Back to Long Tests report for BioC 3.16

This page was generated on 2023-04-15 21:30:03 -0400 (Sat, 15 Apr 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.5 LTS)x86_644.2.3 (2023-03-15) -- "Shortstop Beagle" 4502
palomino4Windows Server 2022 Datacenterx644.2.3 (2023-03-15 ucrt) -- "Shortstop Beagle" 4282
lconwaymacOS 12.5.1 Montereyx86_644.2.3 (2023-03-15) -- "Shortstop Beagle" 4310
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

CHECK results for biodbExpasy on lconway


To the developers/maintainers of the biodbExpasy package:
Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 6/28HostnameOS / ArchCHECK
biodbExpasy 1.2.0  (landing page)
Pierrick Roger
Snapshot Date: 2023-04-15 06:55:01 -0400 (Sat, 15 Apr 2023)
git_url: https://git.bioconductor.org/packages/biodbExpasy
git_branch: RELEASE_3_16
git_last_commit: ef6c7ee
git_last_commit_date: 2022-11-01 11:26:41 -0400 (Tue, 01 Nov 2022)
nebbiolo2Linux (Ubuntu 20.04.5 LTS) / x86_64  OK  
palomino4Windows Server 2022 Datacenter / x64  OK  
lconwaymacOS 12.5.1 Monterey / x86_64  OK  

Summary

Package: biodbExpasy
Version: 1.2.0
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_1.2.0.tar.gz
StartedAt: 2023-04-15 08:01:34 -0400 (Sat, 15 Apr 2023)
EndedAt: 2023-04-15 08:02:28 -0400 (Sat, 15 Apr 2023)
EllapsedTime: 53.9 seconds
RetCode: 0
Status:   OK  
CheckDir: biodbExpasy.Rcheck
Warnings: 0

Tests output

biodbExpasy.Rcheck/tests/testthat.Rout


R version 4.2.3 (2023-03-15) -- "Shortstop Beagle"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (64-bit)

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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 [2023-04-15 08:02:12.665][biodb::testContext]
biodb.INFO [2023-04-15 08:02:12.689][biodb::testContext] ********************************************************************************
biodb.INFO [2023-04-15 08:02:12.691][biodb::testContext] Test context - Generic long tests
biodb.INFO [2023-04-15 08:02:12.691][biodb::testContext] ********************************************************************************
biodb.INFO [2023-04-15 08:02:12.692][biodb::testContext]
biodb.INFO [2023-04-15 08:02:12.699][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.6.1.
biodb.DEBUG[2023-04-15 08:02:12.700][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.2/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2023-04-15 08:02:12.707][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-04-15 08:02:12.708][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2023-04-15 08:02:12.710][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2023-04-15 08:02:12.710][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:02:12.711][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:02:12.712][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:02:12.713][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2023-04-15 08:02:12.729][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2023-04-15 08:02:12.730][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:02:12.731][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:02:12.731][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:02:12.732][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2023-04-15 08:02:12.733][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2023-04-15 08:02:12.734][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:02:12.735][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:02:12.736][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:02:12.736][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2023-04-15 08:02:12.737][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2023-04-15 08:02:12.738][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2023-04-15 08:02:12.739][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:02:12.740][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:02:12.741][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:02:12.742][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2023-04-15 08:02:12.742][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2023-04-15 08:02:12.743][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2023-04-15 08:02:12.744][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:02:12.745][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:02:12.746][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:02:12.746][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2023-04-15 08:02:12.747][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2023-04-15 08:02:12.748][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:02:12.749][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:02:12.750][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:02:12.750][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2023-04-15 08:02:12.751][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2023-04-15 08:02:12.752][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2023-04-15 08:02:12.753][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:02:12.754][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:02:12.755][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:02:12.756][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2023-04-15 08:02:12.757][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2023-04-15 08:02:12.757][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:02:12.758][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:02:12.759][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:02:12.760][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2023-04-15 08:02:12.760][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2023-04-15 08:02:12.761][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2023-04-15 08:02:12.762][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:02:12.763][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:02:12.764][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:02:12.764][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2023-04-15 08:02:12.765][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2023-04-15 08:02:12.766][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2023-04-15 08:02:12.767][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2023-04-15 08:02:12.768][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2023-04-15 08:02:12.769][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2023-04-15 08:02:12.770][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:02:12.770][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:02:12.771][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[2023-04-15 08:02:12.772][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2023-04-15 08:02:12.773][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2023-04-15 08:02:12.774][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:02:12.774][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:02:12.775][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:02:12.776][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2023-04-15 08:02:12.777][self$set] Set key entries.sep to "|".
biodb.DEBUG[2023-04-15 08:02:12.778][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:02:12.778][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:02:12.779][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:02:12.780][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2023-04-15 08:02:12.781][self$set] Set key offline to FALSE.
biodb.DEBUG[2023-04-15 08:02:12.782][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:02:12.782][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:02:12.783][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:02:12.784][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2023-04-15 08:02:12.785][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2023-04-15 08:02:12.786][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:02:12.787][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:02:12.788][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:02:12.788][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2023-04-15 08:02:12.789][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2023-04-15 08:02:12.790][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:02:12.791][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:02:12.792][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:02:12.793][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2023-04-15 08:02:12.794][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2023-04-15 08:02:12.816][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2023-04-15 08:02:12.817][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:02:12.817][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:02:12.818][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:02:12.819][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2023-04-15 08:02:12.820][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2023-04-15 08:02:12.821][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2023-04-15 08:02:12.822][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:02:12.823][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:02:12.823][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:02:12.827][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2023-04-15 08:02:12.862][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-04-15 08:02:12.873][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2023-04-15 08:02:12.874][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-04-15 08:02:12.875][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-04-15 08:02:12.876][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-04-15 08:02:12.876][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-04-15 08:02:12.877][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-04-15 08:02:12.878][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-04-15 08:02:12.879][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2023-04-15 08:02:12.879][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-04-15 08:02:12.880][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-04-15 08:02:12.881][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2023-04-15 08:02:12.882][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-04-15 08:02:12.883][self$setPropertyValue]
biodb.DEBUG[2023-04-15 08:02:12.884][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-04-15 08:02:12.885][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2023-04-15 08:02:12.885][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2023-04-15 08:02:12.885][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2023-04-15 08:02:12.885][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2023-04-15 08:02:12.885][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2023-04-15 08:02:12.886][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-04-15 08:02:12.887][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-15 08:02:12.888][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-15 08:02:12.889][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-04-15 08:02:12.890][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-15 08:02:12.890][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-15 08:02:12.891][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-04-15 08:02:12.892][self$setPropertyValue]
biodb.DEBUG[2023-04-15 08:02:12.893][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-04-15 08:02:12.893][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-04-15 08:02:12.894][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-04-15 08:02:12.895][self$setPropertyValue]
biodb.DEBUG[2023-04-15 08:02:12.896][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2023-04-15 08:02:12.897][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-04-15 08:02:12.898][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2023-04-15 08:02:12.899][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-04-15 08:02:12.899][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-04-15 08:02:12.900][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-04-15 08:02:12.901][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-04-15 08:02:12.902][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-04-15 08:02:12.903][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-04-15 08:02:12.903][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2023-04-15 08:02:12.904][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-04-15 08:02:12.905][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-04-15 08:02:12.906][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2023-04-15 08:02:12.907][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-04-15 08:02:12.907][self$setPropertyValue]
biodb.DEBUG[2023-04-15 08:02:12.908][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-04-15 08:02:12.909][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2023-04-15 08:02:12.909][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2023-04-15 08:02:12.909][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2023-04-15 08:02:12.909][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2023-04-15 08:02:12.909][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2023-04-15 08:02:12.910][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-04-15 08:02:12.910][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-15 08:02:12.911][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-15 08:02:12.912][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-04-15 08:02:12.913][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-15 08:02:12.913][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-15 08:02:12.914][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-04-15 08:02:12.915][self$setPropertyValue]
biodb.DEBUG[2023-04-15 08:02:12.916][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-04-15 08:02:12.916][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-04-15 08:02:12.917][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-04-15 08:02:12.918][self$setPropertyValue]
biodb.DEBUG[2023-04-15 08:02:12.919][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2023-04-15 08:02:12.920][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2023-04-15 08:02:12.921][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2023-04-15 08:02:12.922][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-04-15 08:02:12.923][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-04-15 08:02:12.923][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-04-15 08:02:12.924][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-04-15 08:02:12.925][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-04-15 08:02:12.926][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-04-15 08:02:12.926][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2023-04-15 08:02:12.927][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-04-15 08:02:12.928][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2023-04-15 08:02:12.929][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2023-04-15 08:02:12.930][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-04-15 08:02:12.930][self$setPropertyValue]
biodb.DEBUG[2023-04-15 08:02:12.931][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-04-15 08:02:12.932][self$setPropertyValue]
biodb.DEBUG[2023-04-15 08:02:12.933][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-04-15 08:02:12.934][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-15 08:02:12.934][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-15 08:02:12.935][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-04-15 08:02:12.936][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-15 08:02:12.937][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-15 08:02:12.937][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-04-15 08:02:12.938][self$setPropertyValue]
biodb.DEBUG[2023-04-15 08:02:12.939][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-04-15 08:02:12.940][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-04-15 08:02:12.940][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-04-15 08:02:12.941][self$setPropertyValue]
biodb.DEBUG[2023-04-15 08:02:12.942][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2023-04-15 08:02:12.943][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2023-04-15 08:02:12.944][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2023-04-15 08:02:12.945][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-04-15 08:02:12.946][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-04-15 08:02:12.947][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-04-15 08:02:12.947][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-04-15 08:02:12.948][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-04-15 08:02:12.949][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-04-15 08:02:12.950][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2023-04-15 08:02:12.950][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-04-15 08:02:12.951][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2023-04-15 08:02:12.952][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2023-04-15 08:02:12.953][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-04-15 08:02:12.953][self$setPropertyValue]
biodb.DEBUG[2023-04-15 08:02:12.954][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-04-15 08:02:12.955][self$setPropertyValue]
biodb.DEBUG[2023-04-15 08:02:12.956][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-04-15 08:02:12.957][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-15 08:02:12.957][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-15 08:02:12.958][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-04-15 08:02:12.959][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-15 08:02:12.960][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-15 08:02:12.960][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-04-15 08:02:12.961][self$setPropertyValue]
biodb.DEBUG[2023-04-15 08:02:12.962][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-04-15 08:02:12.963][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-04-15 08:02:12.963][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-04-15 08:02:12.964][self$setPropertyValue]
