Back to Long Tests report for BioC 3.15

This page was generated on 2022-10-15 21:00:02 -0400 (Sat, 15 Oct 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.5 LTS)x86_644.2.1 (2022-06-23) -- "Funny-Looking Kid" 4383
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 nebbiolo1


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 6/26HostnameOS / ArchCHECK
biodbExpasy 1.0.0  (landing page)
Pierrick Roger
Snapshot Date: 2022-10-15 06:55:01 -0400 (Sat, 15 Oct 2022)
git_url: https://git.bioconductor.org/packages/biodbExpasy
git_branch: RELEASE_3_15
git_last_commit: f09985c
git_last_commit_date: 2022-04-26 12:22:07 -0400 (Tue, 26 Apr 2022)
nebbiolo1Linux (Ubuntu 20.04.5 LTS) / x86_64  OK  

Summary

Package: biodbExpasy
Version: 1.0.0
Command: /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --test-dir=longtests --no-stop-on-test-error --no-codoc --no-examples --no-manual --ignore-vignettes --check-subdirs=no biodbExpasy_1.0.0.tar.gz
StartedAt: 2022-10-15 08:03:22 -0400 (Sat, 15 Oct 2022)
EndedAt: 2022-10-15 08:04:01 -0400 (Sat, 15 Oct 2022)
EllapsedTime: 39.4 seconds
RetCode: 0
Status:   OK  
CheckDir: biodbExpasy.Rcheck
Warnings: 0

Tests output

biodbExpasy.Rcheck/tests/testthat.Rout


R version 4.2.1 (2022-06-23) -- "Funny-Looking Kid"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

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

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

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

> # Script needed to run testthat automatically from ‘R CMD check’. See
> # testthat::test_dir documentation.
> library(testthat)
> library(biodbExpasy)
> Sys.setenv(TESTTHAT_REPORTER="summary")
> Sys.setenv(BIODB_LOG_DST="console")
> test_check("biodbExpasy")
biodb.INFO [2022-10-15 08:03:49.024][biodb::testContext]
biodb.INFO [2022-10-15 08:03:49.026][biodb::testContext] ********************************************************************************
biodb.INFO [2022-10-15 08:03:49.026][biodb::testContext] Test context - Generic long tests
biodb.INFO [2022-10-15 08:03:49.027][biodb::testContext] ********************************************************************************
biodb.INFO [2022-10-15 08:03:49.028][biodb::testContext]
biodb.INFO [2022-10-15 08:03:49.040][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.4.2.
biodb.DEBUG[2022-10-15 08:03:49.042][self$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.15-bioc/R/library/biodb/definitions.yml".
biodb.DEBUG[2022-10-15 08:03:49.047][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2022-10-15 08:03:49.048][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2022-10-15 08:03:49.049][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2022-10-15 08:03:49.050][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-15 08:03:49.050][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-15 08:03:49.051][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-15 08:03:49.052][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2022-10-15 08:03:49.074][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2022-10-15 08:03:49.074][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-15 08:03:49.075][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-15 08:03:49.076][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-15 08:03:49.076][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2022-10-15 08:03:49.077][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2022-10-15 08:03:49.078][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-15 08:03:49.078][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-15 08:03:49.079][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-15 08:03:49.080][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2022-10-15 08:03:49.080][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2022-10-15 08:03:49.081][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2022-10-15 08:03:49.082][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-15 08:03:49.082][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-15 08:03:49.083][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-15 08:03:49.084][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2022-10-15 08:03:49.084][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2022-10-15 08:03:49.085][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2022-10-15 08:03:49.086][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-15 08:03:49.086][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-15 08:03:49.087][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-15 08:03:49.088][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2022-10-15 08:03:49.088][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2022-10-15 08:03:49.089][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-15 08:03:49.090][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-15 08:03:49.090][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-15 08:03:49.091][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2022-10-15 08:03:49.092][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2022-10-15 08:03:49.092][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2022-10-15 08:03:49.093][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-15 08:03:49.094][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-15 08:03:49.094][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-15 08:03:49.095][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2022-10-15 08:03:49.096][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2022-10-15 08:03:49.096][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-15 08:03:49.097][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-15 08:03:49.098][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-15 08:03:49.098][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2022-10-15 08:03:49.099][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2022-10-15 08:03:49.100][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2022-10-15 08:03:49.100][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-15 08:03:49.101][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-15 08:03:49.102][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-15 08:03:49.102][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2022-10-15 08:03:49.103][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2022-10-15 08:03:49.104][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2022-10-15 08:03:49.105][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2022-10-15 08:03:49.105][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2022-10-15 08:03:49.106][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2022-10-15 08:03:49.107][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-15 08:03:49.107][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-15 08:03:49.108][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-15 08:03:49.109][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2022-10-15 08:03:49.109][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2022-10-15 08:03:49.110][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-15 08:03:49.111][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-15 08:03:49.111][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-15 08:03:49.112][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2022-10-15 08:03:49.113][self$set] Set key entries.sep to "|".
biodb.DEBUG[2022-10-15 08:03:49.113][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-15 08:03:49.114][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-15 08:03:49.115][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-15 08:03:49.115][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2022-10-15 08:03:49.116][self$set] Set key offline to FALSE.
biodb.DEBUG[2022-10-15 08:03:49.117][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-15 08:03:49.117][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-15 08:03:49.118][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-15 08:03:49.119][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2022-10-15 08:03:49.119][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2022-10-15 08:03:49.120][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-15 08:03:49.121][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-15 08:03:49.121][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-15 08:03:49.122][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2022-10-15 08:03:49.123][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2022-10-15 08:03:49.123][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-15 08:03:49.124][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-15 08:03:49.125][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-15 08:03:49.125][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2022-10-15 08:03:49.126][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2022-10-15 08:03:49.131][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2022-10-15 08:03:49.131][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-15 08:03:49.132][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-15 08:03:49.133][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-15 08:03:49.133][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2022-10-15 08:03:49.134][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2022-10-15 08:03:49.135][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2022-10-15 08:03:49.136][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-15 08:03:49.136][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-15 08:03:49.137][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-15 08:03:49.140][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2022-10-15 08:03:49.162][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2022-10-15 08:03:49.172][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2022-10-15 08:03:49.173][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2022-10-15 08:03:49.174][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2022-10-15 08:03:49.175][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2022-10-15 08:03:49.175][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2022-10-15 08:03:49.176][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2022-10-15 08:03:49.177][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2022-10-15 08:03:49.177][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2022-10-15 08:03:49.178][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2022-10-15 08:03:49.179][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2022-10-15 08:03:49.180][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2022-10-15 08:03:49.180][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2022-10-15 08:03:49.181][self$setPropertyValue]
biodb.DEBUG[2022-10-15 08:03:49.182][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2022-10-15 08:03:49.182][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2022-10-15 08:03:49.182][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2022-10-15 08:03:49.182][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2022-10-15 08:03:49.182][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2022-10-15 08:03:49.182][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2022-10-15 08:03:49.183][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2022-10-15 08:03:49.184][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-10-15 08:03:49.185][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-10-15 08:03:49.185][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2022-10-15 08:03:49.186][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-10-15 08:03:49.187][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-10-15 08:03:49.187][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2022-10-15 08:03:49.188][self$setPropertyValue]
biodb.DEBUG[2022-10-15 08:03:49.189][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2022-10-15 08:03:49.189][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2022-10-15 08:03:49.190][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2022-10-15 08:03:49.191][self$setPropertyValue]
biodb.DEBUG[2022-10-15 08:03:49.192][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2022-10-15 08:03:49.193][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2022-10-15 08:03:49.194][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2022-10-15 08:03:49.194][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2022-10-15 08:03:49.195][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2022-10-15 08:03:49.196][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2022-10-15 08:03:49.196][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2022-10-15 08:03:49.197][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2022-10-15 08:03:49.198][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2022-10-15 08:03:49.202][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2022-10-15 08:03:49.203][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2022-10-15 08:03:49.204][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2022-10-15 08:03:49.204][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2022-10-15 08:03:49.205][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2022-10-15 08:03:49.206][self$setPropertyValue]
biodb.DEBUG[2022-10-15 08:03:49.207][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2022-10-15 08:03:49.207][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2022-10-15 08:03:49.207][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2022-10-15 08:03:49.207][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2022-10-15 08:03:49.207][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2022-10-15 08:03:49.207][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2022-10-15 08:03:49.208][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2022-10-15 08:03:49.209][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-10-15 08:03:49.209][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-10-15 08:03:49.210][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2022-10-15 08:03:49.211][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-10-15 08:03:49.211][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-10-15 08:03:49.212][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2022-10-15 08:03:49.213][self$setPropertyValue]
biodb.DEBUG[2022-10-15 08:03:49.213][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2022-10-15 08:03:49.214][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2022-10-15 08:03:49.215][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2022-10-15 08:03:49.215][self$setPropertyValue]
biodb.DEBUG[2022-10-15 08:03:49.216][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2022-10-15 08:03:49.217][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2022-10-15 08:03:49.218][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2022-10-15 08:03:49.219][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2022-10-15 08:03:49.220][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2022-10-15 08:03:49.220][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2022-10-15 08:03:49.221][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2022-10-15 08:03:49.222][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2022-10-15 08:03:49.222][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2022-10-15 08:03:49.223][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2022-10-15 08:03:49.224][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2022-10-15 08:03:49.224][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2022-10-15 08:03:49.225][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2022-10-15 08:03:49.226][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2022-10-15 08:03:49.227][self$setPropertyValue]
biodb.DEBUG[2022-10-15 08:03:49.227][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2022-10-15 08:03:49.228][self$setPropertyValue]
biodb.DEBUG[2022-10-15 08:03:49.229][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2022-10-15 08:03:49.229][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-10-15 08:03:49.230][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-10-15 08:03:49.231][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2022-10-15 08:03:49.232][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-10-15 08:03:49.232][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-10-15 08:03:49.233][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2022-10-15 08:03:49.234][self$setPropertyValue]
biodb.DEBUG[2022-10-15 08:03:49.234][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2022-10-15 08:03:49.235][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2022-10-15 08:03:49.236][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2022-10-15 08:03:49.236][self$setPropertyValue]
biodb.DEBUG[2022-10-15 08:03:49.237][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2022-10-15 08:03:49.238][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2022-10-15 08:03:49.239][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2022-10-15 08:03:49.240][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2022-10-15 08:03:49.240][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2022-10-15 08:03:49.241][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2022-10-15 08:03:49.242][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2022-10-15 08:03:49.243][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2022-10-15 08:03:49.243][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2022-10-15 08:03:49.244][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2022-10-15 08:03:49.245][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2022-10-15 08:03:49.245][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2022-10-15 08:03:49.246][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2022-10-15 08:03:49.247][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2022-10-15 08:03:49.248][self$setPropertyValue]
biodb.DEBUG[2022-10-15 08:03:49.248][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2022-10-15 08:03:49.249][self$setPropertyValue]
biodb.DEBUG[2022-10-15 08:03:49.250][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2022-10-15 08:03:49.250][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-10-15 08:03:49.251][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-10-15 08:03:49.252][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2022-10-15 08:03:49.252][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-10-15 08:03:49.253][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-10-15 08:03:49.254][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2022-10-15 08:03:49.254][self$setPropertyValue]
biodb.DEBUG[2022-10-15 08:03:49.255][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2022-10-15 08:03:49.256][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2022-10-15 08:03:49.256][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2022-10-15 08:03:49.257][self$setPropertyValue]
