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
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CHECK results for biodbMirbase on nebbiolo1


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

raw results

Package 10/26HostnameOS / ArchCHECK
biodbMirbase 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/biodbMirbase
git_branch: RELEASE_3_15
git_last_commit: 568294f
git_last_commit_date: 2022-04-26 12:22:00 -0400 (Tue, 26 Apr 2022)
nebbiolo1Linux (Ubuntu 20.04.5 LTS) / x86_64  OK  

Summary

Package: biodbMirbase
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 biodbMirbase_1.0.0.tar.gz
StartedAt: 2022-10-15 08:06:53 -0400 (Sat, 15 Oct 2022)
EndedAt: 2022-10-15 08:07:31 -0400 (Sat, 15 Oct 2022)
EllapsedTime: 38.0 seconds
RetCode: 0
Status:   OK  
CheckDir: biodbMirbase.Rcheck
Warnings: 0

Tests output

biodbMirbase.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)

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> # Script needed to run testthat automatically from ‘R CMD check’. See
> # testthat::test_dir documentation.
> library(testthat)
> library(biodbMirbase)
> Sys.setenv(TESTTHAT_REPORTER="summary")
> Sys.setenv(BIODB_LOG_DST="console")
> test_check("biodbMirbase")
biodb.INFO [2022-10-15 08:07:20.800][biodb::testContext]
biodb.INFO [2022-10-15 08:07:20.802][biodb::testContext] ********************************************************************************
biodb.INFO [2022-10-15 08:07:20.809][biodb::testContext] Test context - Generic long tests
biodb.INFO [2022-10-15 08:07:20.810][biodb::testContext] ********************************************************************************
biodb.INFO [2022-10-15 08:07:20.811][biodb::testContext]
biodb.INFO [2022-10-15 08:07:20.823][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.4.2.
biodb.DEBUG[2022-10-15 08:07:20.824][self$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.15-bioc/R/library/biodb/definitions.yml".
biodb.DEBUG[2022-10-15 08:07:20.838][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2022-10-15 08:07:20.839][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2022-10-15 08:07:20.840][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2022-10-15 08:07:20.841][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-15 08:07:20.841][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-15 08:07:20.842][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-15 08:07:20.843][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2022-10-15 08:07:20.854][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2022-10-15 08:07:20.855][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-15 08:07:20.855][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-15 08:07:20.856][FUN] Functions in observer BiodbConfig: [21]: ".__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 08:07:20.857][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2022-10-15 08:07:20.857][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2022-10-15 08:07:20.858][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-15 08:07:20.859][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-15 08:07:20.859][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-15 08:07:20.860][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2022-10-15 08:07:20.861][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2022-10-15 08:07:20.862][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2022-10-15 08:07:20.862][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-15 08:07:20.863][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-15 08:07:20.864][FUN] Functions in observer BiodbConfig: [21]: ".__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 08:07:20.864][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2022-10-15 08:07:20.865][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2022-10-15 08:07:20.866][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2022-10-15 08:07:20.866][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-15 08:07:20.867][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-15 08:07:20.868][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-15 08:07:20.868][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2022-10-15 08:07:20.869][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2022-10-15 08:07:20.870][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-15 08:07:20.870][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-15 08:07:20.871][FUN] Functions in observer BiodbConfig: [21]: ".__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 08:07:20.872][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2022-10-15 08:07:20.873][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2022-10-15 08:07:20.873][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2022-10-15 08:07:20.874][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-15 08:07:20.875][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-15 08:07:20.875][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-15 08:07:20.876][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2022-10-15 08:07:20.877][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2022-10-15 08:07:20.877][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-15 08:07:20.878][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-15 08:07:20.879][FUN] Functions in observer BiodbConfig: [21]: ".__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 08:07:20.879][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2022-10-15 08:07:20.880][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2022-10-15 08:07:20.881][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2022-10-15 08:07:20.881][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-15 08:07:20.882][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-15 08:07:20.883][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-15 08:07:20.883][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2022-10-15 08:07:20.884][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2022-10-15 08:07:20.885][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2022-10-15 08:07:20.886][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2022-10-15 08:07:20.886][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2022-10-15 08:07:20.887][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2022-10-15 08:07:20.888][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-15 08:07:20.888][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-15 08:07:20.889][FUN] Functions in observer BiodbConfig: [21]: ".__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 08:07:20.890][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2022-10-15 08:07:20.890][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2022-10-15 08:07:20.891][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-15 08:07:20.892][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-15 08:07:20.892][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-15 08:07:20.893][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2022-10-15 08:07:20.894][self$set] Set key entries.sep to "|".
biodb.DEBUG[2022-10-15 08:07:20.894][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-15 08:07:20.895][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-15 08:07:20.896][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-15 08:07:20.896][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2022-10-15 08:07:20.897][self$set] Set key offline to FALSE.
biodb.DEBUG[2022-10-15 08:07:20.898][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-15 08:07:20.898][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-15 08:07:20.899][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-15 08:07:20.900][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2022-10-15 08:07:20.900][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2022-10-15 08:07:20.901][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-15 08:07:20.902][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-15 08:07:20.902][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-15 08:07:20.903][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2022-10-15 08:07:20.904][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2022-10-15 08:07:20.904][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-15 08:07:20.905][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-15 08:07:20.906][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-15 08:07:20.906][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2022-10-15 08:07:20.907][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2022-10-15 08:07:20.912][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2022-10-15 08:07:20.913][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-15 08:07:20.913][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-15 08:07:20.914][FUN] Functions in observer BiodbConfig: [21]: ".__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 08:07:20.915][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2022-10-15 08:07:20.915][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2022-10-15 08:07:20.916][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2022-10-15 08:07:20.917][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-15 08:07:20.917][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-15 08:07:20.918][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-15 08:07:20.921][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2022-10-15 08:07:20.944][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2022-10-15 08:07:20.954][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2022-10-15 08:07:20.954][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2022-10-15 08:07:20.955][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2022-10-15 08:07:20.956][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2022-10-15 08:07:20.957][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2022-10-15 08:07:20.957][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2022-10-15 08:07:20.958][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2022-10-15 08:07:20.959][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2022-10-15 08:07:20.960][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2022-10-15 08:07:20.960][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2022-10-15 08:07:20.961][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2022-10-15 08:07:20.962][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2022-10-15 08:07:20.962][self$setPropertyValue]
biodb.DEBUG[2022-10-15 08:07:20.963][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2022-10-15 08:07:20.964][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2022-10-15 08:07:20.964][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2022-10-15 08:07:20.964][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2022-10-15 08:07:20.964][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2022-10-15 08:07:20.964][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2022-10-15 08:07:20.965][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2022-10-15 08:07:20.965][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-10-15 08:07:20.966][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-10-15 08:07:20.971][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2022-10-15 08:07:20.971][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-10-15 08:07:20.972][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-10-15 08:07:20.973][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2022-10-15 08:07:20.973][self$setPropertyValue]
biodb.DEBUG[2022-10-15 08:07:20.974][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2022-10-15 08:07:20.975][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2022-10-15 08:07:20.975][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2022-10-15 08:07:20.976][self$setPropertyValue]
biodb.DEBUG[2022-10-15 08:07:20.977][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2022-10-15 08:07:20.978][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2022-10-15 08:07:20.979][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2022-10-15 08:07:20.979][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2022-10-15 08:07:20.980][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2022-10-15 08:07:20.981][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2022-10-15 08:07:20.982][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2022-10-15 08:07:20.982][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2022-10-15 08:07:20.983][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2022-10-15 08:07:20.984][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2022-10-15 08:07:20.984][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2022-10-15 08:07:20.985][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2022-10-15 08:07:20.986][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2022-10-15 08:07:20.987][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2022-10-15 08:07:20.987][self$setPropertyValue]
biodb.DEBUG[2022-10-15 08:07:20.988][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2022-10-15 08:07:20.989][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2022-10-15 08:07:20.989][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2022-10-15 08:07:20.989][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2022-10-15 08:07:20.989][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2022-10-15 08:07:20.989][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2022-10-15 08:07:20.989][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2022-10-15 08:07:20.990][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-10-15 08:07:20.991][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-10-15 08:07:20.992][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2022-10-15 08:07:20.992][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-10-15 08:07:20.993][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-10-15 08:07:20.993][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2022-10-15 08:07:20.994][self$setPropertyValue]
biodb.DEBUG[2022-10-15 08:07:20.995][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2022-10-15 08:07:20.996][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2022-10-15 08:07:20.996][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2022-10-15 08:07:20.997][self$setPropertyValue]
biodb.DEBUG[2022-10-15 08:07:20.998][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2022-10-15 08:07:20.999][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2022-10-15 08:07:21.000][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2022-10-15 08:07:21.001][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2022-10-15 08:07:21.001][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2022-10-15 08:07:21.002][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2022-10-15 08:07:21.003][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2022-10-15 08:07:21.003][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2022-10-15 08:07:21.004][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2022-10-15 08:07:21.005][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2022-10-15 08:07:21.006][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2022-10-15 08:07:21.006][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2022-10-15 08:07:21.007][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2022-10-15 08:07:21.008][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2022-10-15 08:07:21.008][self$setPropertyValue]
biodb.DEBUG[2022-10-15 08:07:21.009][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2022-10-15 08:07:21.010][self$setPropertyValue]
biodb.DEBUG[2022-10-15 08:07:21.011][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2022-10-15 08:07:21.011][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-10-15 08:07:21.012][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-10-15 08:07:21.013][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2022-10-15 08:07:21.013][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-10-15 08:07:21.014][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-10-15 08:07:21.015][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2022-10-15 08:07:21.015][self$setPropertyValue]
biodb.DEBUG[2022-10-15 08:07:21.016][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2022-10-15 08:07:21.017][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2022-10-15 08:07:21.017][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2022-10-15 08:07:21.018][self$setPropertyValue]
biodb.DEBUG[2022-10-15 08:07:21.019][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2022-10-15 08:07:21.020][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2022-10-15 08:07:21.021][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2022-10-15 08:07:21.022][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2022-10-15 08:07:21.022][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2022-10-15 08:07:21.023][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2022-10-15 08:07:21.024][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2022-10-15 08:07:21.024][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2022-10-15 08:07:21.025][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2022-10-15 08:07:21.026][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2022-10-15 08:07:21.027][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2022-10-15 08:07:21.027][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2022-10-15 08:07:21.028][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2022-10-15 08:07:21.029][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2022-10-15 08:07:21.029][self$setPropertyValue]
biodb.DEBUG[2022-10-15 08:07:21.030][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2022-10-15 08:07:21.031][self$setPropertyValue]
biodb.DEBUG[2022-10-15 08:07:21.032][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2022-10-15 08:07:21.032][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-10-15 08:07:21.033][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-10-15 08:07:21.034][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2022-10-15 08:07:21.034][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-10-15 08:07:21.035][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-10-15 08:07:21.036][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2022-10-15 08:07:21.036][self$setPropertyValue]
biodb.DEBUG[2022-10-15 08:07:21.037][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2022-10-15 08:07:21.038][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2022-10-15 08:07:21.038][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2022-10-15 08:07:21.039][self$setPropertyValue]