biodb.DEBUG[2023-04-15 08:02:12.968][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-04-15 08:02:12.968][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:02:12.969][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:02:12.970][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:02:12.970][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:02:12.971][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-15 08:02:12.972][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:02:12.972][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:02:12.973][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:02:12.974][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:02:12.974][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-15 08:02:12.975][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:02:12.976][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:02:12.977][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:02:12.977][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:02:12.978][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-15 08:02:12.979][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:02:12.979][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:02:12.980][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:02:12.981][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:02:12.981][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-15 08:02:12.982][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:02:12.983][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:02:12.983][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:02:12.984][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:02:12.985][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-15 08:02:12.985][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:02:12.986][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:02:12.987][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:02:12.987][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:02:12.988][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-15 08:02:12.989][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:02:12.989][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:02:12.990][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:02:12.991][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:02:12.991][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-15 08:02:12.992][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:02:12.993][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:02:12.993][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:02:12.994][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:02:12.995][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-15 08:02:12.995][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:02:12.996][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[2023-04-15 08:02:12.997][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:02:12.997][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:02:12.998][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-15 08:02:12.999][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:02:12.999][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:02:13.000][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:02:13.000][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:02:13.001][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-15 08:02:13.002][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:02:13.003][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:02:13.003][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:02:13.004][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:02:13.005][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-15 08:02:13.005][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:02:13.006][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:02:13.007][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:02:13.007][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:02:13.008][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-15 08:02:13.009][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:02:13.009][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:02:13.010][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:02:13.011][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:02:13.011][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-15 08:02:13.012][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:02:13.013][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:02:13.013][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:02:13.014][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:02:13.015][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-15 08:02:13.015][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:02:13.016][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:02:13.017][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:02:13.017][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:02:13.018][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-15 08:02:13.019][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:02:13.020][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:02:13.020][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:02:13.021][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:02:13.022][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-15 08:02:13.022][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:02:13.023][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:02:13.024][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:02:13.025][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:02:13.025][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-15 08:02:13.026][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:02:13.027][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:02:13.027][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2023-04-15 08:02:13.031][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2023-04-15 08:02:13.032][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2023-04-15 08:02:13.033][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2023-04-15 08:02:13.034][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2023-04-15 08:02:13.035][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2023-04-15 08:02:13.036][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2023-04-15 08:02:13.037][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2023-04-15 08:02:13.038][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2023-04-15 08:02:13.039][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2023-04-15 08:02:13.040][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2023-04-15 08:02:13.042][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2023-04-15 08:02:13.043][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2023-04-15 08:02:13.044][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2023-04-15 08:02:13.049][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2023-04-15 08:02:13.050][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2023-04-15 08:02:13.051][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2023-04-15 08:02:13.052][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2023-04-15 08:02:13.053][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2023-04-15 08:02:13.054][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2023-04-15 08:02:13.055][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2023-04-15 08:02:13.056][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2023-04-15 08:02:13.057][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2023-04-15 08:02:13.058][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2023-04-15 08:02:13.059][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2023-04-15 08:02:13.060][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2023-04-15 08:02:13.061][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2023-04-15 08:02:13.062][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2023-04-15 08:02:13.063][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2023-04-15 08:02:13.064][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2023-04-15 08:02:13.065][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2023-04-15 08:02:13.066][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2023-04-15 08:02:13.067][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2023-04-15 08:02:13.068][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2023-04-15 08:02:13.069][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2023-04-15 08:02:13.070][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2023-04-15 08:02:13.071][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2023-04-15 08:02:13.072][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2023-04-15 08:02:13.073][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2023-04-15 08:02:13.074][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2023-04-15 08:02:13.075][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2023-04-15 08:02:13.076][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2023-04-15 08:02:13.077][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2023-04-15 08:02:13.078][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2023-04-15 08:02:13.079][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2023-04-15 08:02:13.080][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2023-04-15 08:02:13.081][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2023-04-15 08:02:13.082][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2023-04-15 08:02:13.083][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2023-04-15 08:02:13.084][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2023-04-15 08:02:13.085][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2023-04-15 08:02:13.086][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2023-04-15 08:02:13.087][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2023-04-15 08:02:13.088][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2023-04-15 08:02:13.089][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2023-04-15 08:02:13.090][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2023-04-15 08:02:13.091][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2023-04-15 08:02:13.092][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2023-04-15 08:02:13.093][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2023-04-15 08:02:13.094][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2023-04-15 08:02:13.095][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2023-04-15 08:02:13.096][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2023-04-15 08:02:13.097][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2023-04-15 08:02:13.098][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2023-04-15 08:02:13.099][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2023-04-15 08:02:13.100][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2023-04-15 08:02:13.101][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2023-04-15 08:02:13.101][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2023-04-15 08:02:13.102][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2023-04-15 08:02:13.103][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2023-04-15 08:02:13.104][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2023-04-15 08:02:13.105][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2023-04-15 08:02:13.106][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2023-04-15 08:02:13.107][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2023-04-15 08:02:13.108][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2023-04-15 08:02:13.109][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2023-04-15 08:02:13.110][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2023-04-15 08:02:13.111][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2023-04-15 08:02:13.112][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2023-04-15 08:02:13.113][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2023-04-15 08:02:13.114][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2023-04-15 08:02:13.115][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2023-04-15 08:02:13.116][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2023-04-15 08:02:13.120][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2023-04-15 08:02:13.121][initialize] This is biodb version 1.6.1.
biodb.DEBUG[2023-04-15 08:02:13.124][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-04-15 08:02:13.124][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:02:13.125][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-15 08:02:13.126][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:02:13.126][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[2023-04-15 08:02:13.130][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:02:13.130][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-15 08:02:13.131][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-15 08:02:13.132][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:02:13.132][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-15 08:02:13.133][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:02:13.134][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[2023-04-15 08:02:13.134][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:02:13.135][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-15 08:02:13.136][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-15 08:02:13.136][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:02:13.137][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-15 08:02:13.138][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:02:13.138][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[2023-04-15 08:02:13.139][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:02:13.140][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-15 08:02:13.140][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-15 08:02:13.141][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:02:13.142][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-15 08:02:13.142][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:02:13.143][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:02:13.144][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:02:13.144][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-15 08:02:13.145][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-15 08:02:13.146][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:02:13.146][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-15 08:02:13.147][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:02:13.148][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[2023-04-15 08:02:13.148][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:02:13.149][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-15 08:02:13.149][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-15 08:02:13.150][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:02:13.151][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-15 08:02:13.151][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:02:13.152][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[2023-04-15 08:02:13.153][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:02:13.153][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-15 08:02:13.154][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-15 08:02:13.155][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:02:13.155][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-15 08:02:13.156][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:02:13.157][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:02:13.157][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:02:13.158][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-15 08:02:13.158][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-15 08:02:13.159][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:02:13.160][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-15 08:02:13.160][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:02:13.161][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:02:13.162][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:02:13.162][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-15 08:02:13.163][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-15 08:02:13.164][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:02:13.164][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-15 08:02:13.165][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:02:13.166][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:02:13.166][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:02:13.167][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-15 08:02:13.167][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-15 08:02:13.168][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:02:13.169][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-15 08:02:13.169][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:02:13.170][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:02:13.171][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:02:13.171][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-15 08:02:13.172][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-15 08:02:13.173][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:02:13.173][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-15 08:02:13.174][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:02:13.175][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:02:13.175][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:02:13.176][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-15 08:02:13.176][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-15 08:02:13.177][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:02:13.178][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-15 08:02:13.178][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:02:13.179][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:02:13.180][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:02:13.180][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-15 08:02:13.181][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-15 08:02:13.182][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:02:13.182][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-15 08:02:13.183][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:02:13.184][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:02:13.184][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:02:13.185][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-15 08:02:13.186][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-15 08:02:13.186][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:02:13.187][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-15 08:02:13.188][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:02:13.188][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:02:13.189][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:02:13.190][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-15 08:02:13.190][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-15 08:02:13.191][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:02:13.192][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-15 08:02:13.192][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:02:13.193][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:02:13.194][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:02:13.194][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-15 08:02:13.195][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-15 08:02:13.196][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:02:13.196][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-15 08:02:13.197][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:02:13.198][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:02:13.198][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:02:13.199][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-15 08:02:13.200][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-15 08:02:13.200][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:02:13.201][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-15 08:02:13.202][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:02:13.202][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:02:13.203][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:02:13.204][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-15 08:02:13.204][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-15 08:02:13.205][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:02:13.205][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-15 08:02:13.206][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:02:13.207][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:02:13.208][biodb$loadDefinitions] Load definitions from file "/Users/biocbuild/bbs-3.16-bioc-longtests/meat/biodbExpasy.Rcheck/biodbExpasy/definitions.yml".
