Back to Long Tests report for BioC 3.20

This page was generated on 2024-07-06 23:55 -0400 (Sat, 06 Jul 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.4.1 (2024-06-14) -- "Race for Your Life" 4643
palomino6Windows Server 2022 Datacenterx644.4.1 (2024-06-14 ucrt) -- "Race for Your Life" 4414
lconwaymacOS 12.7.1 Montereyx86_644.4.1 (2024-06-14) -- "Race for Your Life" 4442
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 7/32HostnameOS / ArchCHECK
biodbExpasy 1.9.0  (landing page)
Pierrick Roger
Snapshot Date: 2024-07-06 09:55 -0400 (Sat, 06 Jul 2024)
git_url: https://git.bioconductor.org/packages/biodbExpasy
git_branch: devel
git_last_commit: 25fc0fc
git_last_commit_date: 2024-04-30 11:41:12 -0400 (Tue, 30 Apr 2024)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  ERROR  
palomino6Windows Server 2022 Datacenter / x64  ERROR  
lconwaymacOS 12.7.1 Monterey / x86_64  ERROR  


CHECK results for biodbExpasy on lconway

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: 1.9.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --test-dir=longtests --no-stop-on-test-error --no-codoc --no-examples --no-manual --ignore-vignettes --check-subdirs=no biodbExpasy_1.9.0.tar.gz
StartedAt: 2024-07-06 16:01:04 -0400 (Sat, 06 Jul 2024)
EndedAt: 2024-07-06 16:01:52 -0400 (Sat, 06 Jul 2024)
EllapsedTime: 47.7 seconds
RetCode: 1
Status:   ERROR  
CheckDir: biodbExpasy.Rcheck
Warnings: NA

Tests output

biodbExpasy.Rcheck/tests/testthat.Rout.fail


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

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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 [2024-07-06 16:01:38.499][biodb::testContext]
biodb.INFO [2024-07-06 16:01:38.502][biodb::testContext] ********************************************************************************
biodb.INFO [2024-07-06 16:01:38.503][biodb::testContext] Test context - Generic long tests
biodb.INFO [2024-07-06 16:01:38.504][biodb::testContext] ********************************************************************************
biodb.INFO [2024-07-06 16:01:38.505][biodb::testContext]
biodb.INFO [2024-07-06 16:01:38.510][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.13.0.
biodb.DEBUG[2024-07-06 16:01:38.512][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2024-07-06 16:01:38.518][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-07-06 16:01:38.519][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-07-06 16:01:38.520][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-07-06 16:01:38.520][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:01:38.521][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:01:38.522][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:01:38.523][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-07-06 16:01:38.548][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-07-06 16:01:38.549][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:01:38.550][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:01:38.550][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:01:38.551][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-07-06 16:01:38.552][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-07-06 16:01:38.552][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:01:38.553][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:01:38.554][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:01:38.555][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-07-06 16:01:38.555][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-07-06 16:01:38.556][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-07-06 16:01:38.557][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:01:38.557][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:01:38.558][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:01:38.559][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-07-06 16:01:38.560][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-07-06 16:01:38.561][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-07-06 16:01:38.561][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:01:38.562][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:01:38.563][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:01:38.563][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-07-06 16:01:38.564][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-07-06 16:01:38.565][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:01:38.565][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:01:38.566][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:01:38.567][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-07-06 16:01:38.567][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-07-06 16:01:38.568][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-07-06 16:01:38.569][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:01:38.570][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:01:38.570][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:01:38.571][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-07-06 16:01:38.572][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-07-06 16:01:38.573][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:01:38.573][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:01:38.574][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:01:38.575][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-07-06 16:01:38.575][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-07-06 16:01:38.576][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-07-06 16:01:38.577][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:01:38.578][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:01:38.578][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:01:38.579][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-07-06 16:01:38.580][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-07-06 16:01:38.581][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-07-06 16:01:38.582][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-07-06 16:01:38.582][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-07-06 16:01:38.583][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-07-06 16:01:38.584][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:01:38.585][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:01:38.585][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:01:38.586][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-07-06 16:01:38.587][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-07-06 16:01:38.588][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:01:38.588][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:01:38.589][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:01:38.590][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-07-06 16:01:38.590][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-07-06 16:01:38.591][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:01:38.592][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:01:38.592][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:01:38.593][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-07-06 16:01:38.594][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-07-06 16:01:38.595][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:01:38.595][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:01:38.596][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:01:38.597][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-07-06 16:01:38.598][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-07-06 16:01:38.598][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:01:38.599][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:01:38.600][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:01:38.600][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-07-06 16:01:38.601][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-07-06 16:01:38.602][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:01:38.603][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:01:38.603][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:01:38.604][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-07-06 16:01:38.605][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-07-06 16:01:38.620][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-07-06 16:01:38.621][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:01:38.622][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:01:38.622][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:01:38.623][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-07-06 16:01:38.624][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-07-06 16:01:38.625][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-07-06 16:01:38.625][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:01:38.626][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:01:38.626][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:01:38.629][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-07-06 16:01:38.654][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-07-06 16:01:38.665][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2024-07-06 16:01:38.666][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-07-06 16:01:38.667][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-07-06 16:01:38.668][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-07-06 16:01:38.668][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-07-06 16:01:38.669][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-07-06 16:01:38.670][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-07-06 16:01:38.671][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-07-06 16:01:38.671][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-07-06 16:01:38.672][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-07-06 16:01:38.673][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-07-06 16:01:38.673][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-07-06 16:01:38.674][self$setPropertyValue]
biodb.DEBUG[2024-07-06 16:01:38.675][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-07-06 16:01:38.676][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-07-06 16:01:38.676][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-07-06 16:01:38.676][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-07-06 16:01:38.676][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-07-06 16:01:38.676][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-07-06 16:01:38.676][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-07-06 16:01:38.677][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-06 16:01:38.678][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-06 16:01:38.679][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-07-06 16:01:38.680][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-06 16:01:38.680][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-06 16:01:38.681][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-07-06 16:01:38.682][self$setPropertyValue]
biodb.DEBUG[2024-07-06 16:01:38.683][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-07-06 16:01:38.683][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-07-06 16:01:38.684][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-07-06 16:01:38.685][self$setPropertyValue]
biodb.DEBUG[2024-07-06 16:01:38.686][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-07-06 16:01:38.687][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-07-06 16:01:38.688][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-07-06 16:01:38.689][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-07-06 16:01:38.689][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-07-06 16:01:38.690][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-07-06 16:01:38.691][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-07-06 16:01:38.692][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-07-06 16:01:38.692][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-07-06 16:01:38.693][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-07-06 16:01:38.694][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-07-06 16:01:38.695][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-07-06 16:01:38.695][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-07-06 16:01:38.696][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-07-06 16:01:38.697][self$setPropertyValue]
biodb.DEBUG[2024-07-06 16:01:38.697][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-07-06 16:01:38.698][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-07-06 16:01:38.698][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-07-06 16:01:38.698][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-07-06 16:01:38.698][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-07-06 16:01:38.698][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-07-06 16:01:38.703][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-07-06 16:01:38.704][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-06 16:01:38.705][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-06 16:01:38.705][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-07-06 16:01:38.706][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-06 16:01:38.707][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-06 16:01:38.707][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-07-06 16:01:38.708][self$setPropertyValue]
biodb.DEBUG[2024-07-06 16:01:38.709][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-07-06 16:01:38.710][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-07-06 16:01:38.710][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-07-06 16:01:38.711][self$setPropertyValue]
biodb.DEBUG[2024-07-06 16:01:38.712][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-07-06 16:01:38.713][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-07-06 16:01:38.714][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2024-07-06 16:01:38.715][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-07-06 16:01:38.716][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-07-06 16:01:38.716][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-07-06 16:01:38.717][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-07-06 16:01:38.718][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-07-06 16:01:38.719][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-07-06 16:01:38.719][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-07-06 16:01:38.720][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-07-06 16:01:38.721][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-07-06 16:01:38.722][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-07-06 16:01:38.722][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-07-06 16:01:38.723][self$setPropertyValue]
biodb.DEBUG[2024-07-06 16:01:38.724][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-07-06 16:01:38.725][self$setPropertyValue]
biodb.DEBUG[2024-07-06 16:01:38.725][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-07-06 16:01:38.726][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-06 16:01:38.727][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-06 16:01:38.728][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-07-06 16:01:38.728][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-06 16:01:38.729][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-06 16:01:38.730][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-07-06 16:01:38.731][self$setPropertyValue]
biodb.DEBUG[2024-07-06 16:01:38.731][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-07-06 16:01:38.732][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-07-06 16:01:38.733][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-07-06 16:01:38.733][self$setPropertyValue]
biodb.DEBUG[2024-07-06 16:01:38.734][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-07-06 16:01:38.736][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-07-06 16:01:38.736][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-07-06 16:01:38.737][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-07-06 16:01:38.738][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-07-06 16:01:38.739][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-07-06 16:01:38.740][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-07-06 16:01:38.741][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-07-06 16:01:38.742][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-07-06 16:01:38.743][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-07-06 16:01:38.743][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-07-06 16:01:38.744][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-07-06 16:01:38.745][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-07-06 16:01:38.746][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-07-06 16:01:38.746][self$setPropertyValue]
biodb.DEBUG[2024-07-06 16:01:38.747][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-07-06 16:01:38.748][self$setPropertyValue]
biodb.DEBUG[2024-07-06 16:01:38.749][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-07-06 16:01:38.749][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-06 16:01:38.750][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-06 16:01:38.751][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-07-06 16:01:38.751][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-06 16:01:38.752][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-06 16:01:38.753][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-07-06 16:01:38.754][self$setPropertyValue]
biodb.DEBUG[2024-07-06 16:01:38.754][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-07-06 16:01:38.755][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-07-06 16:01:38.756][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-07-06 16:01:38.756][self$setPropertyValue]