biodb.DEBUG[2022-10-15 08:07:21.042][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2022-10-15 08:07:21.043][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2022-10-15 08:07:21.043][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-15 08:07:21.044][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-15 08:07:21.044][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-15 08:07:21.045][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 08:07:21.046][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-15 08:07:21.046][FUN] Functions in observer BiodbConfig: [21]: ".__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 08:07:21.047][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-15 08:07:21.048][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-15 08:07:21.048][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 08:07:21.049][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-15 08:07:21.050][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-15 08:07:21.050][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-15 08:07:21.051][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-15 08:07:21.052][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 08:07:21.052][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-15 08:07:21.053][FUN] Functions in observer BiodbConfig: [21]: ".__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 08:07:21.054][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-15 08:07:21.054][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-15 08:07:21.055][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 08:07:21.055][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-15 08:07:21.056][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-15 08:07:21.057][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-15 08:07:21.057][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-15 08:07:21.058][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 08:07:21.059][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-15 08:07:21.059][FUN] Functions in observer BiodbConfig: [21]: ".__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 08:07:21.060][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-15 08:07:21.061][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-15 08:07:21.061][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 08:07:21.062][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-15 08:07:21.063][FUN] Functions in observer BiodbConfig: [21]: ".__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 08:07:21.063][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-15 08:07:21.064][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-15 08:07:21.064][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-15 08:07:21.065][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-15 08:07:21.066][FUN] Functions in observer BiodbConfig: [21]: ".__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 08:07:21.066][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-15 08:07:21.067][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-15 08:07:21.068][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 08:07:21.068][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-15 08:07:21.069][FUN] Functions in observer BiodbConfig: [21]: ".__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 08:07:21.070][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-15 08:07:21.070][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-15 08:07:21.071][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-15 08:07:21.072][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-15 08:07:21.072][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-15 08:07:21.073][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-15 08:07:21.073][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-15 08:07:21.074][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 08:07:21.075][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-15 08:07:21.075][FUN] Functions in observer BiodbConfig: [21]: ".__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 08:07:21.076][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-15 08:07:21.077][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-15 08:07:21.077][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 08:07:21.078][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-15 08:07:21.079][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 08:07:21.079][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-15 08:07:21.080][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-15 08:07:21.081][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 08:07:21.081][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-15 08:07:21.082][FUN] Functions in observer BiodbConfig: [21]: ".__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 08:07:21.083][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-15 08:07:21.083][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-15 08:07:21.084][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 08:07:21.084][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-15 08:07:21.085][FUN] Functions in observer BiodbConfig: [21]: ".__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 08:07:21.086][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-15 08:07:21.086][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-15 08:07:21.087][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 08:07:21.088][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-15 08:07:21.088][FUN] Functions in observer BiodbConfig: [21]: ".__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 08:07:21.089][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-15 08:07:21.090][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-15 08:07:21.090][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 08:07:21.091][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-15 08:07:21.091][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-15 08:07:21.092][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-15 08:07:21.093][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-15 08:07:21.093][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-15 08:07:21.094][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-15 08:07:21.095][FUN] Functions in observer BiodbConfig: [21]: ".__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 08:07:21.095][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-15 08:07:21.096][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-15 08:07:21.097][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 08:07:21.097][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-15 08:07:21.098][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 08:07:21.099][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2022-10-15 08:07:21.102][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2022-10-15 08:07:21.103][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2022-10-15 08:07:21.104][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2022-10-15 08:07:21.108][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2022-10-15 08:07:21.109][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2022-10-15 08:07:21.110][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2022-10-15 08:07:21.111][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2022-10-15 08:07:21.112][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2022-10-15 08:07:21.113][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2022-10-15 08:07:21.114][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2022-10-15 08:07:21.115][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2022-10-15 08:07:21.116][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2022-10-15 08:07:21.117][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2022-10-15 08:07:21.118][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2022-10-15 08:07:21.119][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2022-10-15 08:07:21.120][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2022-10-15 08:07:21.121][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2022-10-15 08:07:21.122][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2022-10-15 08:07:21.123][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2022-10-15 08:07:21.124][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2022-10-15 08:07:21.125][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2022-10-15 08:07:21.126][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2022-10-15 08:07:21.127][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2022-10-15 08:07:21.128][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2022-10-15 08:07:21.129][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2022-10-15 08:07:21.130][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2022-10-15 08:07:21.131][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2022-10-15 08:07:21.132][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2022-10-15 08:07:21.132][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2022-10-15 08:07:21.133][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2022-10-15 08:07:21.134][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2022-10-15 08:07:21.135][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2022-10-15 08:07:21.136][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2022-10-15 08:07:21.137][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2022-10-15 08:07:21.138][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2022-10-15 08:07:21.139][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2022-10-15 08:07:21.140][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2022-10-15 08:07:21.141][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2022-10-15 08:07:21.142][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2022-10-15 08:07:21.143][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2022-10-15 08:07:21.144][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2022-10-15 08:07:21.145][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2022-10-15 08:07:21.146][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2022-10-15 08:07:21.147][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2022-10-15 08:07:21.148][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2022-10-15 08:07:21.149][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2022-10-15 08:07:21.150][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2022-10-15 08:07:21.151][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2022-10-15 08:07:21.152][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2022-10-15 08:07:21.153][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2022-10-15 08:07:21.154][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2022-10-15 08:07:21.155][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2022-10-15 08:07:21.156][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2022-10-15 08:07:21.157][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2022-10-15 08:07:21.158][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2022-10-15 08:07:21.159][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2022-10-15 08:07:21.160][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2022-10-15 08:07:21.161][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2022-10-15 08:07:21.162][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2022-10-15 08:07:21.163][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2022-10-15 08:07:21.164][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2022-10-15 08:07:21.165][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2022-10-15 08:07:21.166][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2022-10-15 08:07:21.167][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2022-10-15 08:07:21.168][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2022-10-15 08:07:21.169][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2022-10-15 08:07:21.170][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2022-10-15 08:07:21.171][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2022-10-15 08:07:21.172][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2022-10-15 08:07:21.173][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2022-10-15 08:07:21.174][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2022-10-15 08:07:21.175][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2022-10-15 08:07:21.176][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2022-10-15 08:07:21.177][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2022-10-15 08:07:21.178][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2022-10-15 08:07:21.179][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2022-10-15 08:07:21.180][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2022-10-15 08:07:21.181][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2022-10-15 08:07:21.182][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2022-10-15 08:07:21.183][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2022-10-15 08:07:21.184][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2022-10-15 08:07:21.185][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2022-10-15 08:07:21.189][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2022-10-15 08:07:21.190][initialize] This is biodb version 1.4.2.
biodb.DEBUG[2022-10-15 08:07:21.192][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2022-10-15 08:07:21.193][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2022-10-15 08:07:21.193][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 08:07:21.194][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2022-10-15 08:07:21.195][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-15 08:07:21.198][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-15 08:07:21.198][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-15 08:07:21.199][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-15 08:07:21.200][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-15 08:07:21.200][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 08:07:21.201][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-15 08:07:21.202][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-15 08:07:21.202][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-15 08:07:21.203][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-15 08:07:21.203][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-15 08:07:21.204][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-15 08:07:21.205][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-15 08:07:21.205][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-15 08:07:21.206][FUN] Functions in observer BiodbConfig: [21]: ".__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 08:07:21.207][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-15 08:07:21.207][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-15 08:07:21.208][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-15 08:07:21.209][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-15 08:07:21.209][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 08:07:21.210][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-15 08:07:21.211][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-15 08:07:21.211][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-15 08:07:21.212][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-15 08:07:21.212][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-15 08:07:21.213][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-15 08:07:21.214][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 08:07:21.214][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-15 08:07:21.215][FUN] Functions in observer BiodbConfig: [21]: ".__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 08:07:21.216][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-15 08:07:21.216][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-15 08:07:21.217][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-15 08:07:21.218][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-15 08:07:21.218][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-15 08:07:21.219][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-15 08:07:21.220][FUN] Functions in observer BiodbConfig: [21]: ".__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 08:07:21.220][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-15 08:07:21.221][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-15 08:07:21.221][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-15 08:07:21.222][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-15 08:07:21.223][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 08:07:21.223][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-15 08:07:21.224][FUN] Functions in observer BiodbConfig: [21]: ".__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 08:07:21.225][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-15 08:07:21.225][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-15 08:07:21.226][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-15 08:07:21.227][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-15 08:07:21.227][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 08:07:21.228][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-15 08:07:21.229][FUN] Functions in observer BiodbConfig: [21]: ".__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 08:07:21.229][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-15 08:07:21.230][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-15 08:07:21.230][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-15 08:07:21.231][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-15 08:07:21.232][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 08:07:21.232][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-15 08:07:21.233][FUN] Functions in observer BiodbConfig: [21]: ".__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 08:07:21.237][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-15 08:07:21.238][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-15 08:07:21.239][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-15 08:07:21.239][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-15 08:07:21.240][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 08:07:21.240][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-15 08:07:21.241][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-15 08:07:21.242][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-15 08:07:21.242][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-15 08:07:21.243][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-15 08:07:21.244][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-15 08:07:21.244][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 08:07:21.245][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-15 08:07:21.245][FUN] Functions in observer BiodbConfig: [21]: ".__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 08:07:21.246][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-15 08:07:21.247][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-15 08:07:21.247][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-15 08:07:21.248][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-15 08:07:21.249][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-15 08:07:21.249][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-15 08:07:21.250][FUN] Functions in observer BiodbConfig: [21]: ".__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 08:07:21.251][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-15 08:07:21.251][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-15 08:07:21.252][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-15 08:07:21.252][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-15 08:07:21.253][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 08:07:21.254][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-15 08:07:21.254][FUN] Functions in observer BiodbConfig: [21]: ".__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 08:07:21.255][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-15 08:07:21.256][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-15 08:07:21.256][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-15 08:07:21.257][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-15 08:07:21.257][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-15 08:07:21.258][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-15 08:07:21.259][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-15 08:07:21.259][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-15 08:07:21.260][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-15 08:07:21.261][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-15 08:07:21.261][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-15 08:07:21.262][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-15 08:07:21.263][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-15 08:07:21.263][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-15 08:07:21.264][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-15 08:07:21.265][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-15 08:07:21.265][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-15 08:07:21.266][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-15 08:07:21.267][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 08:07:21.267][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-15 08:07:21.268][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 08:07:21.269][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-15 08:07:21.269][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-15 08:07:21.270][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-15 08:07:21.270][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-15 08:07:21.271][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 08:07:21.272][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-15 08:07:21.272][FUN] Functions in observer BiodbConfig: [21]: ".__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 08:07:21.273][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-15 08:07:21.274][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-15 08:07:21.274][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-15 08:07:21.275][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-15 08:07:21.276][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 08:07:21.276][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-15 08:07:21.277][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 08:07:21.278][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.15-bioc-longtests/meat/biodbMirbase.Rcheck/biodbMirbase/definitions.yml".