biodb.DEBUG[2022-10-15 08:03:49.260][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2022-10-15 08:03:49.261][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2022-10-15 08:03:49.261][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-15 08:03:49.262][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-15 08:03:49.262][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-15 08:03:49.263][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-15 08:03:49.264][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-15 08:03:49.264][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-15 08:03:49.265][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-15 08:03:49.266][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-15 08:03:49.266][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-15 08:03:49.267][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-15 08:03:49.268][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-15 08:03:49.268][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-15 08:03:49.269][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-15 08:03:49.270][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-15 08:03:49.270][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-15 08:03:49.271][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-15 08:03:49.271][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-15 08:03:49.272][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-15 08:03:49.273][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-15 08:03:49.273][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-15 08:03:49.274][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-15 08:03:49.275][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-15 08:03:49.275][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-15 08:03:49.276][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-15 08:03:49.277][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-15 08:03:49.277][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-15 08:03:49.278][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-15 08:03:49.278][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-15 08:03:49.279][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-15 08:03:49.280][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-15 08:03:49.280][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-15 08:03:49.281][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-15 08:03:49.282][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-15 08:03:49.282][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-15 08:03:49.283][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-15 08:03:49.284][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-15 08:03:49.284][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-15 08:03:49.285][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-15 08:03:49.285][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-15 08:03:49.286][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-15 08:03:49.287][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-15 08:03:49.287][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-15 08:03:49.288][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-15 08:03:49.289][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-15 08:03:49.289][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-15 08:03:49.290][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-15 08:03:49.291][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-15 08:03:49.291][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-15 08:03:49.292][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-15 08:03:49.293][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-15 08:03:49.293][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-15 08:03:49.294][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-15 08:03:49.295][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-15 08:03:49.295][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-15 08:03:49.296][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-15 08:03:49.296][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-15 08:03:49.297][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-15 08:03:49.298][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-15 08:03:49.298][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-15 08:03:49.299][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-15 08:03:49.300][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-15 08:03:49.300][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-15 08:03:49.301][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-15 08:03:49.302][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-15 08:03:49.302][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-15 08:03:49.303][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-15 08:03:49.304][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-15 08:03:49.304][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-15 08:03:49.305][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-15 08:03:49.305][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-15 08:03:49.306][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-15 08:03:49.307][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-15 08:03:49.307][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-15 08:03:49.308][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-15 08:03:49.309][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-15 08:03:49.309][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-15 08:03:49.310][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-15 08:03:49.311][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-15 08:03:49.311][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-15 08:03:49.312][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-15 08:03:49.313][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[2022-10-15 08:03:49.313][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-15 08:03:49.314][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-15 08:03:49.315][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-15 08:03:49.315][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-15 08:03:49.316][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[2022-10-15 08:03:49.317][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2022-10-15 08:03:49.320][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2022-10-15 08:03:49.321][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2022-10-15 08:03:49.322][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2022-10-15 08:03:49.323][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2022-10-15 08:03:49.324][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2022-10-15 08:03:49.325][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2022-10-15 08:03:49.326][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2022-10-15 08:03:49.327][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2022-10-15 08:03:49.328][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2022-10-15 08:03:49.329][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2022-10-15 08:03:49.330][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2022-10-15 08:03:49.331][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2022-10-15 08:03:49.332][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2022-10-15 08:03:49.333][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2022-10-15 08:03:49.334][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2022-10-15 08:03:49.335][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2022-10-15 08:03:49.339][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2022-10-15 08:03:49.340][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2022-10-15 08:03:49.341][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2022-10-15 08:03:49.342][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2022-10-15 08:03:49.343][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2022-10-15 08:03:49.344][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2022-10-15 08:03:49.345][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2022-10-15 08:03:49.346][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2022-10-15 08:03:49.347][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2022-10-15 08:03:49.348][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2022-10-15 08:03:49.349][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2022-10-15 08:03:49.350][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2022-10-15 08:03:49.351][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2022-10-15 08:03:49.351][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2022-10-15 08:03:49.352][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2022-10-15 08:03:49.353][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2022-10-15 08:03:49.354][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2022-10-15 08:03:49.355][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2022-10-15 08:03:49.356][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2022-10-15 08:03:49.357][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2022-10-15 08:03:49.358][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2022-10-15 08:03:49.359][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2022-10-15 08:03:49.360][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2022-10-15 08:03:49.361][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2022-10-15 08:03:49.362][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2022-10-15 08:03:49.363][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2022-10-15 08:03:49.364][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2022-10-15 08:03:49.365][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2022-10-15 08:03:49.366][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2022-10-15 08:03:49.367][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2022-10-15 08:03:49.368][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2022-10-15 08:03:49.369][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2022-10-15 08:03:49.370][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2022-10-15 08:03:49.371][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2022-10-15 08:03:49.372][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2022-10-15 08:03:49.373][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2022-10-15 08:03:49.374][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2022-10-15 08:03:49.375][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2022-10-15 08:03:49.376][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2022-10-15 08:03:49.377][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2022-10-15 08:03:49.378][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2022-10-15 08:03:49.379][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2022-10-15 08:03:49.380][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2022-10-15 08:03:49.381][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2022-10-15 08:03:49.382][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2022-10-15 08:03:49.383][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2022-10-15 08:03:49.384][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2022-10-15 08:03:49.384][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2022-10-15 08:03:49.385][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2022-10-15 08:03:49.386][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2022-10-15 08:03:49.387][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2022-10-15 08:03:49.388][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2022-10-15 08:03:49.389][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2022-10-15 08:03:49.390][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2022-10-15 08:03:49.391][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2022-10-15 08:03:49.392][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2022-10-15 08:03:49.393][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2022-10-15 08:03:49.394][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2022-10-15 08:03:49.395][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2022-10-15 08:03:49.396][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2022-10-15 08:03:49.397][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2022-10-15 08:03:49.398][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2022-10-15 08:03:49.399][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2022-10-15 08:03:49.400][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2022-10-15 08:03:49.401][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2022-10-15 08:03:49.402][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2022-10-15 08:03:49.406][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2022-10-15 08:03:49.407][initialize] This is biodb version 1.4.2.
biodb.DEBUG[2022-10-15 08:03:49.409][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2022-10-15 08:03:49.410][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2022-10-15 08:03:49.411][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-15 08:03:49.411][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2022-10-15 08:03:49.412][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-15 08:03:49.415][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-15 08:03:49.416][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-15 08:03:49.416][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-15 08:03:49.417][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-15 08:03:49.418][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-15 08:03:49.418][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-15 08:03:49.419][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-15 08:03:49.420][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-15 08:03:49.420][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-15 08:03:49.421][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-15 08:03:49.421][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-15 08:03:49.422][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-15 08:03:49.423][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-15 08:03:49.423][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-15 08:03:49.424][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-15 08:03:49.425][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-15 08:03:49.425][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-15 08:03:49.426][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-15 08:03:49.427][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-15 08:03:49.427][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-15 08:03:49.428][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-15 08:03:49.428][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-15 08:03:49.429][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-15 08:03:49.430][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-15 08:03:49.430][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-15 08:03:49.431][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-15 08:03:49.432][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-15 08:03:49.432][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-15 08:03:49.433][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-15 08:03:49.434][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-15 08:03:49.434][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-15 08:03:49.435][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-15 08:03:49.435][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-15 08:03:49.436][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-15 08:03:49.437][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-15 08:03:49.437][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-15 08:03:49.438][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-15 08:03:49.439][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-15 08:03:49.439][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-15 08:03:49.440][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-15 08:03:49.441][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-15 08:03:49.441][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-15 08:03:49.442][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-15 08:03:49.442][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-15 08:03:49.443][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-15 08:03:49.444][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-15 08:03:49.444][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-15 08:03:49.445][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-15 08:03:49.446][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-15 08:03:49.446][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-15 08:03:49.447][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-15 08:03:49.448][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-15 08:03:49.448][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-15 08:03:49.449][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-15 08:03:49.450][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-15 08:03:49.450][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-15 08:03:49.451][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-15 08:03:49.452][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-15 08:03:49.452][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-15 08:03:49.453][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-15 08:03:49.453][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-15 08:03:49.454][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-15 08:03:49.455][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-15 08:03:49.455][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-15 08:03:49.456][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-15 08:03:49.457][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-15 08:03:49.457][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-15 08:03:49.458][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-15 08:03:49.459][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-15 08:03:49.459][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-15 08:03:49.460][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-15 08:03:49.461][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-15 08:03:49.461][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-15 08:03:49.462][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-15 08:03:49.463][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-15 08:03:49.467][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-15 08:03:49.468][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-15 08:03:49.468][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-15 08:03:49.469][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-15 08:03:49.469][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-15 08:03:49.470][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-15 08:03:49.471][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-15 08:03:49.471][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-15 08:03:49.472][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-15 08:03:49.473][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-15 08:03:49.473][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-15 08:03:49.474][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-15 08:03:49.474][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-15 08:03:49.475][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-15 08:03:49.476][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-15 08:03:49.476][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[2022-10-15 08:03:49.477][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-15 08:03:49.478][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-15 08:03:49.478][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-15 08:03:49.479][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-15 08:03:49.479][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-15 08:03:49.480][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-15 08:03:49.481][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-15 08:03:49.481][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-15 08:03:49.482][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-15 08:03:49.483][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-15 08:03:49.483][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-15 08:03:49.484][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-15 08:03:49.485][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-15 08:03:49.485][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-15 08:03:49.486][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-15 08:03:49.486][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-15 08:03:49.487][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-15 08:03:49.488][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-15 08:03:49.488][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-15 08:03:49.489][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-15 08:03:49.490][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-15 08:03:49.490][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-15 08:03:49.491][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-15 08:03:49.491][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-15 08:03:49.492][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-15 08:03:49.493][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-15 08:03:49.493][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-15 08:03:49.494][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-15 08:03:49.495][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.15-bioc-longtests/meat/biodbExpasy.Rcheck/biodbExpasy/definitions.yml".