biodb.DEBUG[2024-07-06 16:01:38.760][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-07-06 16:01:38.760][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:01:38.761][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:01:38.761][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:01:38.762][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-06 16:01:38.763][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-06 16:01:38.763][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:01:38.764][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[2024-07-06 16:01:38.765][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:01:38.766][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-06 16:01:38.766][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-06 16:01:38.767][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:01:38.768][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:01:38.768][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:01:38.769][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-06 16:01:38.770][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-06 16:01:38.770][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:01:38.771][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[2024-07-06 16:01:38.772][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:01:38.773][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-06 16:01:38.773][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-06 16:01:38.774][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:01:38.775][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:01:38.775][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:01:38.776][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-06 16:01:38.776][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-06 16:01:38.777][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:01:38.778][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[2024-07-06 16:01:38.778][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:01:38.779][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-06 16:01:38.780][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-06 16:01:38.780][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:01:38.781][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:01:38.782][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:01:38.782][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-06 16:01:38.783][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-06 16:01:38.783][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:01:38.784][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:01:38.785][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:01:38.785][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-06 16:01:38.786][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-06 16:01:38.787][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:01:38.787][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:01:38.788][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:01:38.789][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-06 16:01:38.789][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-06 16:01:38.790][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:01:38.790][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:01:38.791][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:01:38.792][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-06 16:01:38.792][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-06 16:01:38.793][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:01:38.794][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[2024-07-06 16:01:38.794][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:01:38.795][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-06 16:01:38.796][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-06 16:01:38.796][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:01:38.797][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:01:38.798][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:01:38.798][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-06 16:01:38.799][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-06 16:01:38.800][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:01:38.800][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:01:38.801][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:01:38.802][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-06 16:01:38.802][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-06 16:01:38.803][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:01:38.804][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[2024-07-06 16:01:38.804][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:01:38.805][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-06 16:01:38.806][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-06 16:01:38.806][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:01:38.807][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:01:38.807][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:01:38.808][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-06 16:01:38.809][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-06 16:01:38.809][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:01:38.810][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[2024-07-06 16:01:38.811][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:01:38.812][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-06 16:01:38.812][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-06 16:01:38.813][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:01:38.814][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:01:38.814][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:01:38.815][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-06 16:01:38.816][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-06 16:01:38.816][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:01:38.817][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:01:38.818][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-07-06 16:01:38.821][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-07-06 16:01:38.822][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-07-06 16:01:38.823][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-07-06 16:01:38.824][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-07-06 16:01:38.825][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-07-06 16:01:38.826][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-07-06 16:01:38.827][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-07-06 16:01:38.828][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-07-06 16:01:38.829][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-07-06 16:01:38.830][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-07-06 16:01:38.831][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-07-06 16:01:38.832][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-07-06 16:01:38.833][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-07-06 16:01:38.834][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-07-06 16:01:38.835][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-07-06 16:01:38.836][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-07-06 16:01:38.837][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-07-06 16:01:38.838][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-07-06 16:01:38.839][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-07-06 16:01:38.840][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-07-06 16:01:38.841][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-07-06 16:01:38.842][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-07-06 16:01:38.847][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-07-06 16:01:38.848][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-07-06 16:01:38.849][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-07-06 16:01:38.850][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-07-06 16:01:38.851][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-07-06 16:01:38.852][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-07-06 16:01:38.853][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-07-06 16:01:38.854][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-07-06 16:01:38.855][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-07-06 16:01:38.856][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-07-06 16:01:38.857][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-07-06 16:01:38.858][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-07-06 16:01:38.859][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-07-06 16:01:38.860][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-07-06 16:01:38.861][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-07-06 16:01:38.862][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-07-06 16:01:38.864][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-07-06 16:01:38.865][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-07-06 16:01:38.866][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-07-06 16:01:38.867][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-07-06 16:01:38.868][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-07-06 16:01:38.869][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-07-06 16:01:38.870][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-07-06 16:01:38.871][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-07-06 16:01:38.872][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-07-06 16:01:38.873][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-07-06 16:01:38.874][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-07-06 16:01:38.875][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-07-06 16:01:38.876][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-07-06 16:01:38.877][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-07-06 16:01:38.878][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-07-06 16:01:38.879][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-07-06 16:01:38.880][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-07-06 16:01:38.881][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-07-06 16:01:38.882][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-07-06 16:01:38.884][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-07-06 16:01:38.885][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-07-06 16:01:38.886][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-07-06 16:01:38.887][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-07-06 16:01:38.888][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-07-06 16:01:38.889][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-07-06 16:01:38.890][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-07-06 16:01:38.891][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-07-06 16:01:38.892][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-07-06 16:01:38.893][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-07-06 16:01:38.894][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-07-06 16:01:38.895][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-07-06 16:01:38.896][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-07-06 16:01:38.897][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-07-06 16:01:38.898][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-07-06 16:01:38.899][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-07-06 16:01:38.900][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-07-06 16:01:38.901][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-07-06 16:01:38.902][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-07-06 16:01:38.903][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-07-06 16:01:38.904][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-07-06 16:01:38.905][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-07-06 16:01:38.907][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-07-06 16:01:38.908][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-07-06 16:01:38.908][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-07-06 16:01:38.913][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-07-06 16:01:38.914][initialize] This is biodb version 1.13.0.
biodb.DEBUG[2024-07-06 16:01:38.917][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-07-06 16:01:38.917][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-07-06 16:01:38.918][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-06 16:01:38.918][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:01:38.919][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:01:38.922][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:01:38.923][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-06 16:01:38.924][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-06 16:01:38.924][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-06 16:01:38.925][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-06 16:01:38.926][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:01:38.926][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:01:38.927][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:01:38.928][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-06 16:01:38.929][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-06 16:01:38.929][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-06 16:01:38.930][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-06 16:01:38.930][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:01:38.931][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:01:38.932][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:01:38.933][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-06 16:01:38.933][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-06 16:01:38.934][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-06 16:01:38.935][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-06 16:01:38.935][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:01:38.936][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:01:38.937][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:01:38.937][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-06 16:01:38.938][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-06 16:01:38.939][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-06 16:01:38.939][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-06 16:01:38.940][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:01:38.941][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:01:38.941][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:01:38.942][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-06 16:01:38.943][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-06 16:01:38.943][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-06 16:01:38.944][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-06 16:01:38.944][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:01:38.945][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:01:38.946][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:01:38.946][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-06 16:01:38.947][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-06 16:01:38.948][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-06 16:01:38.948][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-06 16:01:38.949][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:01:38.949][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:01:38.950][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:01:38.951][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-06 16:01:38.951][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-06 16:01:38.952][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-06 16:01:38.953][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-06 16:01:38.953][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:01:38.954][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:01:38.955][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:01:38.956][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-06 16:01:38.956][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-06 16:01:38.957][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-06 16:01:38.957][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-06 16:01:38.958][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:01:38.959][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:01:38.959][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:01:38.960][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-06 16:01:38.961][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-06 16:01:38.961][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-06 16:01:38.962][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-06 16:01:38.963][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:01:38.964][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:01:38.964][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:01:38.965][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-06 16:01:38.965][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-06 16:01:38.966][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-06 16:01:38.967][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-06 16:01:38.968][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:01:38.968][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:01:38.969][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:01:38.970][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-06 16:01:38.970][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-06 16:01:38.971][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-06 16:01:38.972][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-06 16:01:38.973][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:01:38.973][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:01:38.974][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:01:38.975][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-06 16:01:38.976][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-06 16:01:38.976][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-06 16:01:38.977][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-06 16:01:38.978][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:01:38.978][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:01:38.979][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:01:38.980][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-06 16:01:38.980][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-06 16:01:38.985][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-06 16:01:38.986][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-06 16:01:38.987][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:01:38.987][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:01:38.988][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:01:38.988][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-06 16:01:38.989][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-06 16:01:38.990][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-06 16:01:38.990][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-06 16:01:38.991][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:01:38.992][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:01:38.992][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:01:38.993][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-06 16:01:38.993][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-06 16:01:38.994][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-06 16:01:38.995][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-06 16:01:38.995][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:01:38.996][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:01:38.997][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:01:38.997][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-06 16:01:38.998][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-06 16:01:38.998][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-06 16:01:38.999][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-06 16:01:39.000][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:01:39.000][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:01:39.001][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:01:39.002][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-06 16:01:39.002][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-06 16:01:39.003][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-06 16:01:39.004][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-06 16:01:39.004][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:01:39.005][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:01:39.006][biodb$loadDefinitions] Load definitions from file "/Users/biocbuild/bbs-3.20-bioc-longtests/meat/biodbExpasy.Rcheck/biodbExpasy/definitions.yml".