biodb.DEBUG[2022-10-15 08:07:21.284][self$getDbsInfo()$define] Define connector mirbase.mature.
biodb.DEBUG[2022-10-15 08:07:21.286][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2022-10-15 08:07:21.286][self$setPropertyValue] Setting property "description" to "Write here the description of this database.".
biodb.DEBUG[2022-10-15 08:07:21.287][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2022-10-15 08:07:21.288][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2022-10-15 08:07:21.289][self$setPropertyValue] Setting property "downloadable" to "TRUE".
biodb.DEBUG[2022-10-15 08:07:21.289][self$setPropertyValue] Setting property "dwnld.ext" to "gz".
biodb.DEBUG[2022-10-15 08:07:21.290][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2022-10-15 08:07:21.291][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2022-10-15 08:07:21.291][self$setPropertyValue] Setting property "entry.content.type" to "txt".
biodb.DEBUG[2022-10-15 08:07:21.292][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2022-10-15 08:07:21.293][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2022-10-15 08:07:21.294][self$setPropertyValue] Setting property "name" to "miRBase mature database".
biodb.DEBUG[2022-10-15 08:07:21.294][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2022-10-15 08:07:21.295][self$setPropertyValue] Setting property "parsing.expr" to "^>[^ ]+ *(MIMAT[0-9]+) .*$".
biodb.DEBUG[2022-10-15 08:07:21.295][self$setPropertyValue] Setting property "parsing.expr" to "^>[^ ]+ *MIMAT[0-9]+ (.*)$".
biodb.DEBUG[2022-10-15 08:07:21.295][self$setPropertyValue] Setting property "parsing.expr" to "^>([^ ]+) *MIMAT[0-9]+ .*$".
biodb.DEBUG[2022-10-15 08:07:21.295][self$setPropertyValue] Setting property "parsing.expr" to "^([ACGU]+)$".
biodb.DEBUG[2022-10-15 08:07:21.296][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2022-10-15 08:07:21.297][self$setPropertyValue]
biodb.DEBUG[2022-10-15 08:07:21.297][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2022-10-15 08:07:21.298][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-10-15 08:07:21.299][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-10-15 08:07:21.299][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2022-10-15 08:07:21.300][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-10-15 08:07:21.301][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-10-15 08:07:21.301][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2022-10-15 08:07:21.302][self$setPropertyValue] Setting property "urls" to "http://www.mirbase.org/".
biodb.DEBUG[2022-10-15 08:07:21.302][self$setPropertyValue] Setting property "urls" to "https://www.mirbase.org/ftp/CURRENT/mature.fa.gz".
biodb.DEBUG[2022-10-15 08:07:21.303][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2022-10-15 08:07:21.303][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2022-10-15 08:07:21.304][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2022-10-15 08:07:21.305][self$setPropertyValue]
biodb.DEBUG[2022-10-15 08:07:21.309][self$getEntryFields()$define] Define field mirbase.mature.id.
biodb.DEBUG[2022-10-15 08:07:21.325][initialize] Initialize connector mirbase.mature.
biodb.DEBUG[2022-10-15 08:07:21.326][initialize] Register connector mirbase.mature with the request scheduler
biodb.DEBUG[2022-10-15 08:07:21.329][private$bdb$getRequestScheduler()$re ...] Register connector mirbase.mature.
biodb.DEBUG[2022-10-15 08:07:21.332][private$addConnectorRules] Create new rule for URL "www.mirbase.org" of connector "mirbase.mature".
biodb.DEBUG[2022-10-15 08:07:21.335][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2022-10-15 08:07:21.336][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2022-10-15 08:07:21.336][rule$addConnector] Connector "mirbase.mature" is already listed in rule "www.mirbase.org".
biodb.DEBUG[2022-10-15 08:07:21.337][biodb$getFactory()$createConn] Creating new connector mirbase.mature for database class mirbase.mature .
biodb.INFO [2022-10-15 08:07:21.349][biodb::testThat]
biodb.INFO [2022-10-15 08:07:21.349][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2022-10-15 08:07:21.350][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2022-10-15 08:07:21.351][biodb::testThat]
biodb.TRACE[2022-10-15 08:07:21.353][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/bbs-3.15-bioc-longtests/meat/biodbMirbase.Rcheck/biodbMirbase/testref/entry-mirbase.mature-MIMAT0000433-content.txt".
biodb.DEBUG[2022-10-15 08:07:21.356][biodb$getFactory()$createEntryFromCo ...] Creating miRBase mature database entries from 1 content(s).
biodb.DEBUG[2022-10-15 08:07:21.359][biodb$getFactory()$createEntryFromCo ...] Parsing 1 miRBase mature database entries.
biodb.DEBUG[2022-10-15 08:07:21.365][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-15 08:07:21.365][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-15 08:07:21.366][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-15 08:07:21.375][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-15 08:07:21.376][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 08:07:21.376][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-15 08:07:21.377][FUN] Functions in observer BiodbConfig: [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 08:07:21.410][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-15 08:07:21.411][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-15 08:07:21.412][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:07:21.413][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:07:21.431][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2022-10-15 08:07:21.439][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2022-10-15 08:07:21.440][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:07:21.441][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:07:21.444][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-15 08:07:21.444][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-15 08:07:21.445][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:07:21.446][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:07:21.448][self$getBiodb()$getEntryFields()$get] Asked field names are: sequence.
biodb.TRACE[2022-10-15 08:07:21.449][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2022-10-15 08:07:21.450][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:07:21.451][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:07:21.453][self$getBiodb()$getEntryFields()$get] Asked field names are: mirbase.mature.id.
biodb.TRACE[2022-10-15 08:07:21.454][self$getBiodb()$getEntryFields()$get] Realnames of fields are: mirbase.mature.id.
biodb.TRACE[2022-10-15 08:07:21.455][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:07:21.455][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:07:21.456][self$getBiodb()$getEntryFields()$get] Asked field names are: mirbase.mature.id.
biodb.TRACE[2022-10-15 08:07:21.457][self$getBiodb()$getEntryFields()$get] Realnames of fields are: mirbase.mature.id.
biodb.TRACE[2022-10-15 08:07:21.458][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:07:21.458][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:07:21.459][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-15 08:07:21.460][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-15 08:07:21.460][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:07:21.461][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:07:21.462][self$getBiodb()$getEntryFields()$get] Asked field names are: mirbase.mature.id.
biodb.TRACE[2022-10-15 08:07:21.463][self$getBiodb()$getEntryFields()$get] Realnames of fields are: mirbase.mature.id.
biodb.TRACE[2022-10-15 08:07:21.463][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:07:21.464][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:07:21.465][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-15 08:07:21.465][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-15 08:07:21.466][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:07:21.467][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:07:21.468][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-15 08:07:21.468][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-15 08:07:21.469][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:07:21.470][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:07:21.471][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-15 08:07:21.471][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-15 08:07:21.472][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:07:21.473][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:07:21.496][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-15 08:07:21.497][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-15 08:07:21.497][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:07:21.498][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:07:21.499][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-15 08:07:21.503][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-15 08:07:21.504][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:07:21.505][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:07:21.505][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-15 08:07:21.506][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-15 08:07:21.507][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:07:21.508][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-10-15 08:07:21.508][biodb$getFactory()$createEntryFromCo ...] Accession numbers: MIMAT0000433.
biodb.TRACE[2022-10-15 08:07:21.512][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2022-10-15 08:07:21.513][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2022-10-15 08:07:21.513][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:07:21.514][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:07:21.515][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2022-10-15 08:07:21.515][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2022-10-15 08:07:21.516][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:07:21.517][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:07:21.518][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2022-10-15 08:07:21.518][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2022-10-15 08:07:21.519][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:07:21.520][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:07:21.520][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2022-10-15 08:07:21.521][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2022-10-15 08:07:21.522][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:07:21.522][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:07:21.533][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-15 08:07:21.534][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-15 08:07:21.535][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:07:21.535][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:07:21.544][self$getBiodb()$getEntryFields()$get] Asked field names are: mirbase.mature.id.
biodb.TRACE[2022-10-15 08:07:21.545][self$getBiodb()$getEntryFields()$get] Realnames of fields are: mirbase.mature.id.
biodb.TRACE[2022-10-15 08:07:21.546][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:07:21.550][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:07:21.555][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-15 08:07:21.556][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-15 08:07:21.557][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:07:21.557][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:07:21.558][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-15 08:07:21.559][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-15 08:07:21.560][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:07:21.561][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:07:21.561][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-15 08:07:21.562][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-15 08:07:21.563][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:07:21.564][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:07:21.566][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-15 08:07:21.566][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-15 08:07:21.567][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:07:21.568][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:07:21.569][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-15 08:07:21.569][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-15 08:07:21.570][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:07:21.571][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:07:21.572][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-15 08:07:21.573][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-15 08:07:21.573][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:07:21.574][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:07:21.575][self$getBiodb()$getEntryFields()$get] Asked field names are: mirbase.mature.id.
biodb.TRACE[2022-10-15 08:07:21.576][self$getBiodb()$getEntryFields()$get] Realnames of fields are: mirbase.mature.id.
biodb.TRACE[2022-10-15 08:07:21.577][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:07:21.577][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:07:21.578][self$getBiodb()$getEntryFields()$get] Asked field names are: mirbase.mature.id.
biodb.TRACE[2022-10-15 08:07:21.579][self$getBiodb()$getEntryFields()$get] Realnames of fields are: mirbase.mature.id.
biodb.TRACE[2022-10-15 08:07:21.580][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:07:21.581][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:07:21.581][self$getBiodb()$getEntryFields()$get] Asked field names are: mirbase.mature.id.
biodb.TRACE[2022-10-15 08:07:21.582][self$getBiodb()$getEntryFields()$get] Realnames of fields are: mirbase.mature.id.
biodb.TRACE[2022-10-15 08:07:21.583][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:07:21.584][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:07:21.590][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-15 08:07:21.591][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-15 08:07:21.592][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:07:21.592][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:07:21.593][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-15 08:07:21.594][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-15 08:07:21.595][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:07:21.596][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:07:21.596][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-15 08:07:21.597][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-15 08:07:21.598][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:07:21.599][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:07:21.599][ef$get] Asked field names are: accession.