biodb.DEBUG[2022-10-15 08:03:49.501][self$getDbsInfo()$define] Define connector expasy.enzyme.
biodb.DEBUG[2022-10-15 08:03:49.503][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2022-10-15 08:03:49.503][self$setPropertyValue] Setting property "description" to "Write here the description of this database.".
biodb.DEBUG[2022-10-15 08:03:49.504][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2022-10-15 08:03:49.505][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2022-10-15 08:03:49.505][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2022-10-15 08:03:49.506][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2022-10-15 08:03:49.507][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2022-10-15 08:03:49.508][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2022-10-15 08:03:49.508][self$setPropertyValue] Setting property "entry.content.type" to "txt".
biodb.DEBUG[2022-10-15 08:03:49.509][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2022-10-15 08:03:49.510][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2022-10-15 08:03:49.511][self$setPropertyValue] Setting property "name" to "Expasy ENZYME database.".
biodb.DEBUG[2022-10-15 08:03:49.511][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2022-10-15 08:03:49.512][self$setPropertyValue] Setting property "parsing.expr" to "^ID\s+([0-9.]+)$".
biodb.DEBUG[2022-10-15 08:03:49.512][self$setPropertyValue] Setting property "parsing.expr" to "^CA\s+(.+?)\.?$".
biodb.DEBUG[2022-10-15 08:03:49.512][self$setPropertyValue] Setting property "parsing.expr" to "^CF\s+(.+?)\.?$".
biodb.DEBUG[2022-10-15 08:03:49.512][self$setPropertyValue] Setting property "parsing.expr" to "^DE\s+(.+?)\.?$".
biodb.DEBUG[2022-10-15 08:03:49.513][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2022-10-15 08:03:49.513][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2022-10-15 08:03:49.514][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2022-10-15 08:03:49.515][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-10-15 08:03:49.516][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-10-15 08:03:49.516][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2022-10-15 08:03:49.517][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-10-15 08:03:49.518][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-10-15 08:03:49.518][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2022-10-15 08:03:49.519][self$setPropertyValue] Setting property "urls" to "https://enzyme.expasy.org/".
biodb.DEBUG[2022-10-15 08:03:49.520][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2022-10-15 08:03:49.520][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2022-10-15 08:03:49.521][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2022-10-15 08:03:49.522][self$setPropertyValue]
biodb.DEBUG[2022-10-15 08:03:49.526][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2022-10-15 08:03:49.543][super$initialize] Initialize connector expasy.enzyme.
biodb.DEBUG[2022-10-15 08:03:49.543][super$initialize] Register connector expasy.enzyme with the request scheduler
biodb.DEBUG[2022-10-15 08:03:49.546][private$bdb$getRequestScheduler()$re ...] Register connector expasy.enzyme.
biodb.DEBUG[2022-10-15 08:03:49.549][private$addConnectorRules] Create new rule for URL "enzyme.expasy.org" of connector "expasy.enzyme".
biodb.DEBUG[2022-10-15 08:03:49.552][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2022-10-15 08:03:49.553][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2022-10-15 08:03:49.554][biodb$getFactory()$createConn] Creating new connector expasy.enzyme for database class expasy.enzyme .
biodb.INFO [2022-10-15 08:03:49.566][biodb::testThat]
biodb.INFO [2022-10-15 08:03:49.566][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2022-10-15 08:03:49.567][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2022-10-15 08:03:49.568][biodb::testThat]
biodb.TRACE[2022-10-15 08:03:49.570][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/bbs-3.15-bioc-longtests/meat/biodbExpasy.Rcheck/biodbExpasy/testref/entry-expasy.enzyme-1.1.1.1-content.txt".
biodb.DEBUG[2022-10-15 08:03:49.573][biodb$getFactory()$createEntryFromCo ...] Creating Expasy ENZYME database. entries from 1 content(s).
biodb.DEBUG[2022-10-15 08:03:49.576][biodb$getFactory()$createEntryFromCo ...] Parsing 1 Expasy ENZYME database. entries.
biodb.DEBUG[2022-10-15 08:03:49.582][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-15 08:03:49.583][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-15 08:03:49.583][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-15 08:03:49.592][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-15 08:03:49.593][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-15 08:03:49.593][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-15 08:03:49.594][FUN] Functions in observer BiodbConfig: [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[2022-10-15 08:03:49.602][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-15 08:03:49.603][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-15 08:03:49.603][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:03:49.604][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:03:49.650][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2022-10-15 08:03:49.658][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2022-10-15 08:03:49.658][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:03:49.659][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:03:49.662][self$getBiodb()$getEntryFields()$get] Asked field names are: cofactor.
biodb.TRACE[2022-10-15 08:03:49.663][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2022-10-15 08:03:49.664][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:03:49.664][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:03:49.667][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-15 08:03:49.668][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-15 08:03:49.669][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:03:49.669][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:03:49.672][self$getBiodb()$getEntryFields()$get] Asked field names are: COFACTOR.
biodb.TRACE[2022-10-15 08:03:49.673][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2022-10-15 08:03:49.673][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:03:49.674][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:03:49.675][self$getBiodb()$getEntryFields()$get] Asked field names are: cofactor.
biodb.TRACE[2022-10-15 08:03:49.675][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2022-10-15 08:03:49.676][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:03:49.677][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:03:49.678][self$getBiodb()$getEntryFields()$get] Asked field names are: cofactor.
biodb.TRACE[2022-10-15 08:03:49.678][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2022-10-15 08:03:49.679][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:03:49.680][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:03:49.680][self$getBiodb()$getEntryFields()$get] Asked field names are: cofactor.
biodb.TRACE[2022-10-15 08:03:49.681][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2022-10-15 08:03:49.682][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:03:49.683][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:03:49.683][self$getBiodb()$getEntryFields()$get] Asked field names are: COFACTOR.
biodb.TRACE[2022-10-15 08:03:49.684][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2022-10-15 08:03:49.685][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:03:49.685][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:03:49.698][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-15 08:03:49.699][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-15 08:03:49.700][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:03:49.701][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:03:49.701][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-15 08:03:49.702][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-15 08:03:49.703][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:03:49.704][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:03:49.734][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-15 08:03:49.735][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-15 08:03:49.736][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:03:49.737][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:03:49.737][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-15 08:03:49.738][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-15 08:03:49.739][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:03:49.740][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:03:49.740][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-15 08:03:49.741][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-15 08:03:49.742][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:03:49.743][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:03:49.746][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2022-10-15 08:03:49.746][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2022-10-15 08:03:49.747][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:03:49.748][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:03:49.749][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2022-10-15 08:03:49.749][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2022-10-15 08:03:49.750][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:03:49.751][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:03:49.752][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-15 08:03:49.753][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-15 08:03:49.753][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:03:49.754][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:03:49.755][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2022-10-15 08:03:49.756][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2022-10-15 08:03:49.756][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:03:49.757][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:03:49.758][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-15 08:03:49.762][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-15 08:03:49.764][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:03:49.764][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:03:49.765][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-15 08:03:49.766][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-15 08:03:49.767][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:03:49.768][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:03:49.769][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-15 08:03:49.770][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-15 08:03:49.771][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:03:49.772][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:03:49.776][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-15 08:03:49.777][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-15 08:03:49.778][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:03:49.779][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:03:49.780][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-15 08:03:49.781][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-15 08:03:49.781][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:03:49.782][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:03:49.783][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-15 08:03:49.784][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-15 08:03:49.785][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:03:49.785][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-10-15 08:03:49.786][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 1.1.1.1.
biodb.TRACE[2022-10-15 08:03:49.791][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2022-10-15 08:03:49.792][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2022-10-15 08:03:49.793][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:03:49.794][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:03:49.795][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2022-10-15 08:03:49.796][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2022-10-15 08:03:49.796][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:03:49.797][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:03:49.798][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2022-10-15 08:03:49.799][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2022-10-15 08:03:49.800][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:03:49.801][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:03:49.801][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2022-10-15 08:03:49.802][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2022-10-15 08:03:49.803][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:03:49.804][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:03:49.818][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-15 08:03:49.819][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-15 08:03:49.820][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:03:49.821][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:03:49.833][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2022-10-15 08:03:49.834][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2022-10-15 08:03:49.834][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:03:49.835][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:03:49.839][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-15 08:03:49.840][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-15 08:03:49.841][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:03:49.842][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:03:49.843][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-15 08:03:49.843][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-15 08:03:49.844][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:03:49.845][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:03:49.846][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-15 08:03:49.847][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-15 08:03:49.847][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:03:49.848][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:03:49.850][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-15 08:03:49.851][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-15 08:03:49.851][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:03:49.852][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:03:49.853][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-15 08:03:49.854][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-15 08:03:49.854][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:03:49.855][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:03:49.856][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-15 08:03:49.857][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-15 08:03:49.857][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:03:49.858][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:03:49.859][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2022-10-15 08:03:49.860][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2022-10-15 08:03:49.861][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:03:49.861][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:03:49.862][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2022-10-15 08:03:49.863][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2022-10-15 08:03:49.864][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:03:49.865][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:03:49.872][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2022-10-15 08:03:49.873][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2022-10-15 08:03:49.874][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:03:49.875][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:03:49.880][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-15 08:03:49.881][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-15 08:03:49.882][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:03:49.882][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:03:49.883][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-15 08:03:49.884][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-15 08:03:49.885][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:03:49.885][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:03:49.886][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-15 08:03:49.887][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-15 08:03:49.888][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:03:49.888][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:03:49.889][ef$get] Asked field names are: accession.