biodb.DEBUG[2024-07-06 16:01:39.013][self$getDbsInfo()$define] Define connector expasy.enzyme.
biodb.DEBUG[2024-07-06 16:01:39.015][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-07-06 16:01:39.016][self$setPropertyValue] Setting property "description" to "Write here the description of this database.".
biodb.DEBUG[2024-07-06 16:01:39.017][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-07-06 16:01:39.017][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-07-06 16:01:39.018][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-07-06 16:01:39.019][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-07-06 16:01:39.020][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-07-06 16:01:39.021][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-07-06 16:01:39.021][self$setPropertyValue] Setting property "entry.content.type" to "txt".
biodb.DEBUG[2024-07-06 16:01:39.022][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-07-06 16:01:39.023][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-07-06 16:01:39.024][self$setPropertyValue] Setting property "name" to "Expasy ENZYME database.".
biodb.DEBUG[2024-07-06 16:01:39.024][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-07-06 16:01:39.025][self$setPropertyValue] Setting property "parsing.expr" to "^ID\s+([0-9.]+)$".
biodb.DEBUG[2024-07-06 16:01:39.025][self$setPropertyValue] Setting property "parsing.expr" to "^CA\s+(.+?)\.?$".
biodb.DEBUG[2024-07-06 16:01:39.025][self$setPropertyValue] Setting property "parsing.expr" to "^CF\s+(.+?)\.?$".
biodb.DEBUG[2024-07-06 16:01:39.025][self$setPropertyValue] Setting property "parsing.expr" to "^DE\s+(.+?)\.?$".
biodb.DEBUG[2024-07-06 16:01:39.026][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-07-06 16:01:39.027][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-07-06 16:01:39.028][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2024-07-06 16:01:39.029][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-06 16:01:39.029][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-06 16:01:39.030][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-07-06 16:01:39.031][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-06 16:01:39.031][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-06 16:01:39.032][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-07-06 16:01:39.033][self$setPropertyValue] Setting property "urls" to "https://enzyme.expasy.org/".
biodb.DEBUG[2024-07-06 16:01:39.034][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-07-06 16:01:39.034][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-07-06 16:01:39.035][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-07-06 16:01:39.036][self$setPropertyValue]
biodb.DEBUG[2024-07-06 16:01:39.040][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-07-06 16:01:39.058][super$initialize] Initialize connector expasy.enzyme.
biodb.DEBUG[2024-07-06 16:01:39.060][super$initialize] Register connector expasy.enzyme with the request scheduler
biodb.DEBUG[2024-07-06 16:01:39.063][private$bdb$getRequestScheduler()$re ...] Register connector expasy.enzyme.
biodb.DEBUG[2024-07-06 16:01:39.066][private$addConnectorRules] Create new rule for URL "enzyme.expasy.org" of connector "expasy.enzyme".
biodb.DEBUG[2024-07-06 16:01:39.069][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-07-06 16:01:39.069][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-07-06 16:01:39.070][biodb$getFactory()$createConn] Creating new connector expasy.enzyme for database class expasy.enzyme .
biodb.INFO [2024-07-06 16:01:39.078][biodb::testThat]
biodb.INFO [2024-07-06 16:01:39.078][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2024-07-06 16:01:39.079][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-07-06 16:01:39.080][biodb::testThat]
biodb.TRACE[2024-07-06 16:01:39.082][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/bbs-3.20-bioc-longtests/meat/biodbExpasy.Rcheck/biodbExpasy/testref/entry-expasy.enzyme-1.1.1.1-content.txt".
biodb.DEBUG[2024-07-06 16:01:39.084][biodb$getFactory()$createEntryFromCo ...] Creating Expasy ENZYME database. entries from 1 content(s).
biodb.DEBUG[2024-07-06 16:01:39.086][biodb$getFactory()$createEntryFromCo ...] Parsing 1 Expasy ENZYME database. entries.
biodb.DEBUG[2024-07-06 16:01:39.093][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-06 16:01:39.093][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-06 16:01:39.094][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-06 16:01:39.105][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-06 16:01:39.106][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-06 16:01:39.106][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:01:39.107][FUN] Functions in observer BiodbConfig: [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[2024-07-06 16:01:39.115][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-06 16:01:39.116][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-06 16:01:39.117][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:01:39.118][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:01:39.144][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-07-06 16:01:39.153][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-07-06 16:01:39.154][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:01:39.155][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:01:39.156][self$getBiodb()$getEntryFields()$get] Asked field names are: cofactor.
biodb.TRACE[2024-07-06 16:01:39.157][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-07-06 16:01:39.158][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:01:39.158][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:01:39.159][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-06 16:01:39.160][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-06 16:01:39.161][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:01:39.162][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:01:39.163][self$getBiodb()$getEntryFields()$get] Asked field names are: COFACTOR.
biodb.TRACE[2024-07-06 16:01:39.163][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-07-06 16:01:39.164][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:01:39.165][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:01:39.166][self$getBiodb()$getEntryFields()$get] Asked field names are: cofactor.
biodb.TRACE[2024-07-06 16:01:39.167][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-07-06 16:01:39.167][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:01:39.168][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:01:39.169][self$getBiodb()$getEntryFields()$get] Asked field names are: cofactor.
biodb.TRACE[2024-07-06 16:01:39.170][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-07-06 16:01:39.170][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:01:39.171][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:01:39.172][self$getBiodb()$getEntryFields()$get] Asked field names are: cofactor.
biodb.TRACE[2024-07-06 16:01:39.173][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-07-06 16:01:39.174][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:01:39.174][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:01:39.175][self$getBiodb()$getEntryFields()$get] Asked field names are: COFACTOR.
biodb.TRACE[2024-07-06 16:01:39.176][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-07-06 16:01:39.177][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:01:39.178][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:01:39.191][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-06 16:01:39.192][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-06 16:01:39.193][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:01:39.194][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:01:39.195][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-06 16:01:39.196][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-06 16:01:39.197][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:01:39.197][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:01:39.222][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-06 16:01:39.223][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-06 16:01:39.224][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:01:39.224][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:01:39.225][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-06 16:01:39.226][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-06 16:01:39.227][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:01:39.227][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:01:39.228][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-06 16:01:39.229][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-06 16:01:39.230][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:01:39.230][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:01:39.231][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-07-06 16:01:39.232][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-07-06 16:01:39.232][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:01:39.233][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:01:39.234][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-07-06 16:01:39.235][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-07-06 16:01:39.236][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:01:39.236][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:01:39.237][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-06 16:01:39.238][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-06 16:01:39.239][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:01:39.239][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:01:39.240][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-07-06 16:01:39.241][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-07-06 16:01:39.242][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:01:39.243][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:01:39.243][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-06 16:01:39.244][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-06 16:01:39.245][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:01:39.246][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:01:39.274][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-06 16:01:39.275][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-06 16:01:39.275][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:01:39.276][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:01:39.277][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-06 16:01:39.278][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-06 16:01:39.278][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:01:39.279][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:01:39.280][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-06 16:01:39.281][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-06 16:01:39.281][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:01:39.282][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:01:39.283][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-06 16:01:39.284][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-06 16:01:39.284][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:01:39.285][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:01:39.286][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-06 16:01:39.286][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-06 16:01:39.287][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:01:39.288][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-06 16:01:39.289][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 1.1.1.1.
biodb.TRACE[2024-07-06 16:01:39.291][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-07-06 16:01:39.292][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-07-06 16:01:39.292][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:01:39.293][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:01:39.294][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-07-06 16:01:39.295][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-07-06 16:01:39.295][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:01:39.296][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:01:39.297][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-07-06 16:01:39.298][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-07-06 16:01:39.298][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:01:39.299][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:01:39.300][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-07-06 16:01:39.301][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-07-06 16:01:39.301][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:01:39.302][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:01:39.315][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-06 16:01:39.316][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-06 16:01:39.317][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:01:39.318][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:01:39.328][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-07-06 16:01:39.329][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-07-06 16:01:39.330][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:01:39.331][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:01:39.335][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-06 16:01:39.336][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-06 16:01:39.337][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:01:39.337][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:01:39.338][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-06 16:01:39.339][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-06 16:01:39.340][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:01:39.341][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:01:39.341][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-06 16:01:39.342][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-06 16:01:39.343][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:01:39.344][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:01:39.346][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-06 16:01:39.347][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-06 16:01:39.348][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:01:39.349][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:01:39.349][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-06 16:01:39.350][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-06 16:01:39.351][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:01:39.352][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:01:39.353][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-06 16:01:39.353][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-06 16:01:39.354][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:01:39.355][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:01:39.356][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-07-06 16:01:39.357][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-07-06 16:01:39.357][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:01:39.358][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:01:39.359][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-07-06 16:01:39.360][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-07-06 16:01:39.361][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:01:39.361][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:01:39.362][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-07-06 16:01:39.363][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-07-06 16:01:39.364][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:01:39.364][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:01:39.371][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-06 16:01:39.372][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-06 16:01:39.373][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:01:39.374][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:01:39.375][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-06 16:01:39.375][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-06 16:01:39.376][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:01:39.377][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:01:39.378][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-06 16:01:39.379][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-06 16:01:39.379][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:01:39.380][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:01:39.381][ef$get] Asked field names are: accession.