biodb.TRACE[2022-10-15 08:07:21.600][ef$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-15 08:07:21.601][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:07:21.602][ef$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:07:21.602][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-15 08:07:21.603][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-15 08:07:21.604][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:07:21.605][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:07:21.611][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-15 08:07:21.611][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-15 08:07:21.612][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:07:21.613][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:07:21.614][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-15 08:07:21.614][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-15 08:07:21.615][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:07:21.616][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:07:21.617][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-15 08:07:21.617][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-15 08:07:21.618][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:07:21.619][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:07:21.620][ef$get] Asked field names are: name.
biodb.TRACE[2022-10-15 08:07:21.621][ef$get] Realnames of fields are: name.
biodb.TRACE[2022-10-15 08:07:21.621][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:07:21.632][ef$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:07:21.633][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-15 08:07:21.633][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-15 08:07:21.634][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:07:21.635][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:07:21.640][self$getBiodb()$getEntryFields()$get] Asked field names are: sequence.
biodb.TRACE[2022-10-15 08:07:21.641][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2022-10-15 08:07:21.642][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:07:21.642][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:07:21.643][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2022-10-15 08:07:21.644][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2022-10-15 08:07:21.645][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:07:21.646][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:07:21.646][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2022-10-15 08:07:21.647][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2022-10-15 08:07:21.648][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:07:21.649][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:07:21.649][ef$get] Asked field names are: sequence.
biodb.TRACE[2022-10-15 08:07:21.650][ef$get] Realnames of fields are: aa.seq.
biodb.TRACE[2022-10-15 08:07:21.651][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:07:21.652][ef$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:07:21.652][self$getBiodb()$getEntryFields()$get] Asked field names are: sequence.
biodb.TRACE[2022-10-15 08:07:21.653][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2022-10-15 08:07:21.654][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:07:21.655][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:07:21.660][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2022-10-15 08:07:21.661][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2022-10-15 08:07:21.662][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:07:21.663][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:07:21.663][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2022-10-15 08:07:21.664][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2022-10-15 08:07:21.665][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:07:21.666][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:07:21.666][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2022-10-15 08:07:21.667][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2022-10-15 08:07:21.668][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:07:21.669][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:07:21.669][ef$get] Asked field names are: description.
biodb.TRACE[2022-10-15 08:07:21.670][ef$get] Realnames of fields are: description.
biodb.TRACE[2022-10-15 08:07:21.671][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:07:21.672][ef$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:07:21.673][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2022-10-15 08:07:21.673][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2022-10-15 08:07:21.674][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:07:21.675][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:07:21.680][ef$get] Asked field names are: aa.seq.
biodb.TRACE[2022-10-15 08:07:21.681][ef$get] Realnames of fields are: aa.seq.
biodb.TRACE[2022-10-15 08:07:21.682][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:07:21.682][ef$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:07:21.686][ef$get] Asked field names are: accession.
biodb.TRACE[2022-10-15 08:07:21.686][ef$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-15 08:07:21.687][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:07:21.688][ef$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:07:21.691][ef$get] Asked field names are: description.
biodb.TRACE[2022-10-15 08:07:21.692][ef$get] Realnames of fields are: description.
biodb.TRACE[2022-10-15 08:07:21.693][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:07:21.693][ef$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:07:21.697][ef$get] Asked field names are: name.
biodb.TRACE[2022-10-15 08:07:21.697][ef$get] Realnames of fields are: name.
biodb.TRACE[2022-10-15 08:07:21.698][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:07:21.699][ef$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:07:21.711][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/bbs-3.15-bioc-longtests/meat/biodbMirbase.Rcheck/biodbMirbase/testref/entry-mirbase.mature-MIMAT0000434-content.txt".
biodb.DEBUG[2022-10-15 08:07:21.738][biodb$getFactory()$createEntryFromCo ...] Creating miRBase mature database entries from 1 content(s).
biodb.DEBUG[2022-10-15 08:07:21.739][biodb$getFactory()$createEntryFromCo ...] Parsing 1 miRBase mature database entries.
biodb.DEBUG[2022-10-15 08:07:21.740][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-15 08:07:21.741][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-15 08:07:21.742][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-15 08:07:21.745][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-15 08:07:21.746][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-15 08:07:21.746][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-15 08:07:21.747][FUN] Functions in observer BiodbConfig: [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 08:07:21.749][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-15 08:07:21.749][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-15 08:07:21.750][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:07:21.751][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:07:21.764][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2022-10-15 08:07:21.765][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2022-10-15 08:07:21.766][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:07:21.766][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:07:21.769][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-15 08:07:21.770][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-15 08:07:21.771][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:07:21.771][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:07:21.774][self$getBiodb()$getEntryFields()$get] Asked field names are: sequence.
biodb.TRACE[2022-10-15 08:07:21.775][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2022-10-15 08:07:21.775][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:07:21.776][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:07:21.779][self$getBiodb()$getEntryFields()$get] Asked field names are: mirbase.mature.id.
biodb.TRACE[2022-10-15 08:07:21.779][self$getBiodb()$getEntryFields()$get] Realnames of fields are: mirbase.mature.id.
biodb.TRACE[2022-10-15 08:07:21.780][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:07:21.781][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:07:21.781][self$getBiodb()$getEntryFields()$get] Asked field names are: mirbase.mature.id.
biodb.TRACE[2022-10-15 08:07:21.782][self$getBiodb()$getEntryFields()$get] Realnames of fields are: mirbase.mature.id.
biodb.TRACE[2022-10-15 08:07:21.783][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:07:21.784][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:07:21.784][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-15 08:07:21.785][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-15 08:07:21.786][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:07:21.786][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:07:21.787][self$getBiodb()$getEntryFields()$get] Asked field names are: mirbase.mature.id.
biodb.TRACE[2022-10-15 08:07:21.788][self$getBiodb()$getEntryFields()$get] Realnames of fields are: mirbase.mature.id.
biodb.TRACE[2022-10-15 08:07:21.789][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:07:21.789][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:07:21.790][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-15 08:07:21.791][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-15 08:07:21.792][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:07:21.792][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:07:21.793][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-15 08:07:21.794][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-15 08:07:21.794][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:07:21.795][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:07:21.796][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-15 08:07:21.797][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-15 08:07:21.797][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:07:21.798][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:07:21.801][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-15 08:07:21.801][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-15 08:07:21.802][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:07:21.803][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:07:21.804][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-15 08:07:21.804][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-15 08:07:21.805][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:07:21.806][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:07:21.806][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-15 08:07:21.807][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-15 08:07:21.808][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:07:21.809][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-10-15 08:07:21.809][biodb$getFactory()$createEntryFromCo ...] Accession numbers: MIMAT0000434.
biodb.TRACE[2022-10-15 08:07:21.824][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2022-10-15 08:07:21.825][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2022-10-15 08:07:21.826][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:07:21.829][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:07:21.830][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2022-10-15 08:07:21.831][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2022-10-15 08:07:21.832][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:07:21.832][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:07:21.833][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2022-10-15 08:07:21.834][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2022-10-15 08:07:21.834][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:07:21.835][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:07:21.836][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2022-10-15 08:07:21.837][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2022-10-15 08:07:21.837][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:07:21.838][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:07:21.839][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-15 08:07:21.840][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-15 08:07:21.840][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:07:21.841][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:07:21.845][self$getBiodb()$getEntryFields()$get] Asked field names are: mirbase.mature.id.
biodb.TRACE[2022-10-15 08:07:21.845][self$getBiodb()$getEntryFields()$get] Realnames of fields are: mirbase.mature.id.
biodb.TRACE[2022-10-15 08:07:21.846][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:07:21.847][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:07:21.850][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-15 08:07:21.851][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-15 08:07:21.852][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:07:21.852][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:07:21.853][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-15 08:07:21.854][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-15 08:07:21.855][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:07:21.855][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:07:21.856][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-15 08:07:21.857][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-15 08:07:21.857][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:07:21.858][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:07:21.859][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-15 08:07:21.860][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-15 08:07:21.861][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:07:21.862][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:07:21.862][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-15 08:07:21.863][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-15 08:07:21.864][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:07:21.864][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:07:21.865][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-15 08:07:21.866][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-15 08:07:21.867][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:07:21.867][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:07:21.868][self$getBiodb()$getEntryFields()$get] Asked field names are: mirbase.mature.id.
biodb.TRACE[2022-10-15 08:07:21.869][self$getBiodb()$getEntryFields()$get] Realnames of fields are: mirbase.mature.id.
biodb.TRACE[2022-10-15 08:07:21.870][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:07:21.870][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:07:21.871][self$getBiodb()$getEntryFields()$get] Asked field names are: mirbase.mature.id.
biodb.TRACE[2022-10-15 08:07:21.872][self$getBiodb()$getEntryFields()$get] Realnames of fields are: mirbase.mature.id.
biodb.TRACE[2022-10-15 08:07:21.873][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:07:21.873][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:07:21.874][self$getBiodb()$getEntryFields()$get] Asked field names are: mirbase.mature.id.
biodb.TRACE[2022-10-15 08:07:21.875][self$getBiodb()$getEntryFields()$get] Realnames of fields are: mirbase.mature.id.
biodb.TRACE[2022-10-15 08:07:21.875][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:07:21.876][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:07:21.887][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-15 08:07:21.888][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-15 08:07:21.888][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:07:21.889][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:07:21.890][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-15 08:07:21.891][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-15 08:07:21.891][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:07:21.892][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:07:21.893][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-15 08:07:21.894][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-15 08:07:21.894][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:07:21.895][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:07:21.896][ef$get] Asked field names are: accession.
biodb.TRACE[2022-10-15 08:07:21.896][ef$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-15 08:07:21.897][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:07:21.898][ef$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:07:21.899][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-15 08:07:21.899][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-15 08:07:21.900][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:07:21.901][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:07:21.906][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-15 08:07:21.907][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-15 08:07:21.907][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:07:21.908][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:07:21.909][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-15 08:07:21.909][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-15 08:07:21.910][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:07:21.911][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:07:21.911][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-15 08:07:21.912][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-15 08:07:21.913][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:07:21.914][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:07:21.914][ef$get] Asked field names are: name.
biodb.TRACE[2022-10-15 08:07:21.915][ef$get] Realnames of fields are: name.
biodb.TRACE[2022-10-15 08:07:21.916][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:07:21.916][ef$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:07:21.917][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-15 08:07:21.918][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-15 08:07:21.919][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:07:21.919][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:07:21.924][self$getBiodb()$getEntryFields()$get] Asked field names are: sequence.
biodb.TRACE[2022-10-15 08:07:21.925][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2022-10-15 08:07:21.926][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:07:21.926][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:07:21.927][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2022-10-15 08:07:21.928][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2022-10-15 08:07:21.929][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:07:21.929][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:07:21.930][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2022-10-15 08:07:21.931][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2022-10-15 08:07:21.934][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:07:21.935][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:07:21.936][ef$get] Asked field names are: sequence.
biodb.TRACE[2022-10-15 08:07:21.937][ef$get] Realnames of fields are: aa.seq.