biodb.TRACE[2022-10-15 08:03:49.890][ef$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-15 08:03:49.891][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:03:49.891][ef$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:03:49.892][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-15 08:03:49.893][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-15 08:03:49.894][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:03:49.895][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:03:49.900][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-15 08:03:49.901][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-15 08:03:49.902][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:03:49.902][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:03:49.903][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-15 08:03:49.904][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-15 08:03:49.905][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:03:49.905][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:03:49.906][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-15 08:03:49.907][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-15 08:03:49.908][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:03:49.908][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:03:49.909][ef$get] Asked field names are: name.
biodb.TRACE[2022-10-15 08:03:49.910][ef$get] Realnames of fields are: name.
biodb.TRACE[2022-10-15 08:03:49.911][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:03:49.911][ef$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:03:49.912][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-15 08:03:49.913][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-15 08:03:49.914][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:03:49.914][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:03:49.920][self$getBiodb()$getEntryFields()$get] Asked field names are: cofactor.
biodb.TRACE[2022-10-15 08:03:49.920][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2022-10-15 08:03:49.921][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:03:49.922][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:03:49.922][self$getBiodb()$getEntryFields()$get] Asked field names are: cofactor.
biodb.TRACE[2022-10-15 08:03:49.923][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2022-10-15 08:03:49.924][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:03:49.925][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:03:49.925][self$getBiodb()$getEntryFields()$get] Asked field names are: cofactor.
biodb.TRACE[2022-10-15 08:03:49.926][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2022-10-15 08:03:49.927][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:03:49.928][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:03:49.928][ef$get] Asked field names are: cofactor.
biodb.TRACE[2022-10-15 08:03:49.929][ef$get] Realnames of fields are: cofactor.
biodb.TRACE[2022-10-15 08:03:49.930][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:03:49.931][ef$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:03:49.931][self$getBiodb()$getEntryFields()$get] Asked field names are: cofactor.
biodb.TRACE[2022-10-15 08:03:49.932][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2022-10-15 08:03:49.933][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:03:49.934][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:03:49.939][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2022-10-15 08:03:49.940][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2022-10-15 08:03:49.940][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:03:49.941][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:03:49.942][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2022-10-15 08:03:49.943][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2022-10-15 08:03:49.943][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:03:49.944][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:03:49.945][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2022-10-15 08:03:49.945][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2022-10-15 08:03:49.946][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:03:49.947][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:03:49.948][ef$get] Asked field names are: catalytic.activity.
biodb.TRACE[2022-10-15 08:03:49.948][ef$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2022-10-15 08:03:49.949][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:03:49.950][ef$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:03:49.951][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2022-10-15 08:03:49.951][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2022-10-15 08:03:49.952][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:03:49.953][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:03:49.958][ef$get] Asked field names are: accession.
biodb.TRACE[2022-10-15 08:03:49.959][ef$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-15 08:03:49.960][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:03:49.960][ef$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:03:49.964][ef$get] Asked field names are: catalytic.activity.
biodb.TRACE[2022-10-15 08:03:49.965][ef$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2022-10-15 08:03:49.965][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:03:49.966][ef$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:03:49.969][ef$get] Asked field names are: cofactor.
biodb.TRACE[2022-10-15 08:03:49.970][ef$get] Realnames of fields are: cofactor.
biodb.TRACE[2022-10-15 08:03:49.971][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:03:49.972][ef$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:03:49.975][ef$get] Asked field names are: name.
biodb.TRACE[2022-10-15 08:03:49.976][ef$get] Realnames of fields are: name.
biodb.TRACE[2022-10-15 08:03:49.977][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:03:49.977][ef$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:03:49.992][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/bbs-3.15-bioc-longtests/meat/biodbExpasy.Rcheck/biodbExpasy/testref/entry-expasy.enzyme-1.1.1.54-content.txt".
biodb.DEBUG[2022-10-15 08:03:50.018][biodb$getFactory()$createEntryFromCo ...] Creating Expasy ENZYME database. entries from 1 content(s).
biodb.DEBUG[2022-10-15 08:03:50.019][biodb$getFactory()$createEntryFromCo ...] Parsing 1 Expasy ENZYME database. entries.
biodb.DEBUG[2022-10-15 08:03:50.020][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-15 08:03:50.021][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-15 08:03:50.021][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-15 08:03:50.025][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-15 08:03:50.026][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-15 08:03:50.027][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-15 08:03:50.027][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.TRACE[2022-10-15 08:03:50.029][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-15 08:03:50.030][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-15 08:03:50.030][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:03:50.031][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:03:50.034][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2022-10-15 08:03:50.035][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2022-10-15 08:03:50.036][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:03:50.036][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:03:50.039][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-15 08:03:50.040][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-15 08:03:50.041][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:03:50.041][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:03:50.044][self$getBiodb()$getEntryFields()$get] Asked field names are: COFACTOR.
biodb.TRACE[2022-10-15 08:03:50.045][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2022-10-15 08:03:50.046][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:03:50.046][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:03:50.047][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2022-10-15 08:03:50.048][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2022-10-15 08:03:50.049][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:03:50.049][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:03:50.050][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2022-10-15 08:03:50.051][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2022-10-15 08:03:50.052][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:03:50.052][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:03:50.053][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-15 08:03:50.054][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-15 08:03:50.055][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:03:50.056][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:03:50.056][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2022-10-15 08:03:50.057][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2022-10-15 08:03:50.058][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:03:50.058][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:03:50.059][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-15 08:03:50.060][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-15 08:03:50.061][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:03:50.061][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:03:50.062][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-15 08:03:50.063][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-15 08:03:50.064][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:03:50.064][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:03:50.065][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-15 08:03:50.066][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-15 08:03:50.067][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:03:50.067][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:03:50.070][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-15 08:03:50.071][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-15 08:03:50.072][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:03:50.072][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:03:50.073][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-15 08:03:50.074][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-15 08:03:50.075][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:03:50.075][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:03:50.076][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-15 08:03:50.077][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-15 08:03:50.078][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:03:50.078][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-10-15 08:03:50.079][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 1.1.1.54.
biodb.TRACE[2022-10-15 08:03:50.098][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2022-10-15 08:03:50.099][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2022-10-15 08:03:50.100][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:03:50.100][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:03:50.101][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2022-10-15 08:03:50.102][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2022-10-15 08:03:50.103][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:03:50.103][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:03:50.104][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2022-10-15 08:03:50.105][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2022-10-15 08:03:50.105][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:03:50.106][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:03:50.107][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2022-10-15 08:03:50.108][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2022-10-15 08:03:50.108][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:03:50.109][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:03:50.110][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-15 08:03:50.111][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-15 08:03:50.112][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:03:50.113][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:03:50.116][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2022-10-15 08:03:50.117][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2022-10-15 08:03:50.118][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:03:50.119][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:03:50.122][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-15 08:03:50.123][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-15 08:03:50.124][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:03:50.124][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:03:50.125][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-15 08:03:50.126][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-15 08:03:50.127][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:03:50.127][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:03:50.128][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-15 08:03:50.129][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-15 08:03:50.130][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:03:50.130][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:03:50.132][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-15 08:03:50.133][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-15 08:03:50.133][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:03:50.134][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:03:50.135][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-15 08:03:50.136][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-15 08:03:50.136][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:03:50.137][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:03:50.138][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-15 08:03:50.139][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-15 08:03:50.139][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:03:50.140][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:03:50.141][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2022-10-15 08:03:50.142][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2022-10-15 08:03:50.142][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:03:50.143][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:03:50.144][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2022-10-15 08:03:50.145][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2022-10-15 08:03:50.145][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:03:50.146][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:03:50.147][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2022-10-15 08:03:50.148][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2022-10-15 08:03:50.148][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:03:50.149][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:03:50.161][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-15 08:03:50.161][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-15 08:03:50.162][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:03:50.163][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:03:50.163][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-15 08:03:50.164][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-15 08:03:50.165][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:03:50.166][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:03:50.166][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-15 08:03:50.167][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-15 08:03:50.168][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:03:50.169][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:03:50.169][ef$get] Asked field names are: accession.
biodb.TRACE[2022-10-15 08:03:50.170][ef$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-15 08:03:50.171][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:03:50.172][ef$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:03:50.172][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-15 08:03:50.173][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-15 08:03:50.174][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:03:50.175][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:03:50.180][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-15 08:03:50.181][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-15 08:03:50.181][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:03:50.182][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:03:50.183][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-15 08:03:50.183][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-15 08:03:50.184][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:03:50.185][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:03:50.189][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-15 08:03:50.190][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-15 08:03:50.190][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:03:50.191][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:03:50.192][ef$get] Asked field names are: name.
biodb.TRACE[2022-10-15 08:03:50.193][ef$get] Realnames of fields are: name.
biodb.TRACE[2022-10-15 08:03:50.193][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:03:50.194][ef$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:03:50.195][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-15 08:03:50.195][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-15 08:03:50.196][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:03:50.197][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:03:50.202][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2022-10-15 08:03:50.203][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2022-10-15 08:03:50.203][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:03:50.204][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:03:50.205][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2022-10-15 08:03:50.206][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2022-10-15 08:03:50.206][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:03:50.207][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:03:50.208][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2022-10-15 08:03:50.209][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2022-10-15 08:03:50.209][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:03:50.210][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:03:50.211][ef$get] Asked field names are: catalytic.activity.
biodb.TRACE[2022-10-15 08:03:50.211][ef$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2022-10-15 08:03:50.212][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:03:50.213][ef$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:03:50.214][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2022-10-15 08:03:50.214][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2022-10-15 08:03:50.215][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:03:50.216][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:03:50.221][ef$get] Asked field names are: accession.