biodb.TRACE[2024-07-06 16:01:39.382][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-06 16:01:39.382][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:01:39.383][ef$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:01:39.384][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-06 16:01:39.385][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-06 16:01:39.386][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:01:39.386][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:01:39.394][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-06 16:01:39.395][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-06 16:01:39.396][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:01:39.396][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:01:39.397][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-06 16:01:39.398][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-06 16:01:39.399][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:01:39.404][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:01:39.405][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-06 16:01:39.405][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-06 16:01:39.406][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:01:39.407][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:01:39.408][ef$get] Asked field names are: name.
biodb.TRACE[2024-07-06 16:01:39.408][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-07-06 16:01:39.409][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:01:39.410][ef$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:01:39.411][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-06 16:01:39.412][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-06 16:01:39.412][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:01:39.413][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:01:39.421][self$getBiodb()$getEntryFields()$get] Asked field names are: cofactor.
biodb.TRACE[2024-07-06 16:01:39.422][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-07-06 16:01:39.422][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:01:39.423][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:01:39.424][self$getBiodb()$getEntryFields()$get] Asked field names are: cofactor.
biodb.TRACE[2024-07-06 16:01:39.425][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-07-06 16:01:39.425][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:01:39.426][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:01:39.427][self$getBiodb()$getEntryFields()$get] Asked field names are: cofactor.
biodb.TRACE[2024-07-06 16:01:39.428][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-07-06 16:01:39.429][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:01:39.429][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:01:39.430][ef$get] Asked field names are: cofactor.
biodb.TRACE[2024-07-06 16:01:39.431][ef$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-07-06 16:01:39.432][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:01:39.432][ef$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:01:39.433][self$getBiodb()$getEntryFields()$get] Asked field names are: cofactor.
biodb.TRACE[2024-07-06 16:01:39.434][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-07-06 16:01:39.435][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:01:39.436][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:01:39.443][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-07-06 16:01:39.444][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-07-06 16:01:39.445][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:01:39.446][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:01:39.447][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-07-06 16:01:39.448][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-07-06 16:01:39.448][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:01:39.449][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:01:39.450][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-07-06 16:01:39.451][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-07-06 16:01:39.451][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:01:39.452][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:01:39.453][ef$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-07-06 16:01:39.454][ef$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-07-06 16:01:39.454][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:01:39.455][ef$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:01:39.456][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-07-06 16:01:39.457][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-07-06 16:01:39.458][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:01:39.458][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:01:39.466][ef$get] Asked field names are: accession.
biodb.TRACE[2024-07-06 16:01:39.467][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-06 16:01:39.467][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:01:39.468][ef$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:01:39.472][ef$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-07-06 16:01:39.473][ef$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-07-06 16:01:39.474][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:01:39.475][ef$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:01:39.479][ef$get] Asked field names are: cofactor.
biodb.TRACE[2024-07-06 16:01:39.479][ef$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-07-06 16:01:39.480][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:01:39.481][ef$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:01:39.485][ef$get] Asked field names are: name.
biodb.TRACE[2024-07-06 16:01:39.486][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-07-06 16:01:39.487][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:01:39.488][ef$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:01:39.501][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/bbs-3.20-bioc-longtests/meat/biodbExpasy.Rcheck/biodbExpasy/testref/entry-expasy.enzyme-1.1.1.54-content.txt".
biodb.DEBUG[2024-07-06 16:01:39.531][biodb$getFactory()$createEntryFromCo ...] Creating Expasy ENZYME database. entries from 1 content(s).
biodb.DEBUG[2024-07-06 16:01:39.533][biodb$getFactory()$createEntryFromCo ...] Parsing 1 Expasy ENZYME database. entries.
biodb.DEBUG[2024-07-06 16:01:39.534][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-06 16:01:39.535][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-06 16:01:39.535][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-06 16:01:39.539][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-06 16:01:39.540][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-06 16:01:39.541][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:01:39.541][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.TRACE[2024-07-06 16:01:39.543][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-06 16:01:39.544][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-06 16:01:39.544][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:01:39.545][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:01:39.546][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-07-06 16:01:39.547][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-07-06 16:01:39.548][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:01:39.548][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:01:39.549][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-06 16:01:39.550][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-06 16:01:39.551][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:01:39.551][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:01:39.552][self$getBiodb()$getEntryFields()$get] Asked field names are: COFACTOR.
biodb.TRACE[2024-07-06 16:01:39.553][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-07-06 16:01:39.554][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:01:39.554][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:01:39.555][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-07-06 16:01:39.556][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-07-06 16:01:39.557][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:01:39.557][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:01:39.558][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-07-06 16:01:39.559][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-07-06 16:01:39.560][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:01:39.560][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:01:39.561][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-06 16:01:39.562][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-06 16:01:39.563][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:01:39.564][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:01:39.565][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-07-06 16:01:39.565][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-07-06 16:01:39.566][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:01:39.567][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:01:39.568][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-06 16:01:39.569][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-06 16:01:39.569][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:01:39.570][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:01:39.571][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-06 16:01:39.572][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-06 16:01:39.572][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:01:39.573][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:01:39.574][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-06 16:01:39.575][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-06 16:01:39.576][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:01:39.577][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:01:39.578][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-06 16:01:39.578][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-06 16:01:39.579][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:01:39.580][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:01:39.580][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-06 16:01:39.581][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-06 16:01:39.582][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:01:39.583][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:01:39.583][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-06 16:01:39.584][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-06 16:01:39.585][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:01:39.586][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-06 16:01:39.586][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 1.1.1.54.
biodb.TRACE[2024-07-06 16:01:39.603][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-07-06 16:01:39.604][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-07-06 16:01:39.604][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:01:39.605][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:01:39.606][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-07-06 16:01:39.607][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-07-06 16:01:39.608][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:01:39.608][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:01:39.609][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-07-06 16:01:39.610][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-07-06 16:01:39.611][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:01:39.612][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:01:39.612][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-07-06 16:01:39.613][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-07-06 16:01:39.614][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:01:39.615][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:01:39.616][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-06 16:01:39.617][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-06 16:01:39.617][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:01:39.618][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:01:39.623][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-07-06 16:01:39.624][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-07-06 16:01:39.625][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:01:39.626][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:01:39.630][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-06 16:01:39.631][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-06 16:01:39.632][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:01:39.633][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:01:39.633][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-06 16:01:39.634][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-06 16:01:39.635][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:01:39.636][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:01:39.637][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-06 16:01:39.641][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-06 16:01:39.642][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:01:39.642][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:01:39.645][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-06 16:01:39.645][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-06 16:01:39.646][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:01:39.647][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:01:39.647][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-06 16:01:39.648][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-06 16:01:39.649][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:01:39.649][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:01:39.650][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-06 16:01:39.651][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-06 16:01:39.652][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:01:39.653][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:01:39.653][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-07-06 16:01:39.654][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-07-06 16:01:39.655][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:01:39.656][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:01:39.656][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-07-06 16:01:39.657][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-07-06 16:01:39.658][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:01:39.659][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:01:39.659][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-07-06 16:01:39.660][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-07-06 16:01:39.661][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:01:39.662][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:01:39.675][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-06 16:01:39.676][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-06 16:01:39.677][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:01:39.678][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:01:39.679][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-06 16:01:39.680][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-06 16:01:39.680][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:01:39.681][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:01:39.682][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-06 16:01:39.683][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-06 16:01:39.684][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:01:39.684][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:01:39.685][ef$get] Asked field names are: accession.
biodb.TRACE[2024-07-06 16:01:39.686][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-06 16:01:39.687][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:01:39.687][ef$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:01:39.688][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-06 16:01:39.689][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-06 16:01:39.690][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:01:39.690][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:01:39.698][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-06 16:01:39.699][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-06 16:01:39.699][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:01:39.700][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:01:39.701][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-06 16:01:39.701][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-06 16:01:39.702][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:01:39.703][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:01:39.704][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-06 16:01:39.704][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-06 16:01:39.705][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:01:39.706][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:01:39.706][ef$get] Asked field names are: name.
biodb.TRACE[2024-07-06 16:01:39.707][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-07-06 16:01:39.708][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:01:39.708][ef$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:01:39.709][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-06 16:01:39.710][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-06 16:01:39.711][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:01:39.711][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:01:39.719][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-07-06 16:01:39.720][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-07-06 16:01:39.721][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:01:39.721][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:01:39.722][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-07-06 16:01:39.723][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-07-06 16:01:39.724][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:01:39.724][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:01:39.725][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-07-06 16:01:39.726][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-07-06 16:01:39.727][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:01:39.728][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:01:39.728][ef$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-07-06 16:01:39.729][ef$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-07-06 16:01:39.730][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:01:39.731][ef$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:01:39.732][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-07-06 16:01:39.732][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-07-06 16:01:39.733][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:01:39.734][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:01:39.742][ef$get] Asked field names are: accession.
biodb.TRACE[2024-07-06 16:01:39.743][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-06 16:01:39.744][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:01:39.744][ef$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:01:39.749][ef$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-07-06 16:01:39.750][ef$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-07-06 16:01:39.750][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:01:39.751][ef$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:01:39.755][ef$get] Asked field names are: name.
biodb.TRACE[2024-07-06 16:01:39.756][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-07-06 16:01:39.757][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:01:39.758][ef$get] fields variable is a list.