biodb.DEBUG[2023-04-15 08:02:13.215][self$getDbsInfo()$define] Define connector expasy.enzyme.
biodb.DEBUG[2023-04-15 08:02:13.221][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-04-15 08:02:13.222][self$setPropertyValue] Setting property "description" to "Write here the description of this database.".
biodb.DEBUG[2023-04-15 08:02:13.222][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-04-15 08:02:13.223][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-04-15 08:02:13.224][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-04-15 08:02:13.224][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-04-15 08:02:13.225][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2023-04-15 08:02:13.226][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-04-15 08:02:13.226][self$setPropertyValue] Setting property "entry.content.type" to "txt".
biodb.DEBUG[2023-04-15 08:02:13.227][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-04-15 08:02:13.228][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-04-15 08:02:13.229][self$setPropertyValue] Setting property "name" to "Expasy ENZYME database.".
biodb.DEBUG[2023-04-15 08:02:13.229][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-04-15 08:02:13.230][self$setPropertyValue] Setting property "parsing.expr" to "^ID\s+([0-9.]+)$".
biodb.DEBUG[2023-04-15 08:02:13.230][self$setPropertyValue] Setting property "parsing.expr" to "^CA\s+(.+?)\.?$".
biodb.DEBUG[2023-04-15 08:02:13.230][self$setPropertyValue] Setting property "parsing.expr" to "^CF\s+(.+?)\.?$".
biodb.DEBUG[2023-04-15 08:02:13.230][self$setPropertyValue] Setting property "parsing.expr" to "^DE\s+(.+?)\.?$".
biodb.DEBUG[2023-04-15 08:02:13.231][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2023-04-15 08:02:13.231][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2023-04-15 08:02:13.232][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2023-04-15 08:02:13.233][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-15 08:02:13.233][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-15 08:02:13.234][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-04-15 08:02:13.235][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-15 08:02:13.235][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-15 08:02:13.236][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-04-15 08:02:13.237][self$setPropertyValue] Setting property "urls" to "https://enzyme.expasy.org/".
biodb.DEBUG[2023-04-15 08:02:13.238][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-04-15 08:02:13.238][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-04-15 08:02:13.239][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2023-04-15 08:02:13.239][self$setPropertyValue]
biodb.DEBUG[2023-04-15 08:02:13.244][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2023-04-15 08:02:13.262][super$initialize] Initialize connector expasy.enzyme.
biodb.DEBUG[2023-04-15 08:02:13.263][super$initialize] Register connector expasy.enzyme with the request scheduler
biodb.DEBUG[2023-04-15 08:02:13.267][private$bdb$getRequestScheduler()$re ...] Register connector expasy.enzyme.
biodb.DEBUG[2023-04-15 08:02:13.270][private$addConnectorRules] Create new rule for URL "enzyme.expasy.org" of connector "expasy.enzyme".
biodb.DEBUG[2023-04-15 08:02:13.273][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2023-04-15 08:02:13.274][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2023-04-15 08:02:13.274][biodb$getFactory()$createConn] Creating new connector expasy.enzyme for database class expasy.enzyme .
biodb.INFO [2023-04-15 08:02:13.281][biodb::testThat]
biodb.INFO [2023-04-15 08:02:13.282][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2023-04-15 08:02:13.282][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-04-15 08:02:13.283][biodb::testThat]
biodb.TRACE[2023-04-15 08:02:13.286][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/bbs-3.16-bioc-longtests/meat/biodbExpasy.Rcheck/biodbExpasy/testref/entry-expasy.enzyme-1.1.1.1-content.txt".
biodb.DEBUG[2023-04-15 08:02:13.287][biodb$getFactory()$createEntryFromCo ...] Creating Expasy ENZYME database. entries from 1 content(s).
biodb.DEBUG[2023-04-15 08:02:13.290][biodb$getFactory()$createEntryFromCo ...] Parsing 1 Expasy ENZYME database. entries.
biodb.DEBUG[2023-04-15 08:02:13.297][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-15 08:02:13.298][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-15 08:02:13.299][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-15 08:02:13.309][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:02:13.310][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-15 08:02:13.311][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:02:13.312][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-15 08:02:13.320][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-15 08:02:13.321][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-15 08:02:13.322][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:13.323][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:13.341][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2023-04-15 08:02:13.350][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2023-04-15 08:02:13.351][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:13.352][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:13.353][self$getBiodb()$getEntryFields()$get] Asked field names are: cofactor.
biodb.TRACE[2023-04-15 08:02:13.353][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2023-04-15 08:02:13.354][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:13.355][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:13.356][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-15 08:02:13.357][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-15 08:02:13.357][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:13.358][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:13.359][self$getBiodb()$getEntryFields()$get] Asked field names are: COFACTOR.
biodb.TRACE[2023-04-15 08:02:13.360][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2023-04-15 08:02:13.360][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:13.361][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:13.362][self$getBiodb()$getEntryFields()$get] Asked field names are: cofactor.
biodb.TRACE[2023-04-15 08:02:13.363][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2023-04-15 08:02:13.363][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:13.364][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:13.365][self$getBiodb()$getEntryFields()$get] Asked field names are: cofactor.
biodb.TRACE[2023-04-15 08:02:13.366][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2023-04-15 08:02:13.366][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:13.367][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:13.368][self$getBiodb()$getEntryFields()$get] Asked field names are: cofactor.
biodb.TRACE[2023-04-15 08:02:13.369][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2023-04-15 08:02:13.369][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:13.370][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:13.371][self$getBiodb()$getEntryFields()$get] Asked field names are: COFACTOR.
biodb.TRACE[2023-04-15 08:02:13.372][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2023-04-15 08:02:13.372][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:13.373][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:13.385][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-15 08:02:13.386][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-15 08:02:13.387][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:13.388][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:13.388][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-15 08:02:13.389][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-15 08:02:13.390][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:13.391][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:13.432][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-15 08:02:13.433][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-15 08:02:13.434][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:13.435][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:13.435][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-15 08:02:13.436][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-15 08:02:13.437][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:13.438][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:13.439][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-15 08:02:13.439][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-15 08:02:13.440][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:13.441][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:13.442][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2023-04-15 08:02:13.442][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2023-04-15 08:02:13.443][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:13.444][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:13.445][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2023-04-15 08:02:13.446][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2023-04-15 08:02:13.446][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:13.447][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:13.448][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-15 08:02:13.449][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-15 08:02:13.449][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:13.450][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:13.451][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2023-04-15 08:02:13.452][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2023-04-15 08:02:13.452][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:13.453][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:13.454][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-15 08:02:13.455][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-15 08:02:13.456][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:13.456][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:13.457][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-15 08:02:13.458][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-15 08:02:13.459][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:13.459][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:13.460][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-15 08:02:13.461][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-15 08:02:13.461][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:13.462][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:13.463][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-15 08:02:13.464][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-15 08:02:13.465][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:13.465][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:13.466][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-15 08:02:13.467][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-15 08:02:13.468][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:13.469][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:13.469][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-15 08:02:13.470][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-15 08:02:13.471][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:13.472][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-15 08:02:13.472][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 1.1.1.1.
biodb.TRACE[2023-04-15 08:02:13.474][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2023-04-15 08:02:13.475][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2023-04-15 08:02:13.476][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:13.477][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:13.477][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2023-04-15 08:02:13.478][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2023-04-15 08:02:13.479][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:13.480][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:13.481][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2023-04-15 08:02:13.481][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2023-04-15 08:02:13.482][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:13.483][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:13.484][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2023-04-15 08:02:13.485][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2023-04-15 08:02:13.485][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:13.486][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:13.499][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-15 08:02:13.500][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-15 08:02:13.501][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:13.502][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:13.512][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2023-04-15 08:02:13.513][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2023-04-15 08:02:13.514][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:13.515][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:13.519][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-15 08:02:13.520][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-15 08:02:13.521][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:13.521][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:13.522][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-15 08:02:13.523][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-15 08:02:13.524][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:13.525][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:13.525][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-15 08:02:13.526][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-15 08:02:13.527][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:13.527][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:13.529][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-15 08:02:13.530][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-15 08:02:13.531][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:13.532][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:13.532][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-15 08:02:13.533][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-15 08:02:13.534][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:13.535][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:13.535][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-15 08:02:13.536][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-15 08:02:13.537][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:13.538][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:13.539][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2023-04-15 08:02:13.539][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2023-04-15 08:02:13.540][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:13.541][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:13.542][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2023-04-15 08:02:13.543][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2023-04-15 08:02:13.543][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:13.544][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:13.545][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2023-04-15 08:02:13.546][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2023-04-15 08:02:13.546][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:13.547][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:13.553][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-15 08:02:13.554][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-15 08:02:13.555][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:13.556][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:13.556][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-15 08:02:13.557][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-15 08:02:13.558][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:13.559][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:13.559][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-15 08:02:13.560][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-15 08:02:13.561][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:13.562][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:13.562][ef$get] Asked field names are: accession.