biodb.TRACE[2022-10-15 08:03:50.222][ef$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-15 08:03:50.223][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:03:50.223][ef$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:03:50.227][ef$get] Asked field names are: catalytic.activity.
biodb.TRACE[2022-10-15 08:03:50.228][ef$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2022-10-15 08:03:50.228][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:03:50.229][ef$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:03:50.233][ef$get] Asked field names are: name.
biodb.TRACE[2022-10-15 08:03:50.233][ef$get] Realnames of fields are: name.
biodb.TRACE[2022-10-15 08:03:50.234][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:03:50.235][ef$get] fields variable is a list.
biodb.INFO [2022-10-15 08:03:50.239][biodb::testThat]
biodb.INFO [2022-10-15 08:03:50.240][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2022-10-15 08:03:50.240][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2022-10-15 08:03:50.241][biodb::testThat]
biodb.DEBUG[2022-10-15 08:03:50.243][private$loadEntries] Creating entries from ids [2]: "1.1.1.1, 1.1.1.54".
biodb.DEBUG[2022-10-15 08:03:50.248][conn$getEntryContent] Get Expasy ENZYME database. entry content(s) for 2 id(s)...
biodb.TRACE[2022-10-15 08:03:50.251][cch$loadFileContent] Trying to load 2 files from cache: [2]: "1.1.1.1, 1.1.1.54".
biodb.INFO [2022-10-15 08:03:50.252][self$getFolderPath] Create cache folder "/home/biocbuild/.cache/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280" for "expasy.enzyme-b59b84d962b6741050ba8f70ff4db280".
biodb.TRACE[2022-10-15 08:03:50.253][cch$loadFileContent] file.exist = [2]: "FALSE, FALSE".
biodb.TRACE[2022-10-15 08:03:50.254][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2022-10-15 08:03:50.255][conn$getEntryContent] 0 Expasy ENZYME database. entry content(s) loaded from cache.
biodb.DEBUG[2022-10-15 08:03:50.255][conn$getEntryContent] 2 entry content(s) need to be fetched from Expasy ENZYME database. database "https://enzyme.expasy.org/".
biodb.DEBUG[2022-10-15 08:03:50.256][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2022-10-15 08:03:50.257][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2022-10-15 08:03:50.261][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-15 08:03:50.262][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-15 08:03:50.262][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-15 08:03:50.266][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-15 08:03:50.267][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-15 08:03:50.267][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-15 08:03:50.268][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-15 08:03:50.269][scheduler$sendRequest] Getting content of get URL request "https://enzyme.expasy.org/EC/1.1.1.1.txt".
biodb.DEBUG[2022-10-15 08:03:50.282][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-10-15 08:03:50.283][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-10-15 08:03:50.284][private$doSendRequestOnce] Sent URL is "https://enzyme.expasy.org/EC/1.1.1.1.txt".
biodb.TRACE[2022-10-15 08:03:51.828][getRCurlRequestResult] Using RCurl package for sending request (https://enzyme.expasy.org/EC/1.1.1.1.txt).
biodb.DEBUG[2022-10-15 08:03:52.801][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2022-10-15 08:03:52.816][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280/a52675cfd2f0c2b41556caa64d9341e3.content"
biodb.TRACE[2022-10-15 08:03:52.831][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280/a52675cfd2f0c2b41556caa64d9341e3.request"
biodb.DEBUG[2022-10-15 08:03:52.834][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-15 08:03:52.835][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-15 08:03:52.836][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-15 08:03:52.839][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-15 08:03:52.840][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-15 08:03:52.841][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-15 08:03:52.842][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-15 08:03:52.856][scheduler$sendRequest] Getting content of get URL request "https://enzyme.expasy.org/EC/1.1.1.54.txt".
biodb.DEBUG[2022-10-15 08:03:52.866][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-10-15 08:03:52.867][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-10-15 08:03:52.877][private$doSendRequestOnce] Sent URL is "https://enzyme.expasy.org/EC/1.1.1.54.txt".
biodb.TRACE[2022-10-15 08:03:53.519][getRCurlRequestResult] Using RCurl package for sending request (https://enzyme.expasy.org/EC/1.1.1.54.txt).
biodb.DEBUG[2022-10-15 08:03:54.194][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2022-10-15 08:03:54.200][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280/a9b93566a091cbe35a06e4b3871f95c9.content"
biodb.TRACE[2022-10-15 08:03:54.207][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280/a9b93566a091cbe35a06e4b3871f95c9.request"
biodb.TRACE[2022-10-15 08:03:54.214][private$doSaveContentToFile] Saving to cache [2]: "/home/biocbuild/.cache/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280/1.1.1.1.txt, /home/biocbuild/.cache/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280/1.1.1.54.txt"
biodb.DEBUG[2022-10-15 08:03:54.217][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2022-10-15 08:03:54.231][self$createEntryFromContent] Creating Expasy ENZYME database. entries from 2 content(s).
biodb.DEBUG[2022-10-15 08:03:54.232][self$createEntryFromContent] Parsing 2 Expasy ENZYME database. entries.
biodb.DEBUG[2022-10-15 08:03:54.233][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-15 08:03:54.234][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-15 08:03:54.234][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-15 08:03:54.238][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-15 08:03:54.239][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-15 08:03:54.239][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-15 08:03:54.240][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-10-15 08:03:54.241][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-15 08:03:54.242][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-15 08:03:54.243][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:03:54.244][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:03:54.246][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2022-10-15 08:03:54.247][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2022-10-15 08:03:54.248][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:03:54.248][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:03:54.257][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-15 08:03:54.258][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-15 08:03:54.258][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:03:54.259][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:03:54.262][self$getBiodb()$getEntryFields()$get] Asked field names are: COFACTOR.
biodb.TRACE[2022-10-15 08:03:54.262][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2022-10-15 08:03:54.263][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:03:54.264][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:03:54.265][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-15 08:03:54.265][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-15 08:03:54.266][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:03:54.267][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:03:54.267][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-15 08:03:54.268][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-15 08:03:54.269][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:03:54.269][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:03:54.270][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-15 08:03:54.271][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-15 08:03:54.272][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:03:54.272][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:03:54.273][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-15 08:03:54.274][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-15 08:03:54.275][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:03:54.275][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:03:54.276][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-15 08:03:54.277][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-15 08:03:54.277][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:03:54.278][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:03:54.281][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2022-10-15 08:03:54.281][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2022-10-15 08:03:54.282][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:03:54.283][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:03:54.284][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2022-10-15 08:03:54.284][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2022-10-15 08:03:54.285][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:03:54.286][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:03:54.286][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-15 08:03:54.287][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-15 08:03:54.288][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:03:54.289][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:03:54.289][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2022-10-15 08:03:54.290][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2022-10-15 08:03:54.291][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:03:54.291][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:03:54.292][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-15 08:03:54.293][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-15 08:03:54.294][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:03:54.294][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:03:54.295][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-15 08:03:54.296][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-15 08:03:54.296][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:03:54.297][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:03:54.298][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-15 08:03:54.299][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-15 08:03:54.299][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:03:54.300][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-10-15 08:03:54.303][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-15 08:03:54.303][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-15 08:03:54.304][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-15 08:03:54.308][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-15 08:03:54.308][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-15 08:03:54.309][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-15 08:03:54.310][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-10-15 08:03:54.311][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-15 08:03:54.312][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-15 08:03:54.313][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:03:54.313][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:03:54.316][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2022-10-15 08:03:54.317][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2022-10-15 08:03:54.317][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:03:54.318][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:03:54.321][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-15 08:03:54.321][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-15 08:03:54.322][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:03:54.323][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:03:54.325][self$getBiodb()$getEntryFields()$get] Asked field names are: COFACTOR.
biodb.TRACE[2022-10-15 08:03:54.326][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2022-10-15 08:03:54.327][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:03:54.327][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:03:54.328][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2022-10-15 08:03:54.329][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2022-10-15 08:03:54.330][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:03:54.330][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:03:54.331][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2022-10-15 08:03:54.332][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2022-10-15 08:03:54.332][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:03:54.333][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:03:54.334][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-15 08:03:54.335][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-15 08:03:54.335][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:03:54.336][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:03:54.340][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2022-10-15 08:03:54.341][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2022-10-15 08:03:54.341][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:03:54.342][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:03:54.343][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-15 08:03:54.343][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-15 08:03:54.344][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:03:54.345][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:03:54.346][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-15 08:03:54.346][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-15 08:03:54.347][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:03:54.348][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:03:54.348][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-15 08:03:54.349][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-15 08:03:54.350][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:03:54.351][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:03:54.353][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-15 08:03:54.354][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-15 08:03:54.355][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:03:54.355][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:03:54.356][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-15 08:03:54.357][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-15 08:03:54.358][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:03:54.358][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:03:54.359][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-15 08:03:54.360][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-15 08:03:54.361][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:03:54.361][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:03:54.362][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-15 08:03:54.363][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-15 08:03:54.364][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:03:54.364][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:03:54.365][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-15 08:03:54.366][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-15 08:03:54.367][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:03:54.367][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:03:54.368][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-15 08:03:54.369][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-15 08:03:54.370][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:03:54.370][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-10-15 08:03:54.371][self$createEntryFromContent] Accession numbers: 1.1.1.1, 1.1.1.54.
biodb.TRACE[2022-10-15 08:03:54.372][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2022-10-15 08:03:54.373][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2022-10-15 08:03:54.373][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:03:54.374][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:03:54.375][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2022-10-15 08:03:54.376][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2022-10-15 08:03:54.376][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:03:54.377][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:03:54.378][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2022-10-15 08:03:54.379][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2022-10-15 08:03:54.379][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:03:54.380][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:03:54.384][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2022-10-15 08:03:54.385][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2022-10-15 08:03:54.385][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:03:54.386][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:03:54.387][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2022-10-15 08:03:54.388][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2022-10-15 08:03:54.388][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:03:54.389][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:03:54.390][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2022-10-15 08:03:54.391][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2022-10-15 08:03:54.391][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:03:54.392][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2022-10-15 08:03:54.396][biodb::testThat]
biodb.INFO [2022-10-15 08:03:54.397][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2022-10-15 08:03:54.398][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2022-10-15 08:03:54.398][biodb::testThat]
biodb.TRACE[2022-10-15 08:03:54.400][ef$get] Asked field names are: name.
