:03:28.881][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:03:28.882][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-12 16:03:28.884][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:03:28.885][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".
[ 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:
###
###   E:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --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 'E:/biocbuild/bbs-3.19-bioc-longtests/meat/biodbExpasy.Rcheck'
* using R version 4.4.1 (2024-06-14 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.2.0
    GNU Fortran (GCC) 13.2.0
* running under: Windows Server 2022 x64 (build 20348)
* 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 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
  'E:/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)