biodb.INFO [2024-07-06 16:01:39.768][biodb::testThat]
biodb.INFO [2024-07-06 16:01:39.769][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2024-07-06 16:01:39.770][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-07-06 16:01:39.771][biodb::testThat]
biodb.DEBUG[2024-07-06 16:01:39.772][private$loadEntries] Creating entries from ids [2]: "1.1.1.1, 1.1.1.54".
biodb.DEBUG[2024-07-06 16:01:39.778][conn$getEntryContent] Get Expasy ENZYME database. entry content(s) for 2 id(s)...
biodb.TRACE[2024-07-06 16:01:39.782][cch$loadFileContent] Trying to load 2 files from cache: [2]: "1.1.1.1, 1.1.1.54".
biodb.INFO [2024-07-06 16:01:39.783][self$getFolderPath] Create cache folder "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280" for "expasy.enzyme-b59b84d962b6741050ba8f70ff4db280".
biodb.TRACE[2024-07-06 16:01:39.784][cch$loadFileContent] file.exist = [2]: "FALSE, FALSE".
biodb.TRACE[2024-07-06 16:01:39.785][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-07-06 16:01:39.786][conn$getEntryContent] 0 Expasy ENZYME database. entry content(s) loaded from cache.
biodb.DEBUG[2024-07-06 16:01:39.786][conn$getEntryContent] 2 entry content(s) need to be fetched from Expasy ENZYME database. database "https://enzyme.expasy.org/".
biodb.DEBUG[2024-07-06 16:01:39.787][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-07-06 16:01:39.788][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-07-06 16:01:39.792][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-06 16:01:39.792][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-06 16:01:39.793][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-06 16:01:39.797][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-06 16:01:39.798][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-06 16:01:39.799][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:01:39.800][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:01:39.800][scheduler$sendRequest] Getting content of get URL request "https://enzyme.expasy.org/EC/1.1.1.1.txt".
biodb.DEBUG[2024-07-06 16:01:39.816][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-06 16:01:39.817][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-07-06 16:01:39.818][private$doSendRequestOnce] Sent URL is "https://enzyme.expasy.org/EC/1.1.1.1.txt".
biodb.TRACE[2024-07-06 16:01:46.845][getRCurlRequestResult] Using RCurl package for sending request (https://enzyme.expasy.org/EC/1.1.1.1.txt).
biodb.DEBUG[2024-07-06 16:01:47.210][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-07-06 16:01:47.212][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280/a52675cfd2f0c2b41556caa64d9341e3.content"
biodb.TRACE[2024-07-06 16:01:47.222][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280/a52675cfd2f0c2b41556caa64d9341e3.request"
biodb.DEBUG[2024-07-06 16:01:47.224][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-06 16:01:47.225][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-06 16:01:47.225][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-06 16:01:47.230][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-06 16:01:47.230][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-06 16:01:47.231][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:01:47.232][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:01:47.246][scheduler$sendRequest] Getting content of get URL request "https://enzyme.expasy.org/EC/1.1.1.54.txt".
biodb.DEBUG[2024-07-06 16:01:47.257][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-06 16:01:47.258][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-07-06 16:01:47.275][private$doSendRequestOnce] Sent URL is "https://enzyme.expasy.org/EC/1.1.1.54.txt".
biodb.TRACE[2024-07-06 16:01:47.633][getRCurlRequestResult] Using RCurl package for sending request (https://enzyme.expasy.org/EC/1.1.1.54.txt).
biodb.DEBUG[2024-07-06 16:01:48.154][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-07-06 16:01:48.156][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280/a9b93566a091cbe35a06e4b3871f95c9.content"
biodb.TRACE[2024-07-06 16:01:48.158][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280/a9b93566a091cbe35a06e4b3871f95c9.request"
biodb.TRACE[2024-07-06 16:01:48.160][private$doSaveContentToFile] Saving to cache [2]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280/1.1.1.1.txt, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280/1.1.1.54.txt"
biodb.DEBUG[2024-07-06 16:01:48.162][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-07-06 16:01:48.163][self$createEntryFromContent] Creating Expasy ENZYME database. entries from 2 content(s).
biodb.DEBUG[2024-07-06 16:01:48.164][self$createEntryFromContent] Parsing 2 Expasy ENZYME database. entries.
biodb.DEBUG[2024-07-06 16:01:48.165][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-06 16:01:48.166][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-06 16:01:48.166][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-06 16:01:48.171][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-06 16:01:48.171][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-06 16:01:48.172][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:01:48.173][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-06 16:01:48.175][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-06 16:01:48.176][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-06 16:01:48.177][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:01:48.177][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:01:48.178][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-07-06 16:01:48.179][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-07-06 16:01:48.180][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:01:48.181][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:01:48.182][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-06 16:01:48.183][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-06 16:01:48.183][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:01:48.184][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:01:48.185][self$getBiodb()$getEntryFields()$get] Asked field names are: COFACTOR.
biodb.TRACE[2024-07-06 16:01:48.186][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-07-06 16:01:48.187][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:01:48.188][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:01:48.189][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-06 16:01:48.189][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-06 16:01:48.190][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:01:48.191][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:01:48.192][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-06 16:01:48.193][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-06 16:01:48.194][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:01:48.194][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:01:48.195][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-06 16:01:48.196][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-06 16:01:48.197][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:01:48.198][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:01:48.198][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-06 16:01:48.199][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-06 16:01:48.200][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:01:48.201][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:01:48.201][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-06 16:01:48.202][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-06 16:01:48.203][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:01:48.204][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:01:48.205][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-07-06 16:01:48.205][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-07-06 16:01:48.206][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:01:48.207][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:01:48.208][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-07-06 16:01:48.209][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-07-06 16:01:48.209][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:01:48.210][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:01:48.211][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-06 16:01:48.212][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-06 16:01:48.213][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:01:48.214][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:01:48.214][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-07-06 16:01:48.215][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-07-06 16:01:48.216][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:01:48.217][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:01:48.218][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-06 16:01:48.218][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-06 16:01:48.219][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:01:48.220][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:01:48.221][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-06 16:01:48.221][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-06 16:01:48.222][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:01:48.223][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:01:48.224][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-06 16:01:48.225][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-06 16:01:48.225][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:01:48.226][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-06 16:01:48.227][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-06 16:01:48.228][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-06 16:01:48.228][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-06 16:01:48.233][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-06 16:01:48.234][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-06 16:01:48.234][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:01:48.235][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-06 16:01:48.237][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-06 16:01:48.238][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-06 16:01:48.239][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:01:48.239][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:01:48.244][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-07-06 16:01:48.248][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-07-06 16:01:48.249][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:01:48.249][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:01:48.250][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-06 16:01:48.251][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-06 16:01:48.252][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:01:48.252][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:01:48.253][self$getBiodb()$getEntryFields()$get] Asked field names are: COFACTOR.
biodb.TRACE[2024-07-06 16:01:48.254][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-07-06 16:01:48.255][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:01:48.255][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:01:48.256][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-07-06 16:01:48.257][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-07-06 16:01:48.258][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:01:48.259][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:01:48.259][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-07-06 16:01:48.260][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-07-06 16:01:48.261][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:01:48.262][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:01:48.262][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-06 16:01:48.263][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-06 16:01:48.264][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:01:48.265][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:01:48.265][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-07-06 16:01:48.266][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-07-06 16:01:48.267][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:01:48.268][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:01:48.268][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-06 16:01:48.269][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-06 16:01:48.270][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:01:48.271][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:01:48.272][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-06 16:01:48.272][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-06 16:01:48.273][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:01:48.274][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:01:48.275][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-06 16:01:48.275][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-06 16:01:48.276][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:01:48.277][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:01:48.278][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-06 16:01:48.278][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-06 16:01:48.279][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:01:48.280][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:01:48.280][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-06 16:01:48.281][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-06 16:01:48.282][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:01:48.283][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:01:48.284][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-06 16:01:48.284][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-06 16:01:48.285][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:01:48.286][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:01:48.286][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-06 16:01:48.287][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-06 16:01:48.288][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:01:48.289][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:01:48.289][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-06 16:01:48.290][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-06 16:01:48.291][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:01:48.291][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:01:48.292][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-06 16:01:48.293][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-06 16:01:48.293][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:01:48.294][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-06 16:01:48.295][self$createEntryFromContent] Accession numbers: 1.1.1.1, 1.1.1.54.
biodb.TRACE[2024-07-06 16:01:48.296][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2024-07-06 16:01:48.297][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2024-07-06 16:01:48.297][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:01:48.298][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:01:48.299][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2024-07-06 16:01:48.299][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2024-07-06 16:01:48.300][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:01:48.301][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:01:48.301][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2024-07-06 16:01:48.302][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2024-07-06 16:01:48.303][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:01:48.304][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:01:48.308][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2024-07-06 16:01:48.309][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2024-07-06 16:01:48.310][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:01:48.310][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:01:48.311][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2024-07-06 16:01:48.312][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2024-07-06 16:01:48.313][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:01:48.313][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:01:48.314][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2024-07-06 16:01:48.315][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2024-07-06 16:01:48.315][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:01:48.316][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-07-06 16:01:48.323][biodb::testThat]
biodb.INFO [2024-07-06 16:01:48.324][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2024-07-06 16:01:48.325][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-07-06 16:01:48.325][biodb::testThat]
biodb.TRACE[2024-07-06 16:01:48.328][ef$get] Asked field names are: name.