biodb.TRACE[2022-10-15 08:07:21.937][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:07:21.938][ef$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:07:21.939][self$getBiodb()$getEntryFields()$get] Asked field names are: sequence.
biodb.TRACE[2022-10-15 08:07:21.940][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2022-10-15 08:07:21.940][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:07:21.941][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:07:21.946][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2022-10-15 08:07:21.947][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2022-10-15 08:07:21.947][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:07:21.948][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:07:21.949][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2022-10-15 08:07:21.949][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2022-10-15 08:07:21.950][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:07:21.951][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:07:21.951][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2022-10-15 08:07:21.952][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2022-10-15 08:07:21.953][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:07:21.954][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:07:21.954][ef$get] Asked field names are: description.
biodb.TRACE[2022-10-15 08:07:21.955][ef$get] Realnames of fields are: description.
biodb.TRACE[2022-10-15 08:07:21.956][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:07:21.956][ef$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:07:21.957][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2022-10-15 08:07:21.958][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2022-10-15 08:07:21.959][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:07:21.959][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:07:21.964][ef$get] Asked field names are: aa.seq.
biodb.TRACE[2022-10-15 08:07:21.965][ef$get] Realnames of fields are: aa.seq.
biodb.TRACE[2022-10-15 08:07:21.966][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:07:21.967][ef$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:07:21.970][ef$get] Asked field names are: accession.
biodb.TRACE[2022-10-15 08:07:21.971][ef$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-15 08:07:21.971][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:07:21.972][ef$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:07:21.975][ef$get] Asked field names are: description.
biodb.TRACE[2022-10-15 08:07:21.976][ef$get] Realnames of fields are: description.
biodb.TRACE[2022-10-15 08:07:21.977][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:07:21.977][ef$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:07:21.981][ef$get] Asked field names are: name.
biodb.TRACE[2022-10-15 08:07:21.982][ef$get] Realnames of fields are: name.
biodb.TRACE[2022-10-15 08:07:21.982][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:07:21.983][ef$get] fields variable is a list.
biodb.INFO [2022-10-15 08:07:21.987][biodb::testThat]
biodb.INFO [2022-10-15 08:07:21.988][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2022-10-15 08:07:21.988][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2022-10-15 08:07:21.989][biodb::testThat]
biodb.DEBUG[2022-10-15 08:07:21.991][private$loadEntries] Creating entries from ids [2]: "MIMAT0000433, MIMAT0000434".
biodb.DEBUG[2022-10-15 08:07:21.996][conn$getEntryContent] Get miRBase mature database entry content(s) for 2 id(s)...
biodb.INFO [2022-10-15 08:07:21.999][self$getFolderPath] Create cache folder "/home/biocbuild/.cache/R/biodb/mirbase.mature-ecbae556d51779d9d48125ba5a617e19" for "mirbase.mature-ecbae556d51779d9d48125ba5a617e19".
biodb.DEBUG[2022-10-15 08:07:22.000][self$isDownloaded] Database mirbase.mature has not yet been downloaded.
biodb.INFO [2022-10-15 08:07:22.000][self$download] Downloading whole database of mirbase.mature.
biodb.DEBUG[2022-10-15 08:07:22.002][self$getDownloadPath] Download path of mirbase.mature is "/home/biocbuild/.cache/R/biodb/mirbase.mature-ecbae556d51779d9d48125ba5a617e19/download.gz".
biodb.DEBUG[2022-10-15 08:07:22.003][sched$downloadFile] Downloading file "https://www.mirbase.org/ftp/CURRENT/mature.fa.gz".
trying URL 'https://www.mirbase.org/ftp/CURRENT/mature.fa.gz'
Content type 'application/x-gzip' length 803746 bytes (784 KB)
==================================================
downloaded 784 KB

biodb.DEBUG[2022-10-15 08:07:24.674][self$getDownloadPath] Download path of mirbase.mature is "/home/biocbuild/.cache/R/biodb/mirbase.mature-ecbae556d51779d9d48125ba5a617e19/download.gz".
biodb.DEBUG[2022-10-15 08:07:24.677][self$download] Downloading of mirbase.mature completed.
biodb.TRACE[2022-10-15 08:07:24.681][self$addFilesToCache] Moving files to cache [1]: "/home/biocbuild/.cache/R/biodb/tmp/marker23d39a5f3085f9marker".
biodb.TRACE[2022-10-15 08:07:24.683][private$doAddFilesToCache] Destination files are [1]: "/home/biocbuild/.cache/R/biodb/mirbase.mature-ecbae556d51779d9d48125ba5a617e19/downloaded.marker".
biodb.DEBUG[2022-10-15 08:07:24.684][self$addFilesToCache] Done adding files.
biodb.DEBUG[2022-10-15 08:07:24.685][self$isDownloaded] Database mirbase.mature has already been downloaded.
biodb.INFO [2022-10-15 08:07:24.686][self$download] Extract whole database of mirbase.mature.
biodb.DEBUG[2022-10-15 08:07:24.687][self$getDownloadPath] Download path of mirbase.mature is "/home/biocbuild/.cache/R/biodb/mirbase.mature-ecbae556d51779d9d48125ba5a617e19/download.gz".
biodb.DEBUG[2022-10-15 08:07:24.879][self$getDownloadPath] Download path of mirbase.mature is "/home/biocbuild/.cache/R/biodb/mirbase.mature-ecbae556d51779d9d48125ba5a617e19/download.gz".
biodb.DEBUG[2022-10-15 08:07:24.880][private$doExtractDownload] Found 48885 entries in file "/home/biocbuild/.cache/R/biodb/mirbase.mature-ecbae556d51779d9d48125ba5a617e19/download.gz".
biodb.TRACE[2022-10-15 08:07:25.101][private$doSaveContentToFile] Saving to cache [48885]: "/home/biocbuild/.cache/R/biodb/mirbase.mature-ecbae556d51779d9d48125ba5a617e19/MIMAT0000001.txt, /home/biocbuild/.cache/R/biodb/mirbase.mature-ecbae556d51779d9d48125ba5a617e19/MIMAT0015091.txt, /home/biocbuild/.cache/R/biodb/mirbase.mature-ecbae556d51779d9d48125ba5a617e19/MIMAT0000002.txt, /home/biocbuild/.cache/R/biodb/mirbase.mature-ecbae556d51779d9d48125ba5a617e19/MIMAT0015092.txt, /home/biocbuild/.cache/R/biodb/mirbase.mature-ecbae556d51779d9d48125ba5a617e19/MIMAT0020301.txt, /home/biocbuild/.cache/R/biodb/mirbase.mature-ecbae556d51779d9d48125ba5a617e19/MIMAT0000003.txt, /home/biocbuild/.cache/R/biodb/mirbase.mature-ecbae556d51779d9d48125ba5a617e19/MIMAT0020302.txt, /home/biocbuild/.cache/R/biodb/mirbase.mature-ecbae556d51779d9d48125ba5a617e19/MIMAT0000004.txt, /home/biocbuild/.cache/R/biodb/mirbase.mature-ecbae556d51779d9d48125ba5a617e19/MIMAT0000005.txt, /home/biocbuild/.cache/R/biodb/mirbase.mature-ecbae556d51779d9d48125ba5a617e19/MIMAT0015093.txt, ..."
biodb.TRACE[2022-10-15 08:07:28.881][self$addFilesToCache] Moving files to cache [1]: "/home/biocbuild/.cache/R/biodb/tmp/marker23d39a5b3949c0marker".
biodb.TRACE[2022-10-15 08:07:28.883][private$doAddFilesToCache] Destination files are [1]: "/home/biocbuild/.cache/R/biodb/mirbase.mature-ecbae556d51779d9d48125ba5a617e19/extracted.marker".
biodb.DEBUG[2022-10-15 08:07:28.883][self$addFilesToCache] Done adding files.
biodb.TRACE[2022-10-15 08:07:28.885][cch$loadFileContent] Trying to load 2 files from cache: [2]: "MIMAT0000433, MIMAT0000434".
biodb.TRACE[2022-10-15 08:07:28.886][cch$loadFileContent] file.exist = [2]: "TRUE, TRUE".
biodb.TRACE[2022-10-15 08:07:28.887][loadFileContents] Loaded 2 files from cache: [2]: "/home/biocbuild/.cache/R/biodb/mirbase.mature-ecbae556d51779d9d48125ba5a617e19/MIMAT0000433.txt, /home/biocbuild/.cache/R/biodb/mirbase.mature-ecbae556d51779d9d48125ba5a617e19/MIMAT0000434.txt".
biodb.DEBUG[2022-10-15 08:07:28.888][conn$getEntryContent] 2 miRBase mature database entry content(s) loaded from cache.
biodb.DEBUG[2022-10-15 08:07:28.904][self$createEntryFromContent] Creating miRBase mature database entries from 2 content(s).
biodb.DEBUG[2022-10-15 08:07:28.905][self$createEntryFromContent] Parsing 2 miRBase mature database entries.
biodb.DEBUG[2022-10-15 08:07:28.906][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-15 08:07:28.907][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-15 08:07:28.908][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-15 08:07:28.912][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-15 08:07:28.913][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-15 08:07:28.913][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-15 08:07:28.914][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-10-15 08:07:28.916][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-15 08:07:28.917][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-15 08:07:28.917][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:07:28.918][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:07:28.921][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2022-10-15 08:07:28.922][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2022-10-15 08:07:28.923][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:07:28.924][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:07:28.927][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-15 08:07:28.927][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-15 08:07:28.928][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:07:28.929][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:07:28.932][self$getBiodb()$getEntryFields()$get] Asked field names are: sequence.
biodb.TRACE[2022-10-15 08:07:28.933][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2022-10-15 08:07:28.933][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:07:28.934][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:07:28.937][self$getBiodb()$getEntryFields()$get] Asked field names are: mirbase.mature.id.
biodb.TRACE[2022-10-15 08:07:28.938][self$getBiodb()$getEntryFields()$get] Realnames of fields are: mirbase.mature.id.
biodb.TRACE[2022-10-15 08:07:28.938][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:07:28.939][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:07:28.940][self$getBiodb()$getEntryFields()$get] Asked field names are: mirbase.mature.id.
biodb.TRACE[2022-10-15 08:07:28.941][self$getBiodb()$getEntryFields()$get] Realnames of fields are: mirbase.mature.id.
biodb.TRACE[2022-10-15 08:07:28.941][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:07:28.942][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:07:28.943][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-15 08:07:28.943][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-15 08:07:28.944][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:07:28.945][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:07:28.946][self$getBiodb()$getEntryFields()$get] Asked field names are: mirbase.mature.id.
biodb.TRACE[2022-10-15 08:07:28.947][self$getBiodb()$getEntryFields()$get] Realnames of fields are: mirbase.mature.id.