biodb.TRACE[2023-04-15 08:02:13.563][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-15 08:02:13.564][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:13.565][ef$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:13.565][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-15 08:02:13.566][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-15 08:02:13.567][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:13.567][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:13.574][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-15 08:02:13.574][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-15 08:02:13.575][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:13.576][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:13.577][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-15 08:02:13.577][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-15 08:02:13.578][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:13.584][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:13.585][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-15 08:02:13.585][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-15 08:02:13.586][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:13.587][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:13.588][ef$get] Asked field names are: name.
biodb.TRACE[2023-04-15 08:02:13.588][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-04-15 08:02:13.589][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:13.590][ef$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:13.590][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-15 08:02:13.591][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-15 08:02:13.592][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:13.593][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:13.598][self$getBiodb()$getEntryFields()$get] Asked field names are: cofactor.
biodb.TRACE[2023-04-15 08:02:13.599][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2023-04-15 08:02:13.600][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:13.601][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:13.602][self$getBiodb()$getEntryFields()$get] Asked field names are: cofactor.
biodb.TRACE[2023-04-15 08:02:13.602][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2023-04-15 08:02:13.603][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:13.604][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:13.605][self$getBiodb()$getEntryFields()$get] Asked field names are: cofactor.
biodb.TRACE[2023-04-15 08:02:13.606][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2023-04-15 08:02:13.606][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:13.607][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:13.608][ef$get] Asked field names are: cofactor.
biodb.TRACE[2023-04-15 08:02:13.609][ef$get] Realnames of fields are: cofactor.
biodb.TRACE[2023-04-15 08:02:13.609][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:13.610][ef$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:13.611][self$getBiodb()$getEntryFields()$get] Asked field names are: cofactor.
biodb.TRACE[2023-04-15 08:02:13.612][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2023-04-15 08:02:13.612][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:13.613][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:13.619][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2023-04-15 08:02:13.620][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2023-04-15 08:02:13.620][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:13.621][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:13.622][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2023-04-15 08:02:13.623][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2023-04-15 08:02:13.623][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:13.624][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:13.625][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2023-04-15 08:02:13.626][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2023-04-15 08:02:13.626][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:13.627][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:13.628][ef$get] Asked field names are: catalytic.activity.
biodb.TRACE[2023-04-15 08:02:13.629][ef$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2023-04-15 08:02:13.629][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:13.630][ef$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:13.631][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2023-04-15 08:02:13.631][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2023-04-15 08:02:13.632][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:13.633][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:13.638][ef$get] Asked field names are: accession.
biodb.TRACE[2023-04-15 08:02:13.639][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-15 08:02:13.640][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:13.640][ef$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:13.644][ef$get] Asked field names are: catalytic.activity.
biodb.TRACE[2023-04-15 08:02:13.645][ef$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2023-04-15 08:02:13.646][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:13.646][ef$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:13.650][ef$get] Asked field names are: cofactor.
biodb.TRACE[2023-04-15 08:02:13.651][ef$get] Realnames of fields are: cofactor.
biodb.TRACE[2023-04-15 08:02:13.651][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:13.652][ef$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:13.656][ef$get] Asked field names are: name.
biodb.TRACE[2023-04-15 08:02:13.657][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-04-15 08:02:13.657][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:13.658][ef$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:13.671][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/bbs-3.16-bioc-longtests/meat/biodbExpasy.Rcheck/biodbExpasy/testref/entry-expasy.enzyme-1.1.1.54-content.txt".
biodb.DEBUG[2023-04-15 08:02:13.696][biodb$getFactory()$createEntryFromCo ...] Creating Expasy ENZYME database. entries from 1 content(s).
biodb.DEBUG[2023-04-15 08:02:13.697][biodb$getFactory()$createEntryFromCo ...] Parsing 1 Expasy ENZYME database. entries.
biodb.DEBUG[2023-04-15 08:02:13.698][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-15 08:02:13.699][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-15 08:02:13.699][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-15 08:02:13.703][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:02:13.704][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-15 08:02:13.705][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:02:13.705][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-15 08:02:13.707][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-15 08:02:13.708][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-15 08:02:13.709][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:13.709][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:13.710][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2023-04-15 08:02:13.711][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2023-04-15 08:02:13.712][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:13.713][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:13.714][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-15 08:02:13.715][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-15 08:02:13.715][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:13.716][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:13.717][self$getBiodb()$getEntryFields()$get] Asked field names are: COFACTOR.
biodb.TRACE[2023-04-15 08:02:13.718][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2023-04-15 08:02:13.719][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:13.719][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:13.720][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2023-04-15 08:02:13.721][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2023-04-15 08:02:13.722][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:13.723][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:13.723][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2023-04-15 08:02:13.724][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2023-04-15 08:02:13.725][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:13.726][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:13.731][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-15 08:02:13.731][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-15 08:02:13.732][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:13.733][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:13.734][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2023-04-15 08:02:13.734][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2023-04-15 08:02:13.735][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:13.736][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:13.736][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-15 08:02:13.737][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-15 08:02:13.738][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:13.738][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:13.739][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-15 08:02:13.740][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-15 08:02:13.741][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:13.741][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:13.742][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-15 08:02:13.743][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-15 08:02:13.743][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:13.744][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:13.745][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-15 08:02:13.746][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-15 08:02:13.746][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:13.747][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:13.748][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-15 08:02:13.749][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-15 08:02:13.749][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:13.750][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:13.751][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-15 08:02:13.752][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-15 08:02:13.752][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:13.753][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-15 08:02:13.754][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 1.1.1.54.
biodb.TRACE[2023-04-15 08:02:13.768][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2023-04-15 08:02:13.769][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2023-04-15 08:02:13.770][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:13.770][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:13.771][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2023-04-15 08:02:13.772][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2023-04-15 08:02:13.772][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:13.773][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:13.774][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2023-04-15 08:02:13.775][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2023-04-15 08:02:13.775][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:13.776][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:13.777][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2023-04-15 08:02:13.778][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2023-04-15 08:02:13.779][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:13.779][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:13.781][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-15 08:02:13.781][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-15 08:02:13.782][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:13.783][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:13.787][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2023-04-15 08:02:13.788][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2023-04-15 08:02:13.788][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:13.789][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:13.793][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-15 08:02:13.794][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-15 08:02:13.794][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:13.795][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:13.796][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-15 08:02:13.797][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-15 08:02:13.798][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:13.798][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:13.799][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-15 08:02:13.800][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-15 08:02:13.801][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:13.801][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:13.803][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-15 08:02:13.804][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-15 08:02:13.805][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:13.805][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:13.806][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-15 08:02:13.807][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-15 08:02:13.808][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:13.808][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:13.809][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-15 08:02:13.810][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-15 08:02:13.811][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:13.811][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:13.812][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2023-04-15 08:02:13.813][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2023-04-15 08:02:13.814][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:13.814][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:13.815][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2023-04-15 08:02:13.816][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2023-04-15 08:02:13.816][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:13.817][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:13.818][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2023-04-15 08:02:13.819][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2023-04-15 08:02:13.819][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:13.820][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:13.832][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-15 08:02:13.833][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-15 08:02:13.834][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:13.834][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:13.835][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-15 08:02:13.836][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-15 08:02:13.836][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:13.837][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:13.838][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-15 08:02:13.839][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-15 08:02:13.839][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:13.840][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:13.841][ef$get] Asked field names are: accession.
biodb.TRACE[2023-04-15 08:02:13.842][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-15 08:02:13.842][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:13.843][ef$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:13.844][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-15 08:02:13.844][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-15 08:02:13.845][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:13.846][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:13.851][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-15 08:02:13.852][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-15 08:02:13.853][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:13.853][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:13.854][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-15 08:02:13.855][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-15 08:02:13.856][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:13.856][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:13.857][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-15 08:02:13.858][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-15 08:02:13.859][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:13.859][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:13.860][ef$get] Asked field names are: name.
biodb.TRACE[2023-04-15 08:02:13.861][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-04-15 08:02:13.862][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:13.862][ef$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:13.863][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-15 08:02:13.864][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-15 08:02:13.864][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:13.865][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:13.871][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2023-04-15 08:02:13.871][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2023-04-15 08:02:13.872][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:13.873][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:13.873][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2023-04-15 08:02:13.874][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2023-04-15 08:02:13.879][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:13.880][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:13.881][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2023-04-15 08:02:13.881][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2023-04-15 08:02:13.882][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:13.883][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:13.883][ef$get] Asked field names are: catalytic.activity.
biodb.TRACE[2023-04-15 08:02:13.884][ef$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2023-04-15 08:02:13.885][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:13.885][ef$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:13.886][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2023-04-15 08:02:13.887][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2023-04-15 08:02:13.888][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:13.888][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:13.894][ef$get] Asked field names are: accession.
biodb.TRACE[2023-04-15 08:02:13.894][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-15 08:02:13.895][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:13.896][ef$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:13.899][ef$get] Asked field names are: catalytic.activity.