biodb.TRACE[2024-07-06 16:01:48.328][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-07-06 16:01:48.329][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:01:48.330][ef$get] fields variable is a list.
biodb.DEBUG[2024-07-06 16:01:48.331][function(conn, opt)] Testing searchForEntries() with entry "1.1.1.1" and field "name".
biodb.TRACE[2024-07-06 16:01:48.354][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-06 16:01:48.355][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-06 16:01:48.356][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:01:48.357][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:01:48.358][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-06 16:01:48.358][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-06 16:01:48.359][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:01:48.360][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:01:48.360][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-06 16:01:48.361][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-06 16:01:48.362][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:01:48.363][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-06 16:01:48.366][function(conn, opt)] With value "alcohol dehydrogenase".
biodb.DEBUG[2024-07-06 16:01:48.367][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://enzyme.expasy.org/enzyme-byname.html?alcohol dehydrogenase".
biodb.DEBUG[2024-07-06 16:01:48.369][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-06 16:01:48.370][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-07-06 16:01:48.371][private$doSendRequestOnce] Sent URL is "https://enzyme.expasy.org/enzyme-byname.html?alcohol%20dehydrogenase".
biodb.TRACE[2024-07-06 16:01:48.764][getRCurlRequestResult] Using RCurl package for sending request (https://enzyme.expasy.org/enzyme-byname.html?alcohol%20dehydrogenase).
biodb.DEBUG[2024-07-06 16:01:49.155][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-07-06 16:01:49.156][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280/f603fa2a57aec59588edc37541c6f6d5.content"
biodb.TRACE[2024-07-06 16:01:49.159][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280/f603fa2a57aec59588edc37541c6f6d5.request"
biodb.DEBUG[2024-07-06 16:01:49.164][function(conn, opt)] With found IDs [1]: "1.1.1.1".
biodb.INFO [2024-07-06 16:01:49.178][biodb::testThat]
biodb.INFO [2024-07-06 16:01:49.179][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2024-07-06 16:01:49.180][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-07-06 16:01:49.181][biodb::testThat]
biodb.TRACE[2024-07-06 16:01:49.200][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-06 16:01:49.201][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-06 16:01:49.201][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:01:49.202][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:01:49.203][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-06 16:01:49.204][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-06 16:01:49.204][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:01:49.205][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:01:49.206][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-06 16:01:49.207][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-06 16:01:49.208][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:01:49.208][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-06 16:01:49.235][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://enzyme.expasy.org/enzyme-byname.html?alcohol dehydrogenase".
biodb.DEBUG[2024-07-06 16:01:49.238][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-07-06 16:01:49.249][cch$loadFileContent] Trying to load 1 files from cache: [1]: "f603fa2a57aec59588edc37541c6f6d5".
biodb.TRACE[2024-07-06 16:01:49.250][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-07-06 16:01:49.251][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280/f603fa2a57aec59588edc37541c6f6d5.content".
biodb.INFO [2024-07-06 16:01:49.267][biodb::testThat]
biodb.INFO [2024-07-06 16:01:49.268][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2024-07-06 16:01:49.269][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-07-06 16:01:49.269][biodb::testThat]
biodb.TRACE[2024-07-06 16:01:49.278][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-07-06 16:01:49.279][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-07-06 16:01:49.279][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:01:49.280][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:01:49.281][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-07-06 16:01:49.282][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-07-06 16:01:49.282][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:01:49.283][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:01:49.284][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-07-06 16:01:49.285][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-07-06 16:01:49.285][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:01:49.287][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:01:49.287][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-07-06 16:01:49.288][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-07-06 16:01:49.289][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:01:49.290][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:01:49.318][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-07-06 16:01:49.319][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-07-06 16:01:49.320][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:01:49.321][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:01:49.321][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-07-06 16:01:49.322][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-07-06 16:01:49.323][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:01:49.323][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:01:49.324][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-07-06 16:01:49.325][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-07-06 16:01:49.326][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:01:49.326][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:01:49.327][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-07-06 16:01:49.328][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-07-06 16:01:49.329][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:01:49.330][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-07-06 16:01:49.335][biodb::testThat]
biodb.INFO [2024-07-06 16:01:49.336][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2024-07-06 16:01:49.337][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-07-06 16:01:49.337][biodb::testThat]
biodb.INFO [2024-07-06 16:01:49.345][biodb::testThat]
biodb.INFO [2024-07-06 16:01:49.346][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2024-07-06 16:01:49.347][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-07-06 16:01:49.348][biodb::testThat]
biodb.INFO [2024-07-06 16:01:49.355][biodb::testThat]
biodb.INFO [2024-07-06 16:01:49.356][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2024-07-06 16:01:49.356][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-07-06 16:01:49.357][biodb::testThat]
biodb.DEBUG[2024-07-06 16:01:49.368][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[2024-07-06 16:01:49.908][getUrlContent] Use RCurl for downloading content of URL https://enzyme.expasy.org/cgi-bin/enzyme/enzyme-search-ec?field1=1&field2=1&field3=1&field4=1.
biodb.INFO [2024-07-06 16:01:50.301][biodb::testThat]
biodb.INFO [2024-07-06 16:01:50.302][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2024-07-06 16:01:50.302][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-07-06 16:01:50.303][biodb::testThat]
biodb.DEBUG[2024-07-06 16:01:50.684][getUrlContent] Use base::url() for downloading content of URL https://enzyme.expasy.org/images/1.1.1.1/image.png.
biodb.TRACE[2024-07-06 16:01:51.078][ef$get] Asked field names are: name.
biodb.TRACE[2024-07-06 16:01:51.079][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-07-06 16:01:51.080][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:01:51.080][ef$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:01:51.081][ef$get] Asked field names are: name.
biodb.TRACE[2024-07-06 16:01:51.082][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-07-06 16:01:51.083][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:01:51.083][ef$get] fields variable is a list.
biodb.INFO [2024-07-06 16:01:51.084][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-07-06 16:01:51.085][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector expasy.enzyme from the request scheduler
biodb.INFO [2024-07-06 16:01:51.086][self$deleteConn] Connector "expasy.enzyme" deleted.
biodb.DEBUG[2024-07-06 16:01:51.087][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-07-06 16:01:51.087][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-06 16:01:51.088][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-06 16:01:51.089][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-06 16:01:51.089][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-06 16:01:51.090][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:01:51.091][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2024-07-06 16:01:51.098][biodb::testContext]
biodb.INFO [2024-07-06 16:01:51.099][biodb::testContext] ********************************************************************************
biodb.INFO [2024-07-06 16:01:51.100][biodb::testContext] Test context - Example long tests
biodb.INFO [2024-07-06 16:01:51.100][biodb::testContext] ********************************************************************************
biodb.INFO [2024-07-06 16:01:51.101][biodb::testContext]
biodb.INFO [2024-07-06 16:01:51.103][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.13.0.