biodb.TRACE[2022-10-15 08:03:54.401][ef$get] Realnames of fields are: name.
biodb.TRACE[2022-10-15 08:03:54.402][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:03:54.402][ef$get] fields variable is a list.
biodb.DEBUG[2022-10-15 08:03:54.403][function(conn, opt)] Testing searchForEntries() with entry "1.1.1.1" and field "name".
biodb.TRACE[2022-10-15 08:03:54.424][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-15 08:03:54.425][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-15 08:03:54.426][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:03:54.426][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:03:54.427][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-15 08:03:54.428][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-15 08:03:54.428][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:03:54.429][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:03:54.430][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-15 08:03:54.431][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-15 08:03:54.431][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:03:54.432][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-10-15 08:03:54.434][function(conn, opt)] With value "alcohol dehydrogenase".
biodb.DEBUG[2022-10-15 08:03:54.441][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://enzyme.expasy.org/enzyme-byname.html?alcohol dehydrogenase".
biodb.DEBUG[2022-10-15 08:03:54.443][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-10-15 08:03:54.443][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-10-15 08:03:54.444][private$doSendRequestOnce] Sent URL is "https://enzyme.expasy.org/enzyme-byname.html?alcohol%20dehydrogenase".
biodb.TRACE[2022-10-15 08:03:55.173][getRCurlRequestResult] Using RCurl package for sending request (https://enzyme.expasy.org/enzyme-byname.html?alcohol%20dehydrogenase).
biodb.DEBUG[2022-10-15 08:03:55.944][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2022-10-15 08:03:55.949][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280/f603fa2a57aec59588edc37541c6f6d5.content"
biodb.TRACE[2022-10-15 08:03:55.957][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280/f603fa2a57aec59588edc37541c6f6d5.request"
biodb.DEBUG[2022-10-15 08:03:55.963][function(conn, opt)] With found IDs [1]: "1.1.1.1".
biodb.INFO [2022-10-15 08:03:55.979][biodb::testThat]
biodb.INFO [2022-10-15 08:03:55.979][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2022-10-15 08:03:55.980][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2022-10-15 08:03:55.981][biodb::testThat]
biodb.TRACE[2022-10-15 08:03:56.001][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-15 08:03:56.001][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-15 08:03:56.002][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:03:56.003][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:03:56.004][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-15 08:03:56.004][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-15 08:03:56.005][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:03:56.006][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:03:56.007][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-15 08:03:56.007][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-15 08:03:56.008][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:03:56.009][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-10-15 08:03:56.031][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://enzyme.expasy.org/enzyme-byname.html?alcohol dehydrogenase".
biodb.DEBUG[2022-10-15 08:03:56.033][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2022-10-15 08:03:56.044][cch$loadFileContent] Trying to load 1 files from cache: [1]: "f603fa2a57aec59588edc37541c6f6d5".
biodb.TRACE[2022-10-15 08:03:56.045][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2022-10-15 08:03:56.049][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280/f603fa2a57aec59588edc37541c6f6d5.content".
biodb.INFO [2022-10-15 08:03:56.060][biodb::testThat]
biodb.INFO [2022-10-15 08:03:56.060][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2022-10-15 08:03:56.061][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2022-10-15 08:03:56.062][biodb::testThat]
biodb.TRACE[2022-10-15 08:03:56.077][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2022-10-15 08:03:56.078][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2022-10-15 08:03:56.079][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:03:56.080][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:03:56.080][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2022-10-15 08:03:56.081][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2022-10-15 08:03:56.082][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:03:56.082][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:03:56.083][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2022-10-15 08:03:56.084][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2022-10-15 08:03:56.085][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:03:56.085][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:03:56.086][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2022-10-15 08:03:56.087][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2022-10-15 08:03:56.087][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:03:56.088][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:03:56.111][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2022-10-15 08:03:56.112][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2022-10-15 08:03:56.112][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:03:56.113][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:03:56.114][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2022-10-15 08:03:56.114][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2022-10-15 08:03:56.115][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:03:56.116][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:03:56.120][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2022-10-15 08:03:56.121][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2022-10-15 08:03:56.122][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:03:56.122][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:03:56.123][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2022-10-15 08:03:56.124][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2022-10-15 08:03:56.124][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:03:56.125][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2022-10-15 08:03:56.127][biodb::testThat]
biodb.INFO [2022-10-15 08:03:56.128][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2022-10-15 08:03:56.129][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2022-10-15 08:03:56.129][biodb::testThat]
biodb.INFO [2022-10-15 08:03:56.133][biodb::testThat]
biodb.INFO [2022-10-15 08:03:56.134][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2022-10-15 08:03:56.135][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2022-10-15 08:03:56.135][biodb::testThat]
biodb.INFO [2022-10-15 08:03:56.139][biodb::testThat]
biodb.INFO [2022-10-15 08:03:56.139][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2022-10-15 08:03:56.140][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2022-10-15 08:03:56.141][biodb::testThat]
biodb.DEBUG[2022-10-15 08:03:56.149][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[2022-10-15 08:03:57.190][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 [2022-10-15 08:03:58.494][biodb::testThat]
biodb.INFO [2022-10-15 08:03:58.495][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2022-10-15 08:03:58.496][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2022-10-15 08:03:58.496][biodb::testThat]
biodb.DEBUG[2022-10-15 08:04:00.407][getUrlContent] Use RCurl for downloading content of URL https://enzyme.expasy.org/images/1.1.1.1/image.png.
biodb.TRACE[2022-10-15 08:04:00.802][ef$get] Asked field names are: name.
biodb.TRACE[2022-10-15 08:04:00.803][ef$get] Realnames of fields are: name.
biodb.TRACE[2022-10-15 08:04:00.804][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:04:00.804][ef$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:04:00.809][ef$get] Asked field names are: name.
biodb.TRACE[2022-10-15 08:04:00.810][ef$get] Realnames of fields are: name.
biodb.TRACE[2022-10-15 08:04:00.810][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:04:00.811][ef$get] fields variable is a list.
biodb.INFO [2022-10-15 08:04:00.812][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2022-10-15 08:04:00.813][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector expasy.enzyme from the request scheduler
biodb.INFO [2022-10-15 08:04:00.813][self$deleteConn] Connector "expasy.enzyme" deleted.
biodb.DEBUG[2022-10-15 08:04:00.822][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2022-10-15 08:04:00.823][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-15 08:04:00.824][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-15 08:04:00.824][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-15 08:04:00.825][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-15 08:04:00.826][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2022-10-15 08:04:00.826][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2022-10-15 08:04:00.833][biodb::testContext]
biodb.INFO [2022-10-15 08:04:00.834][biodb::testContext] ********************************************************************************
biodb.INFO [2022-10-15 08:04:00.834][biodb::testContext] Test context - Example long tests
biodb.INFO [2022-10-15 08:04:00.835][biodb::testContext] ********************************************************************************
biodb.INFO [2022-10-15 08:04:00.836][biodb::testContext]
biodb.INFO [2022-10-15 08:04:00.840][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.4.2.
biodb.DEBUG[2022-10-15 08:04:00.841][self$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.15-bioc/R/library/biodb/definitions.yml".
biodb.DEBUG[2022-10-15 08:04:00.844][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2022-10-15 08:04:00.844][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2022-10-15 08:04:00.845][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2022-10-15 08:04:00.846][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-15 08:04:00.846][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-15 08:04:00.847][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-15 08:04:00.848][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2022-10-15 08:04:00.849][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2022-10-15 08:04:00.849][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-15 08:04:00.850][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-15 08:04:00.851][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-15 08:04:00.851][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2022-10-15 08:04:00.852][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2022-10-15 08:04:00.853][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-15 08:04:00.853][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-15 08:04:00.854][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-15 08:04:00.855][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2022-10-15 08:04:00.856][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2022-10-15 08:04:00.856][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2022-10-15 08:04:00.857][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-15 08:04:00.858][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-15 08:04:00.858][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-15 08:04:00.859][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2022-10-15 08:04:00.860][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2022-10-15 08:04:00.860][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2022-10-15 08:04:00.861][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-15 08:04:00.862][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-15 08:04:00.862][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-15 08:04:00.863][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2022-10-15 08:04:00.864][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2022-10-15 08:04:00.864][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-15 08:04:00.865][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-15 08:04:00.866][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-15 08:04:00.866][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2022-10-15 08:04:00.867][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2022-10-15 08:04:00.868][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2022-10-15 08:04:00.868][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-15 08:04:00.869][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-15 08:04:00.870][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-15 08:04:00.870][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2022-10-15 08:04:00.871][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2022-10-15 08:04:00.872][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-15 08:04:00.872][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-15 08:04:00.873][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-15 08:04:00.874][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2022-10-15 08:04:00.875][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2022-10-15 08:04:00.875][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2022-10-15 08:04:00.876][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-15 08:04:00.877][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-15 08:04:00.877][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-15 08:04:00.878][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2022-10-15 08:04:00.879][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2022-10-15 08:04:00.879][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2022-10-15 08:04:00.880][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2022-10-15 08:04:00.881][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2022-10-15 08:04:00.882][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2022-10-15 08:04:00.882][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-15 08:04:00.883][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-15 08:04:00.884][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-15 08:04:00.884][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2022-10-15 08:04:00.885][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2022-10-15 08:04:00.886][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-15 08:04:00.886][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-15 08:04:00.887][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-15 08:04:00.888][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2022-10-15 08:04:00.889][self$set] Set key entries.sep to "|".
biodb.DEBUG[2022-10-15 08:04:00.889][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-15 08:04:00.890][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-15 08:04:00.890][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-15 08:04:00.891][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2022-10-15 08:04:00.892][self$set] Set key offline to FALSE.