biodb.TRACE[2022-10-15 08:07:28.947][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:07:28.948][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:07:28.949][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-15 08:07:28.950][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-15 08:07:28.950][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:07:28.951][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:07:28.952][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-15 08:07:28.953][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-15 08:07:28.953][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:07:28.954][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:07:28.955][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-15 08:07:28.972][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-15 08:07:28.974][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:07:28.975][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-10-15 08:07:28.978][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-15 08:07:28.979][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-15 08:07:28.979][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-15 08:07:28.983][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-15 08:07:28.984][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-15 08:07:28.984][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-15 08:07:28.985][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-10-15 08:07:28.986][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-15 08:07:28.987][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-15 08:07:28.988][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:07:28.989][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:07:28.992][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2022-10-15 08:07:28.992][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2022-10-15 08:07:28.993][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:07:28.994][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:07:28.996][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-15 08:07:28.997][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-15 08:07:28.998][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:07:28.999][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:07:29.001][self$getBiodb()$getEntryFields()$get] Asked field names are: sequence.
biodb.TRACE[2022-10-15 08:07:29.002][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2022-10-15 08:07:29.003][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:07:29.003][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:07:29.006][self$getBiodb()$getEntryFields()$get] Asked field names are: mirbase.mature.id.
biodb.TRACE[2022-10-15 08:07:29.007][self$getBiodb()$getEntryFields()$get] Realnames of fields are: mirbase.mature.id.
biodb.TRACE[2022-10-15 08:07:29.007][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:07:29.008][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:07:29.009][self$getBiodb()$getEntryFields()$get] Asked field names are: mirbase.mature.id.
biodb.TRACE[2022-10-15 08:07:29.010][self$getBiodb()$getEntryFields()$get] Realnames of fields are: mirbase.mature.id.
biodb.TRACE[2022-10-15 08:07:29.010][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:07:29.011][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:07:29.012][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-15 08:07:29.012][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-15 08:07:29.013][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:07:29.014][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:07:29.014][self$getBiodb()$getEntryFields()$get] Asked field names are: mirbase.mature.id.
biodb.TRACE[2022-10-15 08:07:29.015][self$getBiodb()$getEntryFields()$get] Realnames of fields are: mirbase.mature.id.
biodb.TRACE[2022-10-15 08:07:29.016][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:07:29.016][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:07:29.017][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-15 08:07:29.018][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-15 08:07:29.019][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:07:29.019][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:07:29.020][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-15 08:07:29.021][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-15 08:07:29.021][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:07:29.022][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:07:29.023][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-15 08:07:29.023][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-15 08:07:29.024][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:07:29.025][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:07:29.028][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-15 08:07:29.028][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-15 08:07:29.029][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:07:29.030][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:07:29.030][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-15 08:07:29.031][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-15 08:07:29.032][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:07:29.033][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:07:29.033][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-15 08:07:29.034][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-15 08:07:29.035][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:07:29.035][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:07:29.036][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-15 08:07:29.037][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-15 08:07:29.038][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:07:29.038][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:07:29.039][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-15 08:07:29.040][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-15 08:07:29.041][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:07:29.041][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:07:29.042][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-15 08:07:29.043][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-15 08:07:29.044][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:07:29.044][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-10-15 08:07:29.045][self$createEntryFromContent] Accession numbers: MIMAT0000433, MIMAT0000434.
biodb.TRACE[2022-10-15 08:07:29.046][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2022-10-15 08:07:29.047][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2022-10-15 08:07:29.047][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:07:29.048][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:07:29.049][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2022-10-15 08:07:29.050][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2022-10-15 08:07:29.050][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:07:29.051][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:07:29.052][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2022-10-15 08:07:29.052][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2022-10-15 08:07:29.053][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:07:29.054][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:07:29.058][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2022-10-15 08:07:29.059][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2022-10-15 08:07:29.059][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:07:29.060][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:07:29.061][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2022-10-15 08:07:29.062][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2022-10-15 08:07:29.062][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:07:29.063][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:07:29.064][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2022-10-15 08:07:29.064][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2022-10-15 08:07:29.065][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:07:29.066][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2022-10-15 08:07:29.071][biodb::testThat]
biodb.INFO [2022-10-15 08:07:29.071][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2022-10-15 08:07:29.072][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2022-10-15 08:07:29.073][biodb::testThat]
biodb.INFO [2022-10-15 08:07:29.075][biodb::testThat]
biodb.INFO [2022-10-15 08:07:29.076][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2022-10-15 08:07:29.077][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2022-10-15 08:07:29.077][biodb::testThat]
biodb.WARN [2022-10-15 08:07:29.100][self$searchForEntries] This database is not searchable by field "name".
biodb.WARN [2022-10-15 08:07:29.120][self$searchForEntries] This database is not searchable by field "name".
biodb.INFO [2022-10-15 08:07:29.127][biodb::testThat]
biodb.INFO [2022-10-15 08:07:29.128][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2022-10-15 08:07:29.129][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2022-10-15 08:07:29.129][biodb::testThat]
biodb.TRACE[2022-10-15 08:07:29.150][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2022-10-15 08:07:29.151][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2022-10-15 08:07:29.151][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:07:29.152][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:07:29.153][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2022-10-15 08:07:29.154][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2022-10-15 08:07:29.154][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:07:29.155][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:07:29.156][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2022-10-15 08:07:29.157][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2022-10-15 08:07:29.157][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:07:29.158][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:07:29.159][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2022-10-15 08:07:29.159][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2022-10-15 08:07:29.160][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:07:29.161][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:07:29.184][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2022-10-15 08:07:29.185][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2022-10-15 08:07:29.186][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:07:29.187][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:07:29.188][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2022-10-15 08:07:29.188][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2022-10-15 08:07:29.189][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:07:29.190][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:07:29.190][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2022-10-15 08:07:29.191][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2022-10-15 08:07:29.205][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:07:29.206][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:07:29.206][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2022-10-15 08:07:29.207][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2022-10-15 08:07:29.208][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:07:29.208][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2022-10-15 08:07:29.211][biodb::testThat]
biodb.INFO [2022-10-15 08:07:29.212][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2022-10-15 08:07:29.212][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2022-10-15 08:07:29.213][biodb::testThat]
biodb.INFO [2022-10-15 08:07:29.217][biodb::testThat]
biodb.INFO [2022-10-15 08:07:29.217][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2022-10-15 08:07:29.218][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2022-10-15 08:07:29.219][biodb::testThat]
biodb.INFO [2022-10-15 08:07:29.222][biodb::testThat]
biodb.INFO [2022-10-15 08:07:29.222][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2022-10-15 08:07:29.223][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2022-10-15 08:07:29.224][biodb::testThat]
biodb.DEBUG[2022-10-15 08:07:29.226][function(conn, opt)] Trying to download "http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000433".
biodb.DEBUG[2022-10-15 08:07:30.520][getUrlContent] Use RCurl for downloading content of URL http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000433.
biodb.INFO [2022-10-15 08:07:30.741][biodb::testThat]
biodb.INFO [2022-10-15 08:07:30.742][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2022-10-15 08:07:30.743][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2022-10-15 08:07:30.743][biodb::testThat]
biodb.INFO [2022-10-15 08:07:30.754][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2022-10-15 08:07:30.755][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector mirbase.mature from the request scheduler
biodb.INFO [2022-10-15 08:07:30.756][self$deleteConn] Connector "mirbase.mature" deleted.
biodb.DEBUG[2022-10-15 08:07:30.756][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2022-10-15 08:07:30.757][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-15 08:07:30.758][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-15 08:07:30.758][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-15 08:07:30.759][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 08:07:30.760][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2022-10-15 08:07:30.760][FUN] Functions in observer BiodbConfig: [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 08:07:30.767][biodb::testContext]
biodb.INFO [2022-10-15 08:07:30.768][biodb::testContext] ********************************************************************************
biodb.INFO [2022-10-15 08:07:30.768][biodb::testContext] Test context - Example long tests
biodb.INFO [2022-10-15 08:07:30.769][biodb::testContext] ********************************************************************************
biodb.INFO [2022-10-15 08:07:30.770][biodb::testContext]
biodb.INFO [2022-10-15 08:07:30.773][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.4.2.
biodb.DEBUG[2022-10-15 08:07:30.774][self$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.15-bioc/R/library/biodb/definitions.yml".
biodb.DEBUG[2022-10-15 08:07:30.777][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2022-10-15 08:07:30.778][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2022-10-15 08:07:30.779][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2022-10-15 08:07:30.780][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-15 08:07:30.780][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-15 08:07:30.781][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-15 08:07:30.782][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2022-10-15 08:07:30.782][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2022-10-15 08:07:30.783][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-15 08:07:30.784][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-15 08:07:30.784][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-15 08:07:30.785][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2022-10-15 08:07:30.786][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2022-10-15 08:07:30.786][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-15 08:07:30.787][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-15 08:07:30.788][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-15 08:07:30.788][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2022-10-15 08:07:30.789][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2022-10-15 08:07:30.790][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2022-10-15 08:07:30.791][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-15 08:07:30.791][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-15 08:07:30.792][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-15 08:07:30.793][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2022-10-15 08:07:30.793][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2022-10-15 08:07:30.794][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2022-10-15 08:07:30.795][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-15 08:07:30.795][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-15 08:07:30.796][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-15 08:07:30.797][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2022-10-15 08:07:30.798][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2022-10-15 08:07:30.798][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-15 08:07:30.799][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-15 08:07:30.800][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-15 08:07:30.800][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2022-10-15 08:07:30.801][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2022-10-15 08:07:30.802][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2022-10-15 08:07:30.802][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-15 08:07:30.803][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-15 08:07:30.804][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-15 08:07:30.804][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2022-10-15 08:07:30.805][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2022-10-15 08:07:30.806][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-15 08:07:30.806][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-15 08:07:30.807][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-15 08:07:30.808][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2022-10-15 08:07:30.809][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2022-10-15 08:07:30.809][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2022-10-15 08:07:30.810][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-15 08:07:30.811][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-15 08:07:30.811][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-15 08:07:30.812][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2022-10-15 08:07:30.813][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2022-10-15 08:07:30.814][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2022-10-15 08:07:30.814][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2022-10-15 08:07:30.815][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2022-10-15 08:07:30.816][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2022-10-15 08:07:30.817][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-15 08:07:30.817][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-15 08:07:30.818][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-15 08:07:30.819][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2022-10-15 08:07:30.820][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2022-10-15 08:07:30.820][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-15 08:07:30.821][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-15 08:07:30.822][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-15 08:07:30.822][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2022-10-15 08:07:30.823][self$set] Set key entries.sep to "|".
biodb.DEBUG[2022-10-15 08:07:30.824][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-15 08:07:30.824][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-15 08:07:30.825][FUN] Functions in observer BiodbConfig: [21]: ".__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 08:07:30.826][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2022-10-15 08:07:30.827][self$set] Set key offline to FALSE.