biodb.TRACE[2023-04-15 08:02:13.900][ef$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2023-04-15 08:02:13.900][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:13.901][ef$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:13.905][ef$get] Asked field names are: name.
biodb.TRACE[2023-04-15 08:02:13.905][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-04-15 08:02:13.906][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:13.907][ef$get] fields variable is a list.
biodb.INFO [2023-04-15 08:02:13.911][biodb::testThat]
biodb.INFO [2023-04-15 08:02:13.911][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2023-04-15 08:02:13.912][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-04-15 08:02:13.913][biodb::testThat]
biodb.DEBUG[2023-04-15 08:02:13.915][private$loadEntries] Creating entries from ids [2]: "1.1.1.1, 1.1.1.54".
biodb.DEBUG[2023-04-15 08:02:13.920][conn$getEntryContent] Get Expasy ENZYME database. entry content(s) for 2 id(s)...
biodb.TRACE[2023-04-15 08:02:13.923][cch$loadFileContent] Trying to load 2 files from cache: [2]: "1.1.1.1, 1.1.1.54".
biodb.INFO [2023-04-15 08:02:13.923][self$getFolderPath] Create cache folder "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280" for "expasy.enzyme-b59b84d962b6741050ba8f70ff4db280".
biodb.TRACE[2023-04-15 08:02:13.924][cch$loadFileContent] file.exist = [2]: "FALSE, FALSE".
biodb.TRACE[2023-04-15 08:02:13.925][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2023-04-15 08:02:13.926][conn$getEntryContent] 0 Expasy ENZYME database. entry content(s) loaded from cache.
biodb.DEBUG[2023-04-15 08:02:13.927][conn$getEntryContent] 2 entry content(s) need to be fetched from Expasy ENZYME database. database "https://enzyme.expasy.org/".
biodb.DEBUG[2023-04-15 08:02:13.927][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2023-04-15 08:02:13.928][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2023-04-15 08:02:13.932][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-15 08:02:13.933][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-15 08:02:13.933][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-15 08:02:13.937][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:02:13.938][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-15 08:02:13.938][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:02:13.939][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:02:13.940][scheduler$sendRequest] Getting content of get URL request "https://enzyme.expasy.org/EC/1.1.1.1.txt".
biodb.DEBUG[2023-04-15 08:02:13.954][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-04-15 08:02:13.955][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-04-15 08:02:13.955][private$doSendRequestOnce] Sent URL is "https://enzyme.expasy.org/EC/1.1.1.1.txt".
biodb.TRACE[2023-04-15 08:02:15.255][getRCurlRequestResult] Using RCurl package for sending request (https://enzyme.expasy.org/EC/1.1.1.1.txt).
biodb.DEBUG[2023-04-15 08:02:15.946][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2023-04-15 08:02:15.948][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280/a52675cfd2f0c2b41556caa64d9341e3.content"
biodb.TRACE[2023-04-15 08:02:15.957][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280/a52675cfd2f0c2b41556caa64d9341e3.request"
biodb.DEBUG[2023-04-15 08:02:15.959][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-15 08:02:15.960][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-15 08:02:15.960][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-15 08:02:15.964][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:02:15.965][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-15 08:02:15.965][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:02:15.966][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:02:15.980][scheduler$sendRequest] Getting content of get URL request "https://enzyme.expasy.org/EC/1.1.1.54.txt".
biodb.DEBUG[2023-04-15 08:02:15.990][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-04-15 08:02:15.991][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-04-15 08:02:16.000][private$doSendRequestOnce] Sent URL is "https://enzyme.expasy.org/EC/1.1.1.54.txt".
biodb.TRACE[2023-04-15 08:02:16.967][getRCurlRequestResult] Using RCurl package for sending request (https://enzyme.expasy.org/EC/1.1.1.54.txt).
biodb.DEBUG[2023-04-15 08:02:17.662][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2023-04-15 08:02:17.664][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280/a9b93566a091cbe35a06e4b3871f95c9.content"
biodb.TRACE[2023-04-15 08:02:17.667][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280/a9b93566a091cbe35a06e4b3871f95c9.request"
biodb.TRACE[2023-04-15 08:02:17.669][private$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[2023-04-15 08:02:17.670][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2023-04-15 08:02:17.671][self$createEntryFromContent] Creating Expasy ENZYME database. entries from 2 content(s).
biodb.DEBUG[2023-04-15 08:02:17.672][self$createEntryFromContent] Parsing 2 Expasy ENZYME database. entries.
biodb.DEBUG[2023-04-15 08:02:17.674][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-15 08:02:17.675][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-15 08:02:17.675][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-15 08:02:17.679][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:02:17.680][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-15 08:02:17.681][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:02:17.681][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-15 08:02:17.684][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-15 08:02:17.684][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-15 08:02:17.685][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:17.686][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:17.687][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2023-04-15 08:02:17.688][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2023-04-15 08:02:17.689][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:17.689][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:17.691][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-15 08:02:17.691][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-15 08:02:17.692][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:17.693][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:17.694][self$getBiodb()$getEntryFields()$get] Asked field names are: COFACTOR.
biodb.TRACE[2023-04-15 08:02:17.695][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2023-04-15 08:02:17.695][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:17.696][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:17.697][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-15 08:02:17.698][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-15 08:02:17.699][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:17.699][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:17.700][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-15 08:02:17.701][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-15 08:02:17.702][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:17.702][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:17.703][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-15 08:02:17.704][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-15 08:02:17.705][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:17.706][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:17.706][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-15 08:02:17.707][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-15 08:02:17.708][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:17.713][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:17.719][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-15 08:02:17.720][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-15 08:02:17.721][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:17.722][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:17.722][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2023-04-15 08:02:17.723][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2023-04-15 08:02:17.724][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:17.725][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:17.725][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2023-04-15 08:02:17.726][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2023-04-15 08:02:17.727][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:17.728][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:17.729][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-15 08:02:17.729][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-15 08:02:17.730][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:17.731][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:17.732][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2023-04-15 08:02:17.732][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2023-04-15 08:02:17.733][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:17.734][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:17.735][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-15 08:02:17.735][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-15 08:02:17.736][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:17.737][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:17.738][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-15 08:02:17.738][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-15 08:02:17.739][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:17.740][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:17.741][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-15 08:02:17.742][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-15 08:02:17.742][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:17.743][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-15 08:02:17.744][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-15 08:02:17.745][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-15 08:02:17.745][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-15 08:02:17.749][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:02:17.750][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-15 08:02:17.751][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:02:17.751][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-15 08:02:17.753][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-15 08:02:17.754][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-15 08:02:17.755][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:17.755][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:17.756][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2023-04-15 08:02:17.757][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2023-04-15 08:02:17.758][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:17.759][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:17.760][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-15 08:02:17.760][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-15 08:02:17.761][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:17.762][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:17.763][self$getBiodb()$getEntryFields()$get] Asked field names are: COFACTOR.
biodb.TRACE[2023-04-15 08:02:17.764][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2023-04-15 08:02:17.764][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:17.765][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:17.766][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2023-04-15 08:02:17.767][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2023-04-15 08:02:17.768][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:17.768][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:17.769][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2023-04-15 08:02:17.770][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2023-04-15 08:02:17.771][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:17.771][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:17.772][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-15 08:02:17.773][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-15 08:02:17.774][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:17.774][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:17.775][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2023-04-15 08:02:17.776][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2023-04-15 08:02:17.777][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:17.778][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:17.778][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-15 08:02:17.779][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-15 08:02:17.780][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:17.781][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:17.782][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-15 08:02:17.783][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-15 08:02:17.783][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:17.784][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:17.785][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-15 08:02:17.786][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-15 08:02:17.786][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:17.787][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:17.788][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-15 08:02:17.789][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-15 08:02:17.790][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:17.790][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:17.791][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-15 08:02:17.792][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-15 08:02:17.793][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:17.794][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:17.794][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-15 08:02:17.795][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-15 08:02:17.796][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:17.797][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:17.798][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-15 08:02:17.798][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-15 08:02:17.799][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:17.800][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:17.801][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-15 08:02:17.801][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-15 08:02:17.802][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:17.803][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:17.804][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-15 08:02:17.805][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-15 08:02:17.805][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:17.806][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-15 08:02:17.807][self$createEntryFromContent] Accession numbers: 1.1.1.1, 1.1.1.54.
biodb.TRACE[2023-04-15 08:02:17.808][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2023-04-15 08:02:17.809][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2023-04-15 08:02:17.809][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:17.810][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:17.811][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2023-04-15 08:02:17.812][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2023-04-15 08:02:17.812][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:17.813][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:17.814][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2023-04-15 08:02:17.815][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2023-04-15 08:02:17.816][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:17.816][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:17.821][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2023-04-15 08:02:17.821][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2023-04-15 08:02:17.822][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:17.823][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:17.824][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2023-04-15 08:02:17.825][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2023-04-15 08:02:17.825][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:17.826][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:17.827][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2023-04-15 08:02:17.828][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2023-04-15 08:02:17.828][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:17.829][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2023-04-15 08:02:17.840][biodb::testThat]
biodb.INFO [2023-04-15 08:02:17.841][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2023-04-15 08:02:17.842][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-04-15 08:02:17.842][biodb::testThat]
biodb.TRACE[2023-04-15 08:02:17.845][ef$get] Asked field names are: name.