biodb.DEBUG[2022-10-15 08:04:00.892][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-15 08:04:00.893][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-15 08:04:00.894][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-15 08:04:00.894][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2022-10-15 08:04:00.895][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2022-10-15 08:04:00.896][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-15 08:04:00.897][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-15 08:04:00.897][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-15 08:04:00.898][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2022-10-15 08:04:00.899][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2022-10-15 08:04:00.899][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-15 08:04:00.900][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-15 08:04:00.901][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-15 08:04:00.901][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2022-10-15 08:04:00.902][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2022-10-15 08:04:00.910][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2022-10-15 08:04:00.911][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-15 08:04:00.912][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-15 08:04:00.912][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-15 08:04:00.913][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2022-10-15 08:04:00.914][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2022-10-15 08:04:00.914][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2022-10-15 08:04:00.915][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-15 08:04:00.916][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-15 08:04:00.916][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-15 08:04:00.917][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2022-10-15 08:04:00.919][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2022-10-15 08:04:00.919][self$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[2022-10-15 08:04:00.920][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2022-10-15 08:04:00.921][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2022-10-15 08:04:00.922][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2022-10-15 08:04:00.922][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2022-10-15 08:04:00.923][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2022-10-15 08:04:00.924][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2022-10-15 08:04:00.925][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2022-10-15 08:04:00.925][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2022-10-15 08:04:00.926][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2022-10-15 08:04:00.927][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2022-10-15 08:04:00.928][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2022-10-15 08:04:00.928][self$setPropertyValue]
biodb.DEBUG[2022-10-15 08:04:00.929][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2022-10-15 08:04:00.930][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2022-10-15 08:04:00.930][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2022-10-15 08:04:00.930][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2022-10-15 08:04:00.930][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2022-10-15 08:04:00.930][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2022-10-15 08:04:00.931][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2022-10-15 08:04:00.931][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-10-15 08:04:00.932][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-10-15 08:04:00.933][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2022-10-15 08:04:00.933][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-10-15 08:04:00.934][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-10-15 08:04:00.935][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2022-10-15 08:04:00.935][self$setPropertyValue]
biodb.DEBUG[2022-10-15 08:04:00.936][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2022-10-15 08:04:00.937][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2022-10-15 08:04:00.937][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2022-10-15 08:04:00.938][self$setPropertyValue]
biodb.DEBUG[2022-10-15 08:04:00.939][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2022-10-15 08:04:00.940][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2022-10-15 08:04:00.941][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2022-10-15 08:04:00.942][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2022-10-15 08:04:00.943][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2022-10-15 08:04:00.943][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2022-10-15 08:04:00.944][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2022-10-15 08:04:00.945][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2022-10-15 08:04:00.945][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2022-10-15 08:04:00.946][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2022-10-15 08:04:00.947][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2022-10-15 08:04:00.948][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2022-10-15 08:04:00.948][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2022-10-15 08:04:00.949][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2022-10-15 08:04:00.950][self$setPropertyValue]
biodb.DEBUG[2022-10-15 08:04:00.951][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2022-10-15 08:04:00.951][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2022-10-15 08:04:00.951][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2022-10-15 08:04:00.951][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2022-10-15 08:04:00.951][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2022-10-15 08:04:00.951][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2022-10-15 08:04:00.952][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2022-10-15 08:04:00.953][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-10-15 08:04:00.954][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-10-15 08:04:00.954][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2022-10-15 08:04:00.955][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-10-15 08:04:00.956][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-10-15 08:04:00.956][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2022-10-15 08:04:00.957][self$setPropertyValue]
biodb.DEBUG[2022-10-15 08:04:00.958][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2022-10-15 08:04:00.958][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2022-10-15 08:04:00.959][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2022-10-15 08:04:00.960][self$setPropertyValue]
biodb.DEBUG[2022-10-15 08:04:00.961][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2022-10-15 08:04:00.962][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2022-10-15 08:04:00.963][self$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[2022-10-15 08:04:00.963][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2022-10-15 08:04:00.964][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2022-10-15 08:04:00.965][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2022-10-15 08:04:00.966][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2022-10-15 08:04:00.966][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2022-10-15 08:04:00.967][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2022-10-15 08:04:00.968][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2022-10-15 08:04:00.969][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2022-10-15 08:04:00.969][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2022-10-15 08:04:00.970][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2022-10-15 08:04:00.971][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2022-10-15 08:04:00.972][self$setPropertyValue]
biodb.DEBUG[2022-10-15 08:04:00.972][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2022-10-15 08:04:00.973][self$setPropertyValue]
biodb.DEBUG[2022-10-15 08:04:00.974][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2022-10-15 08:04:00.974][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-10-15 08:04:00.975][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-10-15 08:04:00.976][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2022-10-15 08:04:00.977][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-10-15 08:04:00.977][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-10-15 08:04:00.978][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2022-10-15 08:04:00.979][self$setPropertyValue]
biodb.DEBUG[2022-10-15 08:04:00.979][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2022-10-15 08:04:00.980][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2022-10-15 08:04:00.981][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2022-10-15 08:04:00.981][self$setPropertyValue]
biodb.DEBUG[2022-10-15 08:04:00.982][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2022-10-15 08:04:00.984][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2022-10-15 08:04:00.984][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2022-10-15 08:04:00.985][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2022-10-15 08:04:00.986][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2022-10-15 08:04:00.986][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2022-10-15 08:04:00.987][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2022-10-15 08:04:00.988][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2022-10-15 08:04:00.989][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2022-10-15 08:04:00.989][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2022-10-15 08:04:00.990][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2022-10-15 08:04:00.994][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2022-10-15 08:04:00.995][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2022-10-15 08:04:00.996][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2022-10-15 08:04:00.997][self$setPropertyValue]
biodb.DEBUG[2022-10-15 08:04:00.997][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2022-10-15 08:04:00.998][self$setPropertyValue]
biodb.DEBUG[2022-10-15 08:04:00.999][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2022-10-15 08:04:00.999][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-10-15 08:04:01.000][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-10-15 08:04:01.001][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2022-10-15 08:04:01.001][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-10-15 08:04:01.002][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-10-15 08:04:01.003][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2022-10-15 08:04:01.004][self$setPropertyValue]
biodb.DEBUG[2022-10-15 08:04:01.004][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2022-10-15 08:04:01.005][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2022-10-15 08:04:01.006][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2022-10-15 08:04:01.006][self$setPropertyValue]
biodb.DEBUG[2022-10-15 08:04:01.007][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2022-10-15 08:04:01.008][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2022-10-15 08:04:01.008][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-15 08:04:01.009][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-15 08:04:01.010][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-15 08:04:01.010][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-15 08:04:01.011][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-15 08:04:01.012][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-15 08:04:01.012][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-15 08:04:01.013][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-15 08:04:01.014][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-15 08:04:01.014][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-15 08:04:01.015][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-15 08:04:01.016][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-15 08:04:01.016][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-15 08:04:01.017][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-15 08:04:01.018][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-15 08:04:01.018][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-15 08:04:01.019][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-15 08:04:01.020][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-15 08:04:01.020][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-15 08:04:01.021][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-15 08:04:01.021][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-15 08:04:01.022][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-15 08:04:01.023][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-15 08:04:01.023][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-15 08:04:01.024][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-15 08:04:01.025][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-15 08:04:01.025][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-15 08:04:01.026][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-15 08:04:01.027][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-15 08:04:01.027][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-15 08:04:01.028][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-15 08:04:01.029][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-15 08:04:01.029][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-15 08:04:01.030][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-15 08:04:01.030][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-15 08:04:01.031][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-15 08:04:01.032][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-15 08:04:01.032][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-15 08:04:01.033][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-15 08:04:01.034][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-15 08:04:01.034][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-15 08:04:01.035][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-15 08:04:01.036][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-15 08:04:01.036][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-15 08:04:01.037][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-15 08:04:01.038][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-15 08:04:01.038][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-15 08:04:01.039][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-15 08:04:01.039][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-15 08:04:01.040][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-15 08:04:01.041][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-15 08:04:01.041][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-15 08:04:01.042][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-15 08:04:01.043][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-15 08:04:01.043][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-15 08:04:01.044][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-15 08:04:01.045][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-15 08:04:01.045][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-15 08:04:01.046][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-15 08:04:01.047][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-15 08:04:01.047][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-15 08:04:01.048][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-15 08:04:01.049][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-15 08:04:01.049][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-15 08:04:01.050][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-15 08:04:01.051][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-15 08:04:01.051][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-15 08:04:01.052][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-15 08:04:01.053][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-15 08:04:01.053][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-15 08:04:01.054][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-15 08:04:01.055][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-15 08:04:01.055][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-15 08:04:01.056][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-15 08:04:01.056][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-15 08:04:01.057][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-15 08:04:01.058][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-15 08:04:01.058][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-15 08:04:01.059][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-15 08:04:01.060][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-15 08:04:01.060][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-15 08:04:01.061][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-15 08:04:01.062][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-15 08:04:01.062][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-15 08:04:01.063][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-15 08:04:01.064][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-15 08:04:01.064][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2022-10-15 08:04:01.065][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2022-10-15 08:04:01.066][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2022-10-15 08:04:01.067][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2022-10-15 08:04:01.068][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2022-10-15 08:04:01.069][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2022-10-15 08:04:01.070][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2022-10-15 08:04:01.071][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2022-10-15 08:04:01.072][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2022-10-15 08:04:01.077][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2022-10-15 08:04:01.078][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2022-10-15 08:04:01.079][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2022-10-15 08:04:01.080][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2022-10-15 08:04:01.081][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2022-10-15 08:04:01.082][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2022-10-15 08:04:01.083][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2022-10-15 08:04:01.084][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2022-10-15 08:04:01.085][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2022-10-15 08:04:01.085][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2022-10-15 08:04:01.086][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2022-10-15 08:04:01.087][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2022-10-15 08:04:01.088][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2022-10-15 08:04:01.089][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2022-10-15 08:04:01.090][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2022-10-15 08:04:01.091][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2022-10-15 08:04:01.092][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2022-10-15 08:04:01.093][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2022-10-15 08:04:01.094][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2022-10-15 08:04:01.095][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2022-10-15 08:04:01.096][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2022-10-15 08:04:01.097][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2022-10-15 08:04:01.098][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2022-10-15 08:04:01.099][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2022-10-15 08:04:01.100][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2022-10-15 08:04:01.101][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2022-10-15 08:04:01.102][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2022-10-15 08:04:01.103][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2022-10-15 08:04:01.104][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2022-10-15 08:04:01.105][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2022-10-15 08:04:01.106][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2022-10-15 08:04:01.107][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2022-10-15 08:04:01.108][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2022-10-15 08:04:01.109][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2022-10-15 08:04:01.110][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2022-10-15 08:04:01.111][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2022-10-15 08:04:01.112][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2022-10-15 08:04:01.113][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2022-10-15 08:04:01.114][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2022-10-15 08:04:01.115][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2022-10-15 08:04:01.116][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2022-10-15 08:04:01.117][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2022-10-15 08:04:01.118][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2022-10-15 08:04:01.119][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2022-10-15 08:04:01.120][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2022-10-15 08:04:01.121][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2022-10-15 08:04:01.122][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2022-10-15 08:04:01.123][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2022-10-15 08:04:01.124][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2022-10-15 08:04:01.125][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2022-10-15 08:04:01.126][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2022-10-15 08:04:01.127][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2022-10-15 08:04:01.128][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2022-10-15 08:04:01.129][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2022-10-15 08:04:01.130][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2022-10-15 08:04:01.131][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2022-10-15 08:04:01.132][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2022-10-15 08:04:01.133][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2022-10-15 08:04:01.134][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2022-10-15 08:04:01.135][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2022-10-15 08:04:01.136][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2022-10-15 08:04:01.137][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2022-10-15 08:04:01.138][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2022-10-15 08:04:01.139][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2022-10-15 08:04:01.140][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2022-10-15 08:04:01.141][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2022-10-15 08:04:01.142][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2022-10-15 08:04:01.143][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2022-10-15 08:04:01.144][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2022-10-15 08:04:01.145][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2022-10-15 08:04:01.146][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2022-10-15 08:04:01.147][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2022-10-15 08:04:01.148][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2022-10-15 08:04:01.149][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2022-10-15 08:04:01.150][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2022-10-15 08:04:01.151][initialize] This is biodb version 1.4.2.