biodb.DEBUG[2022-10-15 08:07:30.827][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-15 08:07:30.828][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-15 08:07:30.829][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-15 08:07:30.829][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2022-10-15 08:07:30.830][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2022-10-15 08:07:30.831][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-15 08:07:30.831][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-15 08:07:30.832][FUN] Functions in observer BiodbConfig: [21]: ".__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 08:07:30.833][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2022-10-15 08:07:30.833][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2022-10-15 08:07:30.834][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-15 08:07:30.835][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-15 08:07:30.835][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-15 08:07:30.836][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2022-10-15 08:07:30.837][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2022-10-15 08:07:30.842][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2022-10-15 08:07:30.842][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-15 08:07:30.843][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-15 08:07:30.844][FUN] Functions in observer BiodbConfig: [21]: ".__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 08:07:30.844][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2022-10-15 08:07:30.845][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2022-10-15 08:07:30.846][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2022-10-15 08:07:30.847][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-15 08:07:30.847][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-15 08:07:30.848][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-15 08:07:30.849][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2022-10-15 08:07:30.850][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2022-10-15 08:07:30.851][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2022-10-15 08:07:30.852][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2022-10-15 08:07:30.853][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2022-10-15 08:07:30.854][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2022-10-15 08:07:30.854][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2022-10-15 08:07:30.855][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2022-10-15 08:07:30.856][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2022-10-15 08:07:30.857][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2022-10-15 08:07:30.857][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2022-10-15 08:07:30.858][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2022-10-15 08:07:30.859][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2022-10-15 08:07:30.860][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2022-10-15 08:07:30.860][self$setPropertyValue]
biodb.DEBUG[2022-10-15 08:07:30.861][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2022-10-15 08:07:30.862][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2022-10-15 08:07:30.862][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2022-10-15 08:07:30.862][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2022-10-15 08:07:30.862][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2022-10-15 08:07:30.862][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2022-10-15 08:07:30.863][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2022-10-15 08:07:30.864][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-10-15 08:07:30.864][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-10-15 08:07:30.881][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2022-10-15 08:07:30.882][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-10-15 08:07:30.883][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-10-15 08:07:30.883][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2022-10-15 08:07:30.884][self$setPropertyValue]
biodb.DEBUG[2022-10-15 08:07:30.885][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2022-10-15 08:07:30.885][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2022-10-15 08:07:30.886][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2022-10-15 08:07:30.887][self$setPropertyValue]
biodb.DEBUG[2022-10-15 08:07:30.888][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2022-10-15 08:07:30.889][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2022-10-15 08:07:30.890][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2022-10-15 08:07:30.890][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2022-10-15 08:07:30.891][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2022-10-15 08:07:30.892][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2022-10-15 08:07:30.893][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2022-10-15 08:07:30.893][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2022-10-15 08:07:30.894][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2022-10-15 08:07:30.895][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2022-10-15 08:07:30.895][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2022-10-15 08:07:30.896][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2022-10-15 08:07:30.897][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2022-10-15 08:07:30.898][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2022-10-15 08:07:30.898][self$setPropertyValue]
biodb.DEBUG[2022-10-15 08:07:30.899][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2022-10-15 08:07:30.900][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2022-10-15 08:07:30.900][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2022-10-15 08:07:30.900][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2022-10-15 08:07:30.900][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2022-10-15 08:07:30.900][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2022-10-15 08:07:30.901][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2022-10-15 08:07:30.901][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-10-15 08:07:30.902][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-10-15 08:07:30.903][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2022-10-15 08:07:30.903][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-10-15 08:07:30.904][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-10-15 08:07:30.905][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2022-10-15 08:07:30.906][self$setPropertyValue]
biodb.DEBUG[2022-10-15 08:07:30.906][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2022-10-15 08:07:30.907][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2022-10-15 08:07:30.908][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2022-10-15 08:07:30.908][self$setPropertyValue]
biodb.DEBUG[2022-10-15 08:07:30.909][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2022-10-15 08:07:30.911][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2022-10-15 08:07:30.911][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2022-10-15 08:07:30.912][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2022-10-15 08:07:30.913][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2022-10-15 08:07:30.913][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2022-10-15 08:07:30.914][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2022-10-15 08:07:30.915][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2022-10-15 08:07:30.916][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2022-10-15 08:07:30.916][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2022-10-15 08:07:30.917][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2022-10-15 08:07:30.918][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2022-10-15 08:07:30.919][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2022-10-15 08:07:30.919][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2022-10-15 08:07:30.920][self$setPropertyValue]
biodb.DEBUG[2022-10-15 08:07:30.921][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2022-10-15 08:07:30.921][self$setPropertyValue]
biodb.DEBUG[2022-10-15 08:07:30.922][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2022-10-15 08:07:30.923][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-10-15 08:07:30.924][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-10-15 08:07:30.924][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2022-10-15 08:07:30.925][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-10-15 08:07:30.926][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-10-15 08:07:30.926][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2022-10-15 08:07:30.927][self$setPropertyValue]
biodb.DEBUG[2022-10-15 08:07:30.928][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2022-10-15 08:07:30.929][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2022-10-15 08:07:30.929][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2022-10-15 08:07:30.930][self$setPropertyValue]
biodb.DEBUG[2022-10-15 08:07:30.931][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2022-10-15 08:07:30.932][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2022-10-15 08:07:30.933][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2022-10-15 08:07:30.934][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2022-10-15 08:07:30.934][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2022-10-15 08:07:30.935][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2022-10-15 08:07:30.936][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2022-10-15 08:07:30.937][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2022-10-15 08:07:30.937][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2022-10-15 08:07:30.938][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2022-10-15 08:07:30.939][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2022-10-15 08:07:30.940][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2022-10-15 08:07:30.940][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2022-10-15 08:07:30.941][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2022-10-15 08:07:30.942][self$setPropertyValue]
biodb.DEBUG[2022-10-15 08:07:30.942][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2022-10-15 08:07:30.943][self$setPropertyValue]
biodb.DEBUG[2022-10-15 08:07:30.944][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2022-10-15 08:07:30.945][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-10-15 08:07:30.945][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-10-15 08:07:30.946][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2022-10-15 08:07:30.947][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-10-15 08:07:30.947][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-10-15 08:07:30.948][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2022-10-15 08:07:30.949][self$setPropertyValue]
biodb.DEBUG[2022-10-15 08:07:30.949][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2022-10-15 08:07:30.950][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2022-10-15 08:07:30.951][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2022-10-15 08:07:30.951][self$setPropertyValue]
biodb.DEBUG[2022-10-15 08:07:30.952][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2022-10-15 08:07:30.953][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2022-10-15 08:07:30.954][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-15 08:07:30.954][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-15 08:07:30.955][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-15 08:07:30.956][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-15 08:07:30.956][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-15 08:07:30.957][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-15 08:07:30.958][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-15 08:07:30.958][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-15 08:07:30.959][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 08:07:30.960][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-15 08:07:30.960][FUN] Functions in observer BiodbConfig: [21]: ".__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 08:07:30.961][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-15 08:07:30.962][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-15 08:07:30.962][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-15 08:07:30.963][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-15 08:07:30.964][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-15 08:07:30.964][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-15 08:07:30.965][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-15 08:07:30.965][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-15 08:07:30.966][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-15 08:07:30.967][FUN] Functions in observer BiodbConfig: [21]: ".__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 08:07:30.967][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-15 08:07:30.968][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-15 08:07:30.969][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 08:07:30.969][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-15 08:07:30.970][FUN] Functions in observer BiodbConfig: [21]: ".__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 08:07:30.971][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-15 08:07:30.971][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-15 08:07:30.972][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-15 08:07:30.972][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-15 08:07:30.973][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-15 08:07:30.974][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-15 08:07:30.974][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-15 08:07:30.975][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 08:07:30.976][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-15 08:07:30.976][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-15 08:07:30.977][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-15 08:07:30.978][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-15 08:07:30.978][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-15 08:07:30.979][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-15 08:07:30.980][FUN] Functions in observer BiodbConfig: [21]: ".__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 08:07:30.980][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-15 08:07:30.981][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-15 08:07:30.981][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-15 08:07:30.982][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-15 08:07:30.983][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-15 08:07:30.983][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-15 08:07:30.984][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-15 08:07:30.985][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-15 08:07:30.985][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-15 08:07:30.986][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-15 08:07:30.987][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-15 08:07:30.987][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-15 08:07:30.988][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-15 08:07:30.988][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-15 08:07:30.989][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-15 08:07:30.990][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-15 08:07:30.990][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-15 08:07:30.991][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-15 08:07:30.992][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-15 08:07:30.992][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-15 08:07:30.993][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-15 08:07:30.994][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-15 08:07:30.994][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-15 08:07:30.995][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-15 08:07:30.996][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-15 08:07:30.996][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-15 08:07:30.997][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-15 08:07:30.998][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-15 08:07:30.998][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-15 08:07:30.999][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-15 08:07:31.000][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-15 08:07:31.000][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-15 08:07:31.001][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-15 08:07:31.002][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-15 08:07:31.002][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-15 08:07:31.003][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-15 08:07:31.004][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-15 08:07:31.004][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-15 08:07:31.005][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-15 08:07:31.006][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-15 08:07:31.006][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-15 08:07:31.007][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-15 08:07:31.008][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-15 08:07:31.008][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-15 08:07:31.009][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-15 08:07:31.010][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2022-10-15 08:07:31.011][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2022-10-15 08:07:31.012][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2022-10-15 08:07:31.013][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2022-10-15 08:07:31.014][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2022-10-15 08:07:31.015][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2022-10-15 08:07:31.016][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2022-10-15 08:07:31.017][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2022-10-15 08:07:31.018][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2022-10-15 08:07:31.019][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2022-10-15 08:07:31.020][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2022-10-15 08:07:31.021][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2022-10-15 08:07:31.022][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2022-10-15 08:07:31.023][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2022-10-15 08:07:31.024][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2022-10-15 08:07:31.025][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2022-10-15 08:07:31.026][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2022-10-15 08:07:31.027][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2022-10-15 08:07:31.028][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2022-10-15 08:07:31.029][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2022-10-15 08:07:31.030][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2022-10-15 08:07:31.031][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2022-10-15 08:07:31.032][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2022-10-15 08:07:31.033][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2022-10-15 08:07:31.034][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2022-10-15 08:07:31.035][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2022-10-15 08:07:31.036][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2022-10-15 08:07:31.037][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2022-10-15 08:07:31.038][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2022-10-15 08:07:31.039][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2022-10-15 08:07:31.040][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2022-10-15 08:07:31.041][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2022-10-15 08:07:31.042][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2022-10-15 08:07:31.043][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2022-10-15 08:07:31.044][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2022-10-15 08:07:31.045][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2022-10-15 08:07:31.046][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2022-10-15 08:07:31.047][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2022-10-15 08:07:31.048][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2022-10-15 08:07:31.049][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2022-10-15 08:07:31.050][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2022-10-15 08:07:31.051][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2022-10-15 08:07:31.052][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2022-10-15 08:07:31.053][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2022-10-15 08:07:31.054][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2022-10-15 08:07:31.055][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2022-10-15 08:07:31.056][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2022-10-15 08:07:31.057][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2022-10-15 08:07:31.058][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2022-10-15 08:07:31.059][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2022-10-15 08:07:31.060][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2022-10-15 08:07:31.061][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2022-10-15 08:07:31.062][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2022-10-15 08:07:31.067][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2022-10-15 08:07:31.068][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2022-10-15 08:07:31.069][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2022-10-15 08:07:31.071][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2022-10-15 08:07:31.072][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2022-10-15 08:07:31.073][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2022-10-15 08:07:31.074][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2022-10-15 08:07:31.075][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2022-10-15 08:07:31.076][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2022-10-15 08:07:31.077][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2022-10-15 08:07:31.078][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2022-10-15 08:07:31.079][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2022-10-15 08:07:31.080][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2022-10-15 08:07:31.082][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2022-10-15 08:07:31.083][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2022-10-15 08:07:31.084][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2022-10-15 08:07:31.085][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2022-10-15 08:07:31.086][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2022-10-15 08:07:31.087][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2022-10-15 08:07:31.088][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2022-10-15 08:07:31.089][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2022-10-15 08:07:31.090][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2022-10-15 08:07:31.091][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2022-10-15 08:07:31.093][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2022-10-15 08:07:31.094][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2022-10-15 08:07:31.095][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2022-10-15 08:07:31.096][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2022-10-15 08:07:31.097][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2022-10-15 08:07:31.098][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2022-10-15 08:07:31.126][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2022-10-15 08:07:31.127][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2022-10-15 08:07:31.128][initialize] This is biodb version 1.4.2.