biodb.TRACE[2023-04-15 08:02:17.845][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-04-15 08:02:17.846][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:17.847][ef$get] fields variable is a list.
biodb.DEBUG[2023-04-15 08:02:17.848][function(conn, opt)] Testing searchForEntries() with entry "1.1.1.1" and field "name".
biodb.TRACE[2023-04-15 08:02:17.871][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-15 08:02:17.872][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-15 08:02:17.873][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:17.874][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:17.875][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-15 08:02:17.875][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-15 08:02:17.876][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:17.877][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:17.878][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-15 08:02:17.878][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-15 08:02:17.879][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:17.880][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-15 08:02:17.882][function(conn, opt)] With value "alcohol dehydrogenase".
biodb.DEBUG[2023-04-15 08:02:17.884][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://enzyme.expasy.org/enzyme-byname.html?alcohol dehydrogenase".
biodb.DEBUG[2023-04-15 08:02:17.886][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-04-15 08:02:17.886][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-04-15 08:02:17.887][private$doSendRequestOnce] Sent URL is "https://enzyme.expasy.org/enzyme-byname.html?alcohol%20dehydrogenase".
biodb.TRACE[2023-04-15 08:02:18.625][getRCurlRequestResult] Using RCurl package for sending request (https://enzyme.expasy.org/enzyme-byname.html?alcohol%20dehydrogenase).
biodb.DEBUG[2023-04-15 08:02:19.427][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2023-04-15 08:02:19.428][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280/f603fa2a57aec59588edc37541c6f6d5.content"
biodb.TRACE[2023-04-15 08:02:19.431][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280/f603fa2a57aec59588edc37541c6f6d5.request"
biodb.DEBUG[2023-04-15 08:02:19.436][function(conn, opt)] With found IDs [1]: "1.1.1.1".
biodb.INFO [2023-04-15 08:02:19.446][biodb::testThat]
biodb.INFO [2023-04-15 08:02:19.447][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2023-04-15 08:02:19.448][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-04-15 08:02:19.448][biodb::testThat]
biodb.TRACE[2023-04-15 08:02:19.466][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-15 08:02:19.467][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-15 08:02:19.468][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:19.469][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:19.469][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-15 08:02:19.470][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-15 08:02:19.471][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:19.472][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:19.472][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-15 08:02:19.473][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-15 08:02:19.474][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:19.475][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-15 08:02:19.498][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://enzyme.expasy.org/enzyme-byname.html?alcohol dehydrogenase".
biodb.DEBUG[2023-04-15 08:02:19.500][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-04-15 08:02:19.511][cch$loadFileContent] Trying to load 1 files from cache: [1]: "f603fa2a57aec59588edc37541c6f6d5".
biodb.TRACE[2023-04-15 08:02:19.520][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-04-15 08:02:19.521][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280/f603fa2a57aec59588edc37541c6f6d5.content".
biodb.INFO [2023-04-15 08:02:19.533][biodb::testThat]
biodb.INFO [2023-04-15 08:02:19.533][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2023-04-15 08:02:19.534][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-04-15 08:02:19.535][biodb::testThat]
biodb.TRACE[2023-04-15 08:02:19.542][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2023-04-15 08:02:19.543][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2023-04-15 08:02:19.544][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:19.544][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:19.545][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2023-04-15 08:02:19.546][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2023-04-15 08:02:19.547][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:19.547][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:19.548][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2023-04-15 08:02:19.549][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2023-04-15 08:02:19.550][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:19.551][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:19.551][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2023-04-15 08:02:19.552][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2023-04-15 08:02:19.553][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:19.553][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:19.577][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2023-04-15 08:02:19.578][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2023-04-15 08:02:19.579][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:19.579][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:19.580][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2023-04-15 08:02:19.581][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2023-04-15 08:02:19.582][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:19.583][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:19.583][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2023-04-15 08:02:19.584][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2023-04-15 08:02:19.585][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:19.586][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:19.586][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2023-04-15 08:02:19.587][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2023-04-15 08:02:19.588][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:19.589][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2023-04-15 08:02:19.592][biodb::testThat]
biodb.INFO [2023-04-15 08:02:19.592][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2023-04-15 08:02:19.593][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-04-15 08:02:19.594][biodb::testThat]
biodb.INFO [2023-04-15 08:02:19.599][biodb::testThat]
biodb.INFO [2023-04-15 08:02:19.599][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2023-04-15 08:02:19.600][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-04-15 08:02:19.601][biodb::testThat]
biodb.INFO [2023-04-15 08:02:19.605][biodb::testThat]
biodb.INFO [2023-04-15 08:02:19.605][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2023-04-15 08:02:19.606][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-04-15 08:02:19.607][biodb::testThat]
biodb.DEBUG[2023-04-15 08:02:19.617][function(conn, opt)] Trying to download "https://enzyme.expasy.org/cgi-bin/enzyme/enzyme-search-ec?field1=1&field2=1&field3=1&field4=1".
biodb.DEBUG[2023-04-15 08:02:20.295][getUrlContent] Use RCurl for downloading content of URL https://enzyme.expasy.org/cgi-bin/enzyme/enzyme-search-ec?field1=1&field2=1&field3=1&field4=1.
biodb.INFO [2023-04-15 08:02:21.032][biodb::testThat]
biodb.INFO [2023-04-15 08:02:21.033][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2023-04-15 08:02:21.034][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-04-15 08:02:21.035][biodb::testThat]
biodb.DEBUG[2023-04-15 08:02:26.739][getUrlContent] Use RCurl for downloading content of URL https://enzyme.expasy.org/images/1.1.1.1/image.png.
biodb.TRACE[2023-04-15 08:02:27.110][ef$get] Asked field names are: name.
biodb.TRACE[2023-04-15 08:02:27.111][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-04-15 08:02:27.112][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:27.113][ef$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:27.113][ef$get] Asked field names are: name.
biodb.TRACE[2023-04-15 08:02:27.114][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-04-15 08:02:27.115][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:27.115][ef$get] fields variable is a list.
biodb.INFO [2023-04-15 08:02:27.120][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2023-04-15 08:02:27.127][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector expasy.enzyme from the request scheduler
biodb.INFO [2023-04-15 08:02:27.128][self$deleteConn] Connector "expasy.enzyme" deleted.
biodb.DEBUG[2023-04-15 08:02:27.129][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2023-04-15 08:02:27.129][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-15 08:02:27.130][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-15 08:02:27.130][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:02:27.131][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-15 08:02:27.132][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:02:27.132][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2023-04-15 08:02:27.139][biodb::testContext]
biodb.INFO [2023-04-15 08:02:27.140][biodb::testContext] ********************************************************************************
biodb.INFO [2023-04-15 08:02:27.140][biodb::testContext] Test context - Example long tests
biodb.INFO [2023-04-15 08:02:27.141][biodb::testContext] ********************************************************************************
biodb.INFO [2023-04-15 08:02:27.142][biodb::testContext]
biodb.INFO [2023-04-15 08:02:27.143][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.6.1.
biodb.DEBUG[2023-04-15 08:02:27.144][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.2/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2023-04-15 08:02:27.147][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-04-15 08:02:27.148][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2023-04-15 08:02:27.149][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2023-04-15 08:02:27.149][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:02:27.150][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:02:27.151][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:02:27.151][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2023-04-15 08:02:27.152][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2023-04-15 08:02:27.153][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:02:27.153][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:02:27.154][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:02:27.155][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2023-04-15 08:02:27.155][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2023-04-15 08:02:27.156][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:02:27.157][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:02:27.157][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:02:27.158][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2023-04-15 08:02:27.159][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2023-04-15 08:02:27.159][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2023-04-15 08:02:27.160][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:02:27.161][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:02:27.161][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:02:27.162][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2023-04-15 08:02:27.163][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2023-04-15 08:02:27.163][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2023-04-15 08:02:27.164][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:02:27.165][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:02:27.165][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:02:27.166][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2023-04-15 08:02:27.167][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2023-04-15 08:02:27.167][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:02:27.168][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:02:27.168][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:02:27.169][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2023-04-15 08:02:27.170][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2023-04-15 08:02:27.170][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2023-04-15 08:02:27.171][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:02:27.172][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:02:27.172][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:02:27.173][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2023-04-15 08:02:27.174][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2023-04-15 08:02:27.174][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:02:27.175][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:02:27.175][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:02:27.176][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2023-04-15 08:02:27.177][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2023-04-15 08:02:27.177][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2023-04-15 08:02:27.178][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:02:27.179][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:02:27.179][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:02:27.180][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2023-04-15 08:02:27.181][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2023-04-15 08:02:27.181][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2023-04-15 08:02:27.182][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2023-04-15 08:02:27.183][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2023-04-15 08:02:27.184][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2023-04-15 08:02:27.184][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:02:27.185][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:02:27.185][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:02:27.186][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2023-04-15 08:02:27.187][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2023-04-15 08:02:27.187][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:02:27.188][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:02:27.189][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:02:27.189][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2023-04-15 08:02:27.190][self$set] Set key entries.sep to "|".
biodb.DEBUG[2023-04-15 08:02:27.191][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:02:27.191][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:02:27.192][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:02:27.193][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2023-04-15 08:02:27.193][self$set] Set key offline to FALSE.