biodb.DEBUG[2022-10-15 08:04:01.155][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2022-10-15 08:04:01.156][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2022-10-15 08:04:01.157][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-15 08:04:01.157][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2022-10-15 08:04:01.158][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-15 08:04:01.159][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-15 08:04:01.159][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-15 08:04:01.160][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-15 08:04:01.160][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-15 08:04:01.161][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-15 08:04:01.162][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-15 08:04:01.162][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-15 08:04:01.163][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-15 08:04:01.164][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-15 08:04:01.164][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-15 08:04:01.165][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-15 08:04:01.166][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-15 08:04:01.166][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-15 08:04:01.167][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-15 08:04:01.167][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-15 08:04:01.168][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-15 08:04:01.169][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-15 08:04:01.169][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-15 08:04:01.170][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-15 08:04:01.171][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-15 08:04:01.171][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-15 08:04:01.172][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-15 08:04:01.173][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-15 08:04:01.173][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-15 08:04:01.174][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-15 08:04:01.175][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-15 08:04:01.175][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-15 08:04:01.176][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-15 08:04:01.176][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-15 08:04:01.177][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-15 08:04:01.178][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-15 08:04:01.178][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-15 08:04:01.179][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-15 08:04:01.180][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-15 08:04:01.180][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-15 08:04:01.181][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-15 08:04:01.182][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-15 08:04:01.182][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-15 08:04:01.183][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-15 08:04:01.184][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-15 08:04:01.184][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-15 08:04:01.185][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[2022-10-15 08:04:01.186][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-15 08:04:01.186][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-15 08:04:01.187][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-15 08:04:01.188][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-15 08:04:01.188][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-15 08:04:01.189][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-15 08:04:01.190][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-15 08:04:01.190][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-15 08:04:01.191][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-15 08:04:01.192][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-15 08:04:01.192][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-15 08:04:01.193][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-15 08:04:01.194][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-15 08:04:01.194][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-15 08:04:01.195][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-15 08:04:01.196][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-15 08:04:01.196][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-15 08:04:01.197][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-15 08:04:01.198][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-15 08:04:01.198][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-15 08:04:01.199][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-15 08:04:01.200][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-15 08:04:01.200][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-15 08:04:01.201][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-15 08:04:01.202][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-15 08:04:01.202][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-15 08:04:01.203][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-15 08:04:01.204][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-15 08:04:01.204][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-15 08:04:01.205][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-15 08:04:01.205][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-15 08:04:01.206][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-15 08:04:01.207][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-15 08:04:01.207][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-15 08:04:01.208][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-15 08:04:01.209][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-15 08:04:01.209][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-15 08:04:01.210][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-15 08:04:01.211][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-15 08:04:01.211][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-15 08:04:01.212][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-15 08:04:01.213][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-15 08:04:01.214][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-15 08:04:01.214][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-15 08:04:01.215][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-15 08:04:01.215][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-15 08:04:01.216][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-15 08:04:01.217][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-15 08:04:01.217][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-15 08:04:01.218][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-15 08:04:01.219][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-15 08:04:01.219][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-15 08:04:01.220][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-15 08:04:01.221][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-15 08:04:01.221][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-15 08:04:01.222][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-15 08:04:01.223][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-15 08:04:01.223][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-15 08:04:01.224][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-15 08:04:01.225][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-15 08:04:01.225][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-15 08:04:01.226][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-15 08:04:01.227][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-15 08:04:01.227][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-15 08:04:01.228][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-15 08:04:01.229][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-15 08:04:01.229][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-15 08:04:01.230][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-15 08:04:01.231][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-15 08:04:01.231][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-15 08:04:01.232][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-15 08:04:01.233][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-15 08:04:01.237][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-15 08:04:01.237][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-15 08:04:01.238][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-15 08:04:01.239][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-15 08:04:01.239][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-15 08:04:01.241][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.15-bioc-longtests/meat/biodbExpasy.Rcheck/biodbExpasy/definitions.yml".
biodb.DEBUG[2022-10-15 08:04:01.242][self$getDbsInfo()$define] Define connector expasy.enzyme.
biodb.DEBUG[2022-10-15 08:04:01.243][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2022-10-15 08:04:01.244][self$setPropertyValue] Setting property "description" to "Write here the description of this database.".
biodb.DEBUG[2022-10-15 08:04:01.244][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2022-10-15 08:04:01.245][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2022-10-15 08:04:01.246][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2022-10-15 08:04:01.247][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2022-10-15 08:04:01.247][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2022-10-15 08:04:01.248][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2022-10-15 08:04:01.249][self$setPropertyValue] Setting property "entry.content.type" to "txt".
biodb.DEBUG[2022-10-15 08:04:01.250][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2022-10-15 08:04:01.250][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2022-10-15 08:04:01.251][self$setPropertyValue] Setting property "name" to "Expasy ENZYME database.".
biodb.DEBUG[2022-10-15 08:04:01.252][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2022-10-15 08:04:01.252][self$setPropertyValue] Setting property "parsing.expr" to "^ID\s+([0-9.]+)$".
biodb.DEBUG[2022-10-15 08:04:01.252][self$setPropertyValue] Setting property "parsing.expr" to "^CA\s+(.+?)\.?$".
biodb.DEBUG[2022-10-15 08:04:01.252][self$setPropertyValue] Setting property "parsing.expr" to "^CF\s+(.+?)\.?$".
biodb.DEBUG[2022-10-15 08:04:01.252][self$setPropertyValue] Setting property "parsing.expr" to "^DE\s+(.+?)\.?$".
biodb.DEBUG[2022-10-15 08:04:01.253][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2022-10-15 08:04:01.254][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2022-10-15 08:04:01.255][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2022-10-15 08:04:01.256][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-10-15 08:04:01.256][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-10-15 08:04:01.257][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2022-10-15 08:04:01.258][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-10-15 08:04:01.258][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-10-15 08:04:01.259][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2022-10-15 08:04:01.260][self$setPropertyValue] Setting property "urls" to "https://enzyme.expasy.org/".
biodb.DEBUG[2022-10-15 08:04:01.260][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2022-10-15 08:04:01.261][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2022-10-15 08:04:01.262][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2022-10-15 08:04:01.263][self$setPropertyValue]
biodb.DEBUG[2022-10-15 08:04:01.264][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2022-10-15 08:04:01.266][super$initialize] Initialize connector expasy.enzyme.
biodb.DEBUG[2022-10-15 08:04:01.267][super$initialize] Register connector expasy.enzyme with the request scheduler
biodb.DEBUG[2022-10-15 08:04:01.268][private$bdb$getRequestScheduler()$re ...] Register connector expasy.enzyme.
biodb.DEBUG[2022-10-15 08:04:01.269][private$addConnectorRules] Create new rule for URL "enzyme.expasy.org" of connector "expasy.enzyme".
biodb.DEBUG[2022-10-15 08:04:01.270][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2022-10-15 08:04:01.270][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2022-10-15 08:04:01.271][biodb$getFactory()$createConn] Creating new connector expasy.enzyme for database class expasy.enzyme .
biodb.INFO [2022-10-15 08:04:01.272][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2022-10-15 08:04:01.273][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector expasy.enzyme from the request scheduler
biodb.INFO [2022-10-15 08:04:01.274][self$deleteConn] Connector "expasy.enzyme" deleted.
biodb.DEBUG[2022-10-15 08:04:01.274][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2022-10-15 08:04:01.275][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-15 08:04:01.275][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-15 08:04:01.276][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-15 08:04:01.277][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-15 08:04:01.277][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2022-10-15 08:04:01.278][FUN] Functions in observer 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 
  3.773   0.220  13.538

'R CMD check' output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --test-dir=longtests --no-stop-on-test-error --no-codoc --no-examples --no-manual --ignore-vignettes --check-subdirs=no biodbExpasy_1.0.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.15-bioc-longtests/meat/biodbExpasy.Rcheck’
* using R version 4.2.1 (2022-06-23)
* using platform: x86_64-pc-linux-gnu (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 ‘1.0.0’
* 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
  ‘/home/biocbuild/bbs-3.15-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)