biodb.DEBUG[2022-10-15 08:07:31.129][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2022-10-15 08:07:31.130][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2022-10-15 08:07:31.131][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-15 08:07:31.131][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2022-10-15 08:07:31.132][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-15 08:07:31.133][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-15 08:07:31.133][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-15 08:07:31.134][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-15 08:07:31.135][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-15 08:07:31.135][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-15 08:07:31.136][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-15 08:07:31.137][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 08:07:31.137][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-15 08:07:31.138][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-15 08:07:31.139][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-15 08:07:31.140][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-15 08:07:31.140][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 08:07:31.141][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-15 08:07:31.142][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-15 08:07:31.142][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-15 08:07:31.143][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-15 08:07:31.144][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-15 08:07:31.144][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-15 08:07:31.145][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 08:07:31.146][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-15 08:07:31.146][FUN] Functions in observer BiodbConfig: [21]: ".__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 08:07:31.147][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-15 08:07:31.148][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-15 08:07:31.149][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-15 08:07:31.149][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-15 08:07:31.150][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-15 08:07:31.151][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-15 08:07:31.151][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-15 08:07:31.152][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-15 08:07:31.153][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-15 08:07:31.153][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-15 08:07:31.154][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-15 08:07:31.155][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-15 08:07:31.155][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-15 08:07:31.156][FUN] Functions in observer BiodbConfig: [21]: ".__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 08:07:31.157][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-15 08:07:31.157][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-15 08:07:31.158][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-15 08:07:31.159][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-15 08:07:31.160][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-15 08:07:31.160][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-15 08:07:31.161][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-15 08:07:31.162][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-15 08:07:31.162][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-15 08:07:31.163][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-15 08:07:31.164][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-15 08:07:31.165][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 08:07:31.165][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-15 08:07:31.166][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-15 08:07:31.167][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-15 08:07:31.167][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-15 08:07:31.168][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-15 08:07:31.169][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-15 08:07:31.169][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-15 08:07:31.170][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-15 08:07:31.171][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 08:07:31.172][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-15 08:07:31.172][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-15 08:07:31.173][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-15 08:07:31.174][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-15 08:07:31.174][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 08:07:31.175][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-15 08:07:31.176][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 08:07:31.176][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-15 08:07:31.177][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-15 08:07:31.178][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-15 08:07:31.179][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-15 08:07:31.179][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 08:07:31.180][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-15 08:07:31.181][FUN] Functions in observer BiodbConfig: [21]: ".__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 08:07:31.181][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-15 08:07:31.182][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-15 08:07:31.183][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-15 08:07:31.183][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-15 08:07:31.184][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 08:07:31.185][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-15 08:07:31.186][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-15 08:07:31.186][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-15 08:07:31.187][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-15 08:07:31.188][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-15 08:07:31.189][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-15 08:07:31.189][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 08:07:31.190][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-15 08:07:31.191][FUN] Functions in observer BiodbConfig: [21]: ".__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 08:07:31.191][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-15 08:07:31.192][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-15 08:07:31.193][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-15 08:07:31.193][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-15 08:07:31.194][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 08:07:31.195][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-15 08:07:31.196][FUN] Functions in observer BiodbConfig: [21]: ".__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 08:07:31.196][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-15 08:07:31.197][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-15 08:07:31.198][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-15 08:07:31.198][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-15 08:07:31.199][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 08:07:31.200][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-15 08:07:31.200][FUN] Functions in observer BiodbConfig: [21]: ".__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 08:07:31.201][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-15 08:07:31.202][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-15 08:07:31.203][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-15 08:07:31.203][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-15 08:07:31.204][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 08:07:31.205][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-15 08:07:31.205][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-15 08:07:31.206][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-15 08:07:31.207][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-15 08:07:31.208][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-15 08:07:31.208][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-15 08:07:31.209][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 08:07:31.210][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-15 08:07:31.210][FUN] Functions in observer BiodbConfig: [21]: ".__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 08:07:31.211][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-15 08:07:31.212][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-15 08:07:31.212][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-15 08:07:31.213][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-15 08:07:31.214][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 08:07:31.215][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-15 08:07:31.215][FUN] Functions in observer BiodbConfig: [21]: ".__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 08:07:31.217][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.15-bioc-longtests/meat/biodbMirbase.Rcheck/biodbMirbase/definitions.yml".
biodb.DEBUG[2022-10-15 08:07:31.218][self$getDbsInfo()$define] Define connector mirbase.mature.
biodb.DEBUG[2022-10-15 08:07:31.219][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2022-10-15 08:07:31.220][self$setPropertyValue] Setting property "description" to "Write here the description of this database.".
biodb.DEBUG[2022-10-15 08:07:31.221][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2022-10-15 08:07:31.221][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2022-10-15 08:07:31.222][self$setPropertyValue] Setting property "downloadable" to "TRUE".
biodb.DEBUG[2022-10-15 08:07:31.223][self$setPropertyValue] Setting property "dwnld.ext" to "gz".
biodb.DEBUG[2022-10-15 08:07:31.224][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2022-10-15 08:07:31.224][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2022-10-15 08:07:31.225][self$setPropertyValue] Setting property "entry.content.type" to "txt".
biodb.DEBUG[2022-10-15 08:07:31.226][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2022-10-15 08:07:31.227][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2022-10-15 08:07:31.228][self$setPropertyValue] Setting property "name" to "miRBase mature database".
biodb.DEBUG[2022-10-15 08:07:31.228][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2022-10-15 08:07:31.229][self$setPropertyValue] Setting property "parsing.expr" to "^>[^ ]+ *(MIMAT[0-9]+) .*$".
biodb.DEBUG[2022-10-15 08:07:31.229][self$setPropertyValue] Setting property "parsing.expr" to "^>[^ ]+ *MIMAT[0-9]+ (.*)$".
biodb.DEBUG[2022-10-15 08:07:31.229][self$setPropertyValue] Setting property "parsing.expr" to "^>([^ ]+) *MIMAT[0-9]+ .*$".
biodb.DEBUG[2022-10-15 08:07:31.229][self$setPropertyValue] Setting property "parsing.expr" to "^([ACGU]+)$".
biodb.DEBUG[2022-10-15 08:07:31.230][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2022-10-15 08:07:31.231][self$setPropertyValue]
biodb.DEBUG[2022-10-15 08:07:31.231][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2022-10-15 08:07:31.232][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-10-15 08:07:31.233][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-10-15 08:07:31.234][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2022-10-15 08:07:31.234][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-10-15 08:07:31.235][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-10-15 08:07:31.236][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2022-10-15 08:07:31.237][self$setPropertyValue] Setting property "urls" to "http://www.mirbase.org/".
biodb.DEBUG[2022-10-15 08:07:31.237][self$setPropertyValue] Setting property "urls" to "https://www.mirbase.org/ftp/CURRENT/mature.fa.gz".
biodb.DEBUG[2022-10-15 08:07:31.237][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2022-10-15 08:07:31.238][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2022-10-15 08:07:31.239][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2022-10-15 08:07:31.239][self$setPropertyValue]
biodb.DEBUG[2022-10-15 08:07:31.240][self$getEntryFields()$define] Define field mirbase.mature.id.
biodb.DEBUG[2022-10-15 08:07:31.243][initialize] Initialize connector mirbase.mature.
biodb.DEBUG[2022-10-15 08:07:31.244][initialize] Register connector mirbase.mature with the request scheduler
biodb.DEBUG[2022-10-15 08:07:31.244][private$bdb$getRequestScheduler()$re ...] Register connector mirbase.mature.
biodb.DEBUG[2022-10-15 08:07:31.246][private$addConnectorRules] Create new rule for URL "www.mirbase.org" of connector "mirbase.mature".
biodb.DEBUG[2022-10-15 08:07:31.247][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2022-10-15 08:07:31.247][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2022-10-15 08:07:31.248][rule$addConnector] Connector "mirbase.mature" is already listed in rule "www.mirbase.org".
biodb.DEBUG[2022-10-15 08:07:31.249][biodb$getFactory()$createConn] Creating new connector mirbase.mature for database class mirbase.mature .
biodb.INFO [2022-10-15 08:07:31.250][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2022-10-15 08:07:31.251][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector mirbase.mature from the request scheduler
biodb.INFO [2022-10-15 08:07:31.252][self$deleteConn] Connector "mirbase.mature" deleted.
biodb.DEBUG[2022-10-15 08:07:31.252][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2022-10-15 08:07:31.253][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-15 08:07:31.254][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-15 08:07:31.254][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-15 08:07:31.255][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 08:07:31.256][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2022-10-15 08:07:31.256][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 75 ]
> 
> proc.time()
   user  system elapsed 
  4.983   2.587  11.732

'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 biodbMirbase_1.0.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.15-bioc-longtests/meat/biodbMirbase.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 ‘biodbMirbase/DESCRIPTION’ ... OK
* this is package ‘biodbMirbase’ 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 ‘biodbMirbase’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* 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: OK

Installation output

biodbMirbase.Rcheck/00install.out

* installing *source* package ‘biodbMirbase’ ...
** 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 (biodbMirbase)