biodb.DEBUG[2023-04-15 08:02:27.194][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:02:27.195][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:02:27.195][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:02:27.196][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2023-04-15 08:02:27.197][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2023-04-15 08:02:27.197][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:02:27.198][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:02:27.198][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:02:27.199][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2023-04-15 08:02:27.200][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2023-04-15 08:02:27.200][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:02:27.201][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:02:27.201][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:02:27.202][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2023-04-15 08:02:27.203][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2023-04-15 08:02:27.217][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2023-04-15 08:02:27.218][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:02:27.218][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:02:27.219][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:02:27.220][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2023-04-15 08:02:27.220][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2023-04-15 08:02:27.221][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2023-04-15 08:02:27.222][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:02:27.222][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:02:27.223][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:02:27.224][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2023-04-15 08:02:27.225][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-04-15 08:02:27.226][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2023-04-15 08:02:27.227][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-04-15 08:02:27.227][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-04-15 08:02:27.228][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-04-15 08:02:27.229][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-04-15 08:02:27.230][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-04-15 08:02:27.230][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-04-15 08:02:27.231][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2023-04-15 08:02:27.232][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-04-15 08:02:27.232][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-04-15 08:02:27.233][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2023-04-15 08:02:27.234][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-04-15 08:02:27.234][self$setPropertyValue]
biodb.DEBUG[2023-04-15 08:02:27.235][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-04-15 08:02:27.236][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2023-04-15 08:02:27.236][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2023-04-15 08:02:27.236][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2023-04-15 08:02:27.236][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2023-04-15 08:02:27.236][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2023-04-15 08:02:27.237][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-04-15 08:02:27.237][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-15 08:02:27.238][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-15 08:02:27.239][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-04-15 08:02:27.239][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-15 08:02:27.240][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-15 08:02:27.241][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-04-15 08:02:27.241][self$setPropertyValue]
biodb.DEBUG[2023-04-15 08:02:27.242][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-04-15 08:02:27.243][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-04-15 08:02:27.243][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-04-15 08:02:27.244][self$setPropertyValue]
biodb.DEBUG[2023-04-15 08:02:27.245][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2023-04-15 08:02:27.246][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-04-15 08:02:27.247][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2023-04-15 08:02:27.247][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-04-15 08:02:27.248][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-04-15 08:02:27.249][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-04-15 08:02:27.249][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-04-15 08:02:27.250][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-04-15 08:02:27.251][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-04-15 08:02:27.252][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2023-04-15 08:02:27.252][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-04-15 08:02:27.253][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-04-15 08:02:27.254][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2023-04-15 08:02:27.254][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-04-15 08:02:27.255][self$setPropertyValue]
biodb.DEBUG[2023-04-15 08:02:27.256][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-04-15 08:02:27.256][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2023-04-15 08:02:27.256][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2023-04-15 08:02:27.256][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2023-04-15 08:02:27.256][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2023-04-15 08:02:27.256][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2023-04-15 08:02:27.257][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-04-15 08:02:27.262][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-15 08:02:27.263][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-15 08:02:27.263][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-04-15 08:02:27.264][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-15 08:02:27.264][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-15 08:02:27.265][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-04-15 08:02:27.266][self$setPropertyValue]
biodb.DEBUG[2023-04-15 08:02:27.266][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-04-15 08:02:27.267][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-04-15 08:02:27.267][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-04-15 08:02:27.268][self$setPropertyValue]
biodb.DEBUG[2023-04-15 08:02:27.269][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2023-04-15 08:02:27.270][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2023-04-15 08:02:27.271][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2023-04-15 08:02:27.271][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-04-15 08:02:27.272][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-04-15 08:02:27.273][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-04-15 08:02:27.273][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-04-15 08:02:27.274][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-04-15 08:02:27.275][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-04-15 08:02:27.275][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2023-04-15 08:02:27.276][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-04-15 08:02:27.277][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2023-04-15 08:02:27.277][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2023-04-15 08:02:27.278][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-04-15 08:02:27.279][self$setPropertyValue]
biodb.DEBUG[2023-04-15 08:02:27.279][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-04-15 08:02:27.280][self$setPropertyValue]
biodb.DEBUG[2023-04-15 08:02:27.281][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-04-15 08:02:27.281][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-15 08:02:27.282][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-15 08:02:27.283][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-04-15 08:02:27.283][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-15 08:02:27.284][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-15 08:02:27.285][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-04-15 08:02:27.285][self$setPropertyValue]
biodb.DEBUG[2023-04-15 08:02:27.286][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-04-15 08:02:27.286][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-04-15 08:02:27.287][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-04-15 08:02:27.288][self$setPropertyValue]
biodb.DEBUG[2023-04-15 08:02:27.289][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2023-04-15 08:02:27.290][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2023-04-15 08:02:27.290][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2023-04-15 08:02:27.291][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-04-15 08:02:27.292][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-04-15 08:02:27.292][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-04-15 08:02:27.293][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-04-15 08:02:27.294][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-04-15 08:02:27.294][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-04-15 08:02:27.295][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2023-04-15 08:02:27.296][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-04-15 08:02:27.296][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2023-04-15 08:02:27.297][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2023-04-15 08:02:27.298][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-04-15 08:02:27.298][self$setPropertyValue]
biodb.DEBUG[2023-04-15 08:02:27.299][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-04-15 08:02:27.300][self$setPropertyValue]
biodb.DEBUG[2023-04-15 08:02:27.301][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-04-15 08:02:27.301][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-15 08:02:27.302][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-15 08:02:27.302][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-04-15 08:02:27.303][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-15 08:02:27.304][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-15 08:02:27.304][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-04-15 08:02:27.305][self$setPropertyValue]
biodb.DEBUG[2023-04-15 08:02:27.306][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-04-15 08:02:27.306][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-04-15 08:02:27.307][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-04-15 08:02:27.307][self$setPropertyValue]
biodb.DEBUG[2023-04-15 08:02:27.308][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-04-15 08:02:27.309][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:02:27.310][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:02:27.310][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:02:27.311][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:02:27.311][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-15 08:02:27.312][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:02:27.313][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:02:27.313][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:02:27.314][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:02:27.314][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-15 08:02:27.315][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:02:27.316][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:02:27.316][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:02:27.317][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:02:27.317][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-15 08:02:27.318][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:02:27.319][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:02:27.319][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:02:27.320][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:02:27.320][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-15 08:02:27.321][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:02:27.322][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:02:27.322][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:02:27.323][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:02:27.323][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-15 08:02:27.324][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:02:27.325][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[2023-04-15 08:02:27.325][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:02:27.326][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:02:27.326][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-15 08:02:27.327][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:02:27.328][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[2023-04-15 08:02:27.328][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:02:27.329][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:02:27.329][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-15 08:02:27.330][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:02:27.331][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[2023-04-15 08:02:27.331][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:02:27.332][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:02:27.332][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-15 08:02:27.333][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:02:27.334][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[2023-04-15 08:02:27.334][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:02:27.335][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:02:27.335][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-15 08:02:27.336][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:02:27.337][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:02:27.337][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:02:27.338][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:02:27.338][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-15 08:02:27.339][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:02:27.340][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:02:27.340][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:02:27.341][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:02:27.341][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-15 08:02:27.342][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:02:27.343][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:02:27.343][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:02:27.344][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:02:27.345][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-15 08:02:27.345][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:02:27.346][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:02:27.346][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:02:27.347][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:02:27.348][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-15 08:02:27.348][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:02:27.349][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:02:27.349][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:02:27.350][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:02:27.351][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-15 08:02:27.351][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:02:27.352][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[2023-04-15 08:02:27.353][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:02:27.353][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:02:27.354][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-15 08:02:27.354][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:02:27.355][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:02:27.356][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:02:27.356][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:02:27.357][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-15 08:02:27.357][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:02:27.358][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:02:27.359][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:02:27.359][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:02:27.360][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-15 08:02:27.360][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:02:27.361][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:02:27.362][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2023-04-15 08:02:27.363][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2023-04-15 08:02:27.364][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2023-04-15 08:02:27.365][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2023-04-15 08:02:27.366][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2023-04-15 08:02:27.367][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2023-04-15 08:02:27.368][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2023-04-15 08:02:27.369][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2023-04-15 08:02:27.370][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2023-04-15 08:02:27.371][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2023-04-15 08:02:27.372][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2023-04-15 08:02:27.373][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2023-04-15 08:02:27.378][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2023-04-15 08:02:27.379][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2023-04-15 08:02:27.379][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2023-04-15 08:02:27.380][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2023-04-15 08:02:27.381][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2023-04-15 08:02:27.382][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2023-04-15 08:02:27.383][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2023-04-15 08:02:27.384][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2023-04-15 08:02:27.385][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2023-04-15 08:02:27.386][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2023-04-15 08:02:27.387][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2023-04-15 08:02:27.388][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2023-04-15 08:02:27.389][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2023-04-15 08:02:27.389][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2023-04-15 08:02:27.390][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2023-04-15 08:02:27.391][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2023-04-15 08:02:27.392][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2023-04-15 08:02:27.393][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2023-04-15 08:02:27.394][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2023-04-15 08:02:27.395][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2023-04-15 08:02:27.396][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2023-04-15 08:02:27.397][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2023-04-15 08:02:27.398][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2023-04-15 08:02:27.399][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2023-04-15 08:02:27.400][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2023-04-15 08:02:27.401][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2023-04-15 08:02:27.402][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2023-04-15 08:02:27.403][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2023-04-15 08:02:27.403][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2023-04-15 08:02:27.404][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2023-04-15 08:02:27.405][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2023-04-15 08:02:27.406][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2023-04-15 08:02:27.407][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2023-04-15 08:02:27.408][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2023-04-15 08:02:27.409][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2023-04-15 08:02:27.410][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2023-04-15 08:02:27.411][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2023-04-15 08:02:27.412][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2023-04-15 08:02:27.413][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2023-04-15 08:02:27.414][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2023-04-15 08:02:27.415][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2023-04-15 08:02:27.416][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2023-04-15 08:02:27.417][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2023-04-15 08:02:27.418][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2023-04-15 08:02:27.419][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2023-04-15 08:02:27.420][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2023-04-15 08:02:27.420][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2023-04-15 08:02:27.421][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2023-04-15 08:02:27.422][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2023-04-15 08:02:27.423][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2023-04-15 08:02:27.424][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2023-04-15 08:02:27.425][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2023-04-15 08:02:27.426][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2023-04-15 08:02:27.427][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2023-04-15 08:02:27.428][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2023-04-15 08:02:27.429][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2023-04-15 08:02:27.430][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2023-04-15 08:02:27.431][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2023-04-15 08:02:27.432][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2023-04-15 08:02:27.433][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2023-04-15 08:02:27.434][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2023-04-15 08:02:27.435][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2023-04-15 08:02:27.436][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2023-04-15 08:02:27.437][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2023-04-15 08:02:27.438][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2023-04-15 08:02:27.439][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2023-04-15 08:02:27.440][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2023-04-15 08:02:27.441][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2023-04-15 08:02:27.442][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2023-04-15 08:02:27.443][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2023-04-15 08:02:27.444][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2023-04-15 08:02:27.445][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2023-04-15 08:02:27.446][initialize] This is biodb version 1.6.1.