biodb.DEBUG[2024-07-06 16:01:51.104][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2024-07-06 16:01:51.107][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-07-06 16:01:51.108][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-07-06 16:01:51.109][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-07-06 16:01:51.109][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:01:51.110][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:01:51.111][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:01:51.111][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-07-06 16:01:51.112][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-07-06 16:01:51.113][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:01:51.113][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:01:51.114][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:01:51.115][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-07-06 16:01:51.116][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-07-06 16:01:51.116][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:01:51.117][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:01:51.118][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:01:51.118][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-07-06 16:01:51.119][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-07-06 16:01:51.120][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-07-06 16:01:51.121][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:01:51.121][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:01:51.122][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:01:51.123][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-07-06 16:01:51.123][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-07-06 16:01:51.124][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-07-06 16:01:51.125][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:01:51.126][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:01:51.126][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:01:51.127][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-07-06 16:01:51.128][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-07-06 16:01:51.128][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:01:51.129][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:01:51.130][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:01:51.131][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-07-06 16:01:51.131][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-07-06 16:01:51.132][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-07-06 16:01:51.133][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:01:51.133][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:01:51.134][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:01:51.135][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-07-06 16:01:51.135][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-07-06 16:01:51.136][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:01:51.137][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:01:51.138][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:01:51.138][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-07-06 16:01:51.139][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-07-06 16:01:51.140][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-07-06 16:01:51.140][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:01:51.141][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:01:51.142][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:01:51.142][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-07-06 16:01:51.143][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-07-06 16:01:51.144][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-07-06 16:01:51.145][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-07-06 16:01:51.145][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-07-06 16:01:51.146][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-07-06 16:01:51.147][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:01:51.147][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:01:51.148][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:01:51.149][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-07-06 16:01:51.150][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-07-06 16:01:51.150][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:01:51.151][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:01:51.152][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[2024-07-06 16:01:51.152][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-07-06 16:01:51.153][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-07-06 16:01:51.154][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:01:51.154][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:01:51.155][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:01:51.156][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-07-06 16:01:51.157][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-07-06 16:01:51.161][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:01:51.162][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:01:51.163][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:01:51.163][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-07-06 16:01:51.164][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-07-06 16:01:51.165][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:01:51.165][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:01:51.166][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:01:51.167][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-07-06 16:01:51.167][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-07-06 16:01:51.168][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:01:51.169][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:01:51.169][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:01:51.170][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-07-06 16:01:51.171][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-07-06 16:01:51.187][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-07-06 16:01:51.188][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:01:51.189][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:01:51.190][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:01:51.190][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-07-06 16:01:51.191][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-07-06 16:01:51.192][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-07-06 16:01:51.193][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:01:51.193][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:01:51.194][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:01:51.195][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-07-06 16:01:51.196][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-07-06 16:01:51.197][self$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[2024-07-06 16:01:51.198][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-07-06 16:01:51.199][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-07-06 16:01:51.199][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-07-06 16:01:51.200][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-07-06 16:01:51.201][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-07-06 16:01:51.202][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-07-06 16:01:51.203][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-07-06 16:01:51.203][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-07-06 16:01:51.204][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-07-06 16:01:51.205][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-07-06 16:01:51.206][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-07-06 16:01:51.206][self$setPropertyValue]
biodb.DEBUG[2024-07-06 16:01:51.207][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-07-06 16:01:51.208][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-07-06 16:01:51.208][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-07-06 16:01:51.208][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-07-06 16:01:51.208][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-07-06 16:01:51.208][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-07-06 16:01:51.209][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-07-06 16:01:51.210][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-06 16:01:51.210][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-06 16:01:51.211][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-07-06 16:01:51.212][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-06 16:01:51.212][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-06 16:01:51.213][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-07-06 16:01:51.214][self$setPropertyValue]
biodb.DEBUG[2024-07-06 16:01:51.215][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-07-06 16:01:51.215][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-07-06 16:01:51.216][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-07-06 16:01:51.217][self$setPropertyValue]
biodb.DEBUG[2024-07-06 16:01:51.218][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-07-06 16:01:51.219][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-07-06 16:01:51.220][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-07-06 16:01:51.221][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-07-06 16:01:51.222][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-07-06 16:01:51.222][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-07-06 16:01:51.223][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-07-06 16:01:51.224][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-07-06 16:01:51.225][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-07-06 16:01:51.226][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-07-06 16:01:51.226][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-07-06 16:01:51.227][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-07-06 16:01:51.228][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-07-06 16:01:51.229][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-07-06 16:01:51.230][self$setPropertyValue]
biodb.DEBUG[2024-07-06 16:01:51.230][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-07-06 16:01:51.231][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-07-06 16:01:51.231][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-07-06 16:01:51.231][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-07-06 16:01:51.231][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-07-06 16:01:51.231][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-07-06 16:01:51.232][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-07-06 16:01:51.233][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-06 16:01:51.234][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-06 16:01:51.234][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-07-06 16:01:51.235][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-06 16:01:51.236][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-06 16:01:51.236][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-07-06 16:01:51.237][self$setPropertyValue]
biodb.DEBUG[2024-07-06 16:01:51.238][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-07-06 16:01:51.239][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-07-06 16:01:51.239][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-07-06 16:01:51.240][self$setPropertyValue]
biodb.DEBUG[2024-07-06 16:01:51.241][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-07-06 16:01:51.243][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-07-06 16:01:51.243][self$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[2024-07-06 16:01:51.244][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-07-06 16:01:51.245][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-07-06 16:01:51.246][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-07-06 16:01:51.246][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-07-06 16:01:51.247][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-07-06 16:01:51.248][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-07-06 16:01:51.249][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-07-06 16:01:51.249][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-07-06 16:01:51.250][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-07-06 16:01:51.251][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-07-06 16:01:51.252][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-07-06 16:01:51.252][self$setPropertyValue]
biodb.DEBUG[2024-07-06 16:01:51.253][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-07-06 16:01:51.254][self$setPropertyValue]
biodb.DEBUG[2024-07-06 16:01:51.255][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-07-06 16:01:51.256][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-06 16:01:51.256][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-06 16:01:51.257][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-07-06 16:01:51.258][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-06 16:01:51.259][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-06 16:01:51.259][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-07-06 16:01:51.260][self$setPropertyValue]
biodb.DEBUG[2024-07-06 16:01:51.265][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-07-06 16:01:51.265][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-07-06 16:01:51.266][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-07-06 16:01:51.267][self$setPropertyValue]
biodb.DEBUG[2024-07-06 16:01:51.268][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-07-06 16:01:51.269][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-07-06 16:01:51.270][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-07-06 16:01:51.270][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-07-06 16:01:51.271][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-07-06 16:01:51.272][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-07-06 16:01:51.272][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-07-06 16:01:51.273][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-07-06 16:01:51.274][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-07-06 16:01:51.275][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-07-06 16:01:51.275][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-07-06 16:01:51.276][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-07-06 16:01:51.277][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-07-06 16:01:51.278][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-07-06 16:01:51.278][self$setPropertyValue]
biodb.DEBUG[2024-07-06 16:01:51.279][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-07-06 16:01:51.280][self$setPropertyValue]
biodb.DEBUG[2024-07-06 16:01:51.280][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-07-06 16:01:51.281][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-06 16:01:51.282][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-06 16:01:51.282][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-07-06 16:01:51.283][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-06 16:01:51.284][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-06 16:01:51.285][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-07-06 16:01:51.285][self$setPropertyValue]
biodb.DEBUG[2024-07-06 16:01:51.286][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-07-06 16:01:51.287][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-07-06 16:01:51.287][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-07-06 16:01:51.288][self$setPropertyValue]
biodb.DEBUG[2024-07-06 16:01:51.289][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-07-06 16:01:51.290][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:01:51.291][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:01:51.291][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:01:51.292][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-06 16:01:51.293][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-06 16:01:51.293][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:01:51.294][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:01:51.295][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:01:51.295][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-06 16:01:51.296][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-06 16:01:51.297][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:01:51.298][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:01:51.298][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:01:51.299][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-06 16:01:51.300][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-06 16:01:51.300][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:01:51.301][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:01:51.302][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:01:51.303][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-06 16:01:51.303][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-06 16:01:51.304][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:01:51.304][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:01:51.305][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:01:51.306][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-06 16:01:51.306][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-06 16:01:51.307][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:01:51.308][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:01:51.308][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:01:51.309][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-06 16:01:51.310][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-06 16:01:51.310][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:01:51.311][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:01:51.312][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:01:51.312][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-06 16:01:51.313][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-06 16:01:51.314][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:01:51.315][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:01:51.315][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:01:51.316][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-06 16:01:51.317][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-06 16:01:51.317][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:01:51.318][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:01:51.319][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:01:51.319][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-06 16:01:51.320][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-06 16:01:51.321][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:01:51.321][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:01:51.322][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:01:51.323][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-06 16:01:51.323][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-06 16:01:51.324][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:01:51.325][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:01:51.325][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:01:51.326][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-06 16:01:51.327][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-06 16:01:51.327][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:01:51.328][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:01:51.328][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:01:51.329][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-06 16:01:51.330][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-06 16:01:51.330][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:01:51.331][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:01:51.332][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:01:51.332][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-06 16:01:51.333][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-06 16:01:51.334][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:01:51.334][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:01:51.335][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:01:51.336][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-06 16:01:51.336][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-06 16:01:51.337][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:01:51.338][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:01:51.338][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:01:51.339][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-06 16:01:51.340][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-06 16:01:51.340][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:01:51.341][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:01:51.342][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:01:51.342][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-06 16:01:51.343][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-06 16:01:51.348][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:01:51.348][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:01:51.349][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:01:51.350][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-06 16:01:51.350][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-06 16:01:51.351][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:01:51.352][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:01:51.352][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-07-06 16:01:51.353][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-07-06 16:01:51.354][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-07-06 16:01:51.355][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-07-06 16:01:51.356][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-07-06 16:01:51.357][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-07-06 16:01:51.358][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-07-06 16:01:51.359][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-07-06 16:01:51.360][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-07-06 16:01:51.361][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-07-06 16:01:51.362][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-07-06 16:01:51.363][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-07-06 16:01:51.364][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-07-06 16:01:51.365][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-07-06 16:01:51.366][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-07-06 16:01:51.368][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-07-06 16:01:51.369][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-07-06 16:01:51.370][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-07-06 16:01:51.371][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-07-06 16:01:51.372][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-07-06 16:01:51.373][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-07-06 16:01:51.374][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-07-06 16:01:51.375][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-07-06 16:01:51.376][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-07-06 16:01:51.377][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-07-06 16:01:51.378][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-07-06 16:01:51.379][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-07-06 16:01:51.380][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-07-06 16:01:51.381][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-07-06 16:01:51.382][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-07-06 16:01:51.383][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-07-06 16:01:51.384][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-07-06 16:01:51.385][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-07-06 16:01:51.386][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-07-06 16:01:51.387][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-07-06 16:01:51.388][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-07-06 16:01:51.389][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-07-06 16:01:51.390][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-07-06 16:01:51.391][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-07-06 16:01:51.392][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-07-06 16:01:51.393][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-07-06 16:01:51.395][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-07-06 16:01:51.396][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-07-06 16:01:51.397][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-07-06 16:01:51.398][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-07-06 16:01:51.399][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-07-06 16:01:51.400][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-07-06 16:01:51.401][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-07-06 16:01:51.402][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-07-06 16:01:51.403][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-07-06 16:01:51.404][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-07-06 16:01:51.405][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-07-06 16:01:51.406][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-07-06 16:01:51.407][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-07-06 16:01:51.408][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-07-06 16:01:51.410][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-07-06 16:01:51.411][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-07-06 16:01:51.412][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-07-06 16:01:51.413][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-07-06 16:01:51.414][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-07-06 16:01:51.415][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-07-06 16:01:51.416][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-07-06 16:01:51.417][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-07-06 16:01:51.419][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-07-06 16:01:51.420][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-07-06 16:01:51.421][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-07-06 16:01:51.422][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-07-06 16:01:51.423][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-07-06 16:01:51.424][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-07-06 16:01:51.425][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-07-06 16:01:51.430][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-07-06 16:01:51.431][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-07-06 16:01:51.432][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-07-06 16:01:51.433][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-07-06 16:01:51.434][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-07-06 16:01:51.435][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-07-06 16:01:51.436][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-07-06 16:01:51.437][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-07-06 16:01:51.438][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-07-06 16:01:51.439][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-07-06 16:01:51.440][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-07-06 16:01:51.441][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-07-06 16:01:51.442][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-07-06 16:01:51.443][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-07-06 16:01:51.445][initialize] This is biodb version 1.13.0.