biodb.DEBUG[2023-04-15 08:02:27.447][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-04-15 08:02:27.447][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:02:27.448][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-15 08:02:27.448][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:02:27.449][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:02:27.450][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:02:27.450][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-15 08:02:27.451][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-15 08:02:27.452][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:02:27.452][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-15 08:02:27.453][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:02:27.454][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:02:27.454][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:02:27.455][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-15 08:02:27.456][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-15 08:02:27.456][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:02:27.457][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-15 08:02:27.457][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:02:27.458][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[2023-04-15 08:02:27.459][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:02:27.459][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-15 08:02:27.460][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-15 08:02:27.461][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:02:27.461][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-15 08:02:27.462][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:02:27.462][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[2023-04-15 08:02:27.463][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:02:27.464][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-15 08:02:27.464][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-15 08:02:27.465][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:02:27.466][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-15 08:02:27.466][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:02:27.467][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[2023-04-15 08:02:27.467][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:02:27.468][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-15 08:02:27.469][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-15 08:02:27.469][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:02:27.470][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-15 08:02:27.471][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:02:27.471][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:02:27.472][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:02:27.473][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-15 08:02:27.473][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-15 08:02:27.474][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:02:27.474][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-15 08:02:27.475][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:02:27.476][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:02:27.476][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:02:27.477][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-15 08:02:27.477][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-15 08:02:27.478][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:02:27.479][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-15 08:02:27.479][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:02:27.480][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:02:27.480][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:02:27.481][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-15 08:02:27.482][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-15 08:02:27.482][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:02:27.483][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-15 08:02:27.483][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:02:27.484][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:02:27.485][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:02:27.485][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-15 08:02:27.486][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-15 08:02:27.486][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:02:27.487][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-15 08:02:27.488][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:02:27.488][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:02:27.493][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:02:27.494][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-15 08:02:27.495][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-15 08:02:27.495][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:02:27.496][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-15 08:02:27.496][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:02:27.497][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[2023-04-15 08:02:27.498][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:02:27.498][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-15 08:02:27.499][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-15 08:02:27.499][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:02:27.500][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-15 08:02:27.500][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:02:27.501][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:02:27.502][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:02:27.502][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-15 08:02:27.503][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-15 08:02:27.503][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:02:27.504][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-15 08:02:27.505][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:02:27.505][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:02:27.506][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:02:27.506][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-15 08:02:27.507][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-15 08:02:27.508][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:02:27.508][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-15 08:02:27.509][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:02:27.509][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:02:27.510][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:02:27.511][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-15 08:02:27.511][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-15 08:02:27.512][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:02:27.512][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-15 08:02:27.513][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:02:27.514][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:02:27.514][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:02:27.515][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-15 08:02:27.515][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-15 08:02:27.516][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:02:27.517][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-15 08:02:27.517][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:02:27.518][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:02:27.518][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:02:27.519][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-15 08:02:27.519][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-15 08:02:27.520][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:02:27.521][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-15 08:02:27.521][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:02:27.522][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[2023-04-15 08:02:27.522][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:02:27.523][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-15 08:02:27.524][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-15 08:02:27.524][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:02:27.525][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-15 08:02:27.525][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:02:27.526][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:02:27.527][biodb$loadDefinitions] Load definitions from file "/Users/biocbuild/bbs-3.16-bioc-longtests/meat/biodbExpasy.Rcheck/biodbExpasy/definitions.yml".
biodb.DEBUG[2023-04-15 08:02:27.528][self$getDbsInfo()$define] Define connector expasy.enzyme.
biodb.DEBUG[2023-04-15 08:02:27.530][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-04-15 08:02:27.530][self$setPropertyValue] Setting property "description" to "Write here the description of this database.".
biodb.DEBUG[2023-04-15 08:02:27.531][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-04-15 08:02:27.532][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-04-15 08:02:27.532][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-04-15 08:02:27.533][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-04-15 08:02:27.534][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2023-04-15 08:02:27.534][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-04-15 08:02:27.535][self$setPropertyValue] Setting property "entry.content.type" to "txt".
biodb.DEBUG[2023-04-15 08:02:27.536][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-04-15 08:02:27.536][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-04-15 08:02:27.537][self$setPropertyValue] Setting property "name" to "Expasy ENZYME database.".
biodb.DEBUG[2023-04-15 08:02:27.538][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-04-15 08:02:27.538][self$setPropertyValue] Setting property "parsing.expr" to "^ID\s+([0-9.]+)$".
biodb.DEBUG[2023-04-15 08:02:27.538][self$setPropertyValue] Setting property "parsing.expr" to "^CA\s+(.+?)\.?$".
biodb.DEBUG[2023-04-15 08:02:27.538][self$setPropertyValue] Setting property "parsing.expr" to "^CF\s+(.+?)\.?$".
biodb.DEBUG[2023-04-15 08:02:27.538][self$setPropertyValue] Setting property "parsing.expr" to "^DE\s+(.+?)\.?$".
biodb.DEBUG[2023-04-15 08:02:27.539][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2023-04-15 08:02:27.540][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2023-04-15 08:02:27.540][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2023-04-15 08:02:27.541][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-15 08:02:27.542][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-15 08:02:27.542][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-04-15 08:02:27.543][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-15 08:02:27.544][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-15 08:02:27.544][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-04-15 08:02:27.545][self$setPropertyValue] Setting property "urls" to "https://enzyme.expasy.org/".
biodb.DEBUG[2023-04-15 08:02:27.546][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-04-15 08:02:27.546][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-04-15 08:02:27.547][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2023-04-15 08:02:27.547][self$setPropertyValue]
biodb.DEBUG[2023-04-15 08:02:27.548][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2023-04-15 08:02:27.551][super$initialize] Initialize connector expasy.enzyme.
biodb.DEBUG[2023-04-15 08:02:27.551][super$initialize] Register connector expasy.enzyme with the request scheduler
biodb.DEBUG[2023-04-15 08:02:27.552][private$bdb$getRequestScheduler()$re ...] Register connector expasy.enzyme.
biodb.DEBUG[2023-04-15 08:02:27.553][private$addConnectorRules] Create new rule for URL "enzyme.expasy.org" of connector "expasy.enzyme".
biodb.DEBUG[2023-04-15 08:02:27.554][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2023-04-15 08:02:27.555][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2023-04-15 08:02:27.555][biodb$getFactory()$createConn] Creating new connector expasy.enzyme for database class expasy.enzyme .
biodb.INFO [2023-04-15 08:02:27.556][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2023-04-15 08:02:27.557][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector expasy.enzyme from the request scheduler
biodb.INFO [2023-04-15 08:02:27.558][self$deleteConn] Connector "expasy.enzyme" deleted.
biodb.DEBUG[2023-04-15 08:02:27.558][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2023-04-15 08:02:27.559][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-15 08:02:27.559][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-15 08:02:27.560][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:02:27.561][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-15 08:02:27.561][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:02:27.562][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 86 ]
> 
> proc.time()
   user  system elapsed 
  3.778   0.236  16.504

'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_1.2.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.16-bioc-longtests/meat/biodbExpasy.Rcheck’
* using R version 4.2.3 (2023-03-15)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* 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 ‘1.2.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘biodbExpasy’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Title field: should not end in a period.
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... SKIPPED
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... SKIPPED
* checking examples ... SKIPPED
* checking for unstated dependencies in ‘longtests’ ... OK
* checking tests in ‘longtests’ ...
  Running ‘testthat.R’
 OK
* DONE

Status: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.16-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)