biodb.DEBUG[2024-07-06 16:01:51.445][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-07-06 16:01:51.446][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-07-06 16:01:51.447][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-06 16:01:51.447][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:01:51.448][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:01:51.449][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:01:51.449][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-06 16:01:51.450][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-06 16:01:51.451][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-06 16:01:51.451][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-06 16:01:51.452][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:01:51.453][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:01:51.454][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:01:51.454][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-06 16:01:51.455][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-06 16:01:51.456][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-06 16:01:51.456][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-06 16:01:51.457][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:01:51.458][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:01:51.459][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:01:51.459][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-06 16:01:51.460][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-06 16:01:51.460][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-06 16:01:51.461][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-06 16:01:51.462][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:01:51.462][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:01:51.463][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:01:51.464][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-06 16:01:51.465][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-06 16:01:51.465][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-06 16:01:51.466][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-06 16:01:51.467][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:01:51.467][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:01:51.468][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:01:51.469][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-06 16:01:51.469][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-06 16:01:51.470][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-06 16:01:51.471][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-06 16:01:51.472][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:01:51.472][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:01:51.473][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:01:51.474][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-06 16:01:51.474][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-06 16:01:51.475][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-06 16:01:51.476][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-06 16:01:51.476][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:01:51.477][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:01:51.478][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:01:51.478][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-06 16:01:51.479][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-06 16:01:51.480][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-06 16:01:51.481][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-06 16:01:51.481][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:01:51.482][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[2024-07-06 16:01:51.483][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:01:51.483][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-06 16:01:51.484][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-06 16:01:51.485][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-06 16:01:51.485][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-06 16:01:51.486][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:01:51.487][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[2024-07-06 16:01:51.488][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:01:51.488][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-06 16:01:51.489][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-06 16:01:51.490][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-06 16:01:51.490][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-06 16:01:51.491][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:01:51.492][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:01:51.493][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:01:51.493][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-06 16:01:51.494][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-06 16:01:51.495][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-06 16:01:51.495][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-06 16:01:51.496][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:01:51.497][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:01:51.497][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:01:51.498][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-06 16:01:51.499][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-06 16:01:51.499][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-06 16:01:51.500][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-06 16:01:51.501][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:01:51.502][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:01:51.502][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:01:51.503][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-06 16:01:51.504][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-06 16:01:51.504][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-06 16:01:51.505][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-06 16:01:51.506][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:01:51.506][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[2024-07-06 16:01:51.507][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:01:51.508][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-06 16:01:51.508][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-06 16:01:51.509][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-06 16:01:51.510][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-06 16:01:51.514][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:01:51.515][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:01:51.516][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:01:51.516][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-06 16:01:51.517][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-06 16:01:51.517][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-06 16:01:51.518][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-06 16:01:51.519][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:01:51.519][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:01:51.520][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:01:51.521][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-06 16:01:51.521][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-06 16:01:51.522][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-06 16:01:51.522][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-06 16:01:51.523][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:01:51.524][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:01:51.524][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:01:51.525][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-06 16:01:51.526][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-06 16:01:51.526][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-06 16:01:51.527][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-06 16:01:51.528][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:01:51.528][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:01:51.529][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:01:51.530][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-06 16:01:51.530][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-06 16:01:51.531][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-06 16:01:51.532][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-06 16:01:51.532][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:01:51.533][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:01:51.535][biodb$loadDefinitions] Load definitions from file "/Users/biocbuild/bbs-3.20-bioc-longtests/meat/biodbExpasy.Rcheck/biodbExpasy/definitions.yml".
biodb.DEBUG[2024-07-06 16:01:51.536][self$getDbsInfo()$define] Define connector expasy.enzyme.
biodb.DEBUG[2024-07-06 16:01:51.537][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-07-06 16:01:51.538][self$setPropertyValue] Setting property "description" to "Write here the description of this database.".
biodb.DEBUG[2024-07-06 16:01:51.539][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-07-06 16:01:51.540][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-07-06 16:01:51.540][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-07-06 16:01:51.541][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-07-06 16:01:51.542][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-07-06 16:01:51.543][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-07-06 16:01:51.544][self$setPropertyValue] Setting property "entry.content.type" to "txt".
biodb.DEBUG[2024-07-06 16:01:51.544][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-07-06 16:01:51.545][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-07-06 16:01:51.546][self$setPropertyValue] Setting property "name" to "Expasy ENZYME database.".
biodb.DEBUG[2024-07-06 16:01:51.547][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-07-06 16:01:51.547][self$setPropertyValue] Setting property "parsing.expr" to "^ID\s+([0-9.]+)$".
biodb.DEBUG[2024-07-06 16:01:51.547][self$setPropertyValue] Setting property "parsing.expr" to "^CA\s+(.+?)\.?$".
biodb.DEBUG[2024-07-06 16:01:51.547][self$setPropertyValue] Setting property "parsing.expr" to "^CF\s+(.+?)\.?$".
biodb.DEBUG[2024-07-06 16:01:51.547][self$setPropertyValue] Setting property "parsing.expr" to "^DE\s+(.+?)\.?$".
biodb.DEBUG[2024-07-06 16:01:51.548][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-07-06 16:01:51.549][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-07-06 16:01:51.550][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2024-07-06 16:01:51.551][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-06 16:01:51.551][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-06 16:01:51.552][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-07-06 16:01:51.553][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-06 16:01:51.554][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-06 16:01:51.555][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-07-06 16:01:51.555][self$setPropertyValue] Setting property "urls" to "https://enzyme.expasy.org/".
biodb.DEBUG[2024-07-06 16:01:51.556][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-07-06 16:01:51.557][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-07-06 16:01:51.557][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-07-06 16:01:51.558][self$setPropertyValue]
biodb.DEBUG[2024-07-06 16:01:51.559][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-07-06 16:01:51.561][super$initialize] Initialize connector expasy.enzyme.
biodb.DEBUG[2024-07-06 16:01:51.562][super$initialize] Register connector expasy.enzyme with the request scheduler
biodb.DEBUG[2024-07-06 16:01:51.563][private$bdb$getRequestScheduler()$re ...] Register connector expasy.enzyme.
biodb.DEBUG[2024-07-06 16:01:51.564][private$addConnectorRules] Create new rule for URL "enzyme.expasy.org" of connector "expasy.enzyme".
biodb.DEBUG[2024-07-06 16:01:51.565][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-07-06 16:01:51.566][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-07-06 16:01:51.567][biodb$getFactory()$createConn] Creating new connector expasy.enzyme for database class expasy.enzyme .
biodb.INFO [2024-07-06 16:01:51.567][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-07-06 16:01:51.568][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector expasy.enzyme from the request scheduler
biodb.INFO [2024-07-06 16:01:51.569][self$deleteConn] Connector "expasy.enzyme" deleted.
biodb.DEBUG[2024-07-06 16:01:51.570][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-07-06 16:01:51.570][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-06 16:01:51.571][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-06 16:01:51.572][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-06 16:01:51.572][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-06 16:01:51.573][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:01:51.574][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
[ FAIL 1 | WARN 0 | SKIP 0 | PASS 85 ]

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

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

'R CMD check' output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --test-dir=longtests --no-stop-on-test-error --no-codoc --no-examples --no-manual --ignore-vignettes --check-subdirs=no biodbExpasy_1.9.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.20-bioc-longtests/meat/biodbExpasy.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.1
* 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 ‘1.9.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘biodbExpasy’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Title field: should not end in a period.
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... SKIPPED
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... SKIPPED
* checking examples ... SKIPPED
* checking for unstated dependencies in ‘longtests’ ... OK
* checking tests in ‘longtests’ ...
  Running ‘testthat.R’
 ERROR
Running the tests in ‘longtests/testthat.R’ failed.
Last 13 lines of output:
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test_long_100_generic.R:37:1'): The entry image URL can be downloaded. ──
  Error in `charToRaw(content)`: argument must be a character vector of length 1
  Backtrace:
      ▆
   1. ├─base::do.call(fct, params)
   2. └─biodb (local) `<fn>`(conn = `<ExpsyEnC>`, opt = `<named list>`)
   3.   └─biodb:::getUrlContent(url, binary = TRUE)
   4.     └─biodb:::getBaseUrlContent(u, binary = binary)
   5.       └─base::charToRaw(content)
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 85 ]
  Error: Test failures
  Execution halted
* DONE

Status: 1 ERROR, 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.20-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)