Back to Long Tests report for BioC 3.16

This page was generated on 2023-04-15 21:30:02 -0400 (Sat, 15 Apr 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.5 LTS)x86_644.2.3 (2023-03-15) -- "Shortstop Beagle" 4502
palomino4Windows Server 2022 Datacenterx644.2.3 (2023-03-15 ucrt) -- "Shortstop Beagle" 4282
lconwaymacOS 12.5.1 Montereyx86_644.2.3 (2023-03-15) -- "Shortstop Beagle" 4310
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

CHECK results for biodbMirbase on palomino4


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 10/28HostnameOS / ArchCHECK
biodbMirbase 1.2.2  (landing page)
Pierrick Roger
Snapshot Date: 2023-04-15 06:55:01 -0400 (Sat, 15 Apr 2023)
git_url: https://git.bioconductor.org/packages/biodbMirbase
git_branch: RELEASE_3_16
git_last_commit: 993efd2
git_last_commit_date: 2023-01-09 06:51:56 -0400 (Mon, 09 Jan 2023)
nebbiolo2Linux (Ubuntu 20.04.5 LTS) / x86_64  OK  
palomino4Windows Server 2022 Datacenter / x64  OK  
lconwaymacOS 12.5.1 Monterey / x86_64  OK  

Summary

Package: biodbMirbase
Version: 1.2.2
Command: F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD check --no-multiarch --test-dir=longtests --no-stop-on-test-error --no-codoc --no-examples --no-manual --ignore-vignettes --check-subdirs=no biodbMirbase_1.2.2.tar.gz
StartedAt: 2023-04-15 08:07:20 -0400 (Sat, 15 Apr 2023)
EndedAt: 2023-04-15 08:14:16 -0400 (Sat, 15 Apr 2023)
EllapsedTime: 415.4 seconds
RetCode: 0
Status:   OK  
CheckDir: biodbMirbase.Rcheck
Warnings: 0

Tests output

biodbMirbase.Rcheck/tests/testthat.Rout


R version 4.2.3 (2023-03-15 ucrt) -- "Shortstop Beagle"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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 [2023-04-15 08:08:15.244][biodb::testContext]
biodb.INFO [2023-04-15 08:08:15.247][biodb::testContext] ********************************************************************************
biodb.INFO [2023-04-15 08:08:15.248][biodb::testContext] Test context - Generic long tests
biodb.INFO [2023-04-15 08:08:15.249][biodb::testContext] ********************************************************************************
biodb.INFO [2023-04-15 08:08:15.250][biodb::testContext]
biodb.INFO [2023-04-15 08:08:15.258][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.6.1.
biodb.DEBUG[2023-04-15 08:08:15.260][self$loadDefinitions] Load definitions from file "F:/biocbuild/bbs-3.16-bioc/R/library/biodb/definitions.yml".
biodb.DEBUG[2023-04-15 08:08:15.269][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-04-15 08:08:15.270][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2023-04-15 08:08:15.272][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2023-04-15 08:08:15.273][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:08:15.274][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:08:15.275][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:08:15.277][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2023-04-15 08:08:15.295][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2023-04-15 08:08:15.296][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:08:15.297][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:08:15.298][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:08:15.300][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2023-04-15 08:08:15.301][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2023-04-15 08:08:15.302][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:08:15.303][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:08:15.304][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:08:15.306][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2023-04-15 08:08:15.307][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2023-04-15 08:08:15.308][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2023-04-15 08:08:15.310][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:08:15.311][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:08:15.312][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:08:15.314][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2023-04-15 08:08:15.315][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2023-04-15 08:08:15.316][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2023-04-15 08:08:15.317][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:08:15.318][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:08:15.320][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:08:15.321][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2023-04-15 08:08:15.322][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2023-04-15 08:08:15.323][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:08:15.324][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:08:15.326][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:08:15.327][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2023-04-15 08:08:15.328][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2023-04-15 08:08:15.330][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2023-04-15 08:08:15.331][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:08:15.332][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:08:15.333][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:08:15.335][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2023-04-15 08:08:15.336][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2023-04-15 08:08:15.337][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:08:15.338][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:08:15.339][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:08:15.341][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2023-04-15 08:08:15.342][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2023-04-15 08:08:15.343][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2023-04-15 08:08:15.344][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:08:15.345][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:08:15.347][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:08:15.348][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2023-04-15 08:08:15.349][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2023-04-15 08:08:15.350][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2023-04-15 08:08:15.352][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2023-04-15 08:08:15.353][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2023-04-15 08:08:15.354][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2023-04-15 08:08:15.355][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:08:15.357][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:08:15.358][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:08:15.359][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2023-04-15 08:08:15.360][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2023-04-15 08:08:15.362][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:08:15.363][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:08:15.364][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:08:15.365][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2023-04-15 08:08:15.367][self$set] Set key entries.sep to "|".
biodb.DEBUG[2023-04-15 08:08:15.368][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:08:15.369][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:08:15.370][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:08:15.371][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2023-04-15 08:08:15.373][self$set] Set key offline to FALSE.
biodb.DEBUG[2023-04-15 08:08:15.374][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:08:15.375][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:08:15.376][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:08:15.377][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2023-04-15 08:08:15.379][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2023-04-15 08:08:15.380][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:08:15.381][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:08:15.382][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:08:15.383][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2023-04-15 08:08:15.385][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2023-04-15 08:08:15.386][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:08:15.387][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:08:15.388][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:08:15.389][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2023-04-15 08:08:15.391][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2023-04-15 08:08:15.394][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2023-04-15 08:08:15.395][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:08:15.397][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:08:15.398][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:08:15.399][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2023-04-15 08:08:15.401][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2023-04-15 08:08:15.402][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2023-04-15 08:08:15.403][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:08:15.404][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:08:15.406][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:08:15.410][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2023-04-15 08:08:15.449][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-04-15 08:08:15.462][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2023-04-15 08:08:15.463][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-04-15 08:08:15.465][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-04-15 08:08:15.466][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-04-15 08:08:15.467][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-04-15 08:08:15.468][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-04-15 08:08:15.469][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-04-15 08:08:15.470][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2023-04-15 08:08:15.471][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-04-15 08:08:15.473][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-04-15 08:08:15.474][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2023-04-15 08:08:15.475][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-04-15 08:08:15.476][self$setPropertyValue]
biodb.DEBUG[2023-04-15 08:08:15.477][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-04-15 08:08:15.478][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2023-04-15 08:08:15.478][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2023-04-15 08:08:15.478][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2023-04-15 08:08:15.478][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2023-04-15 08:08:15.478][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2023-04-15 08:08:15.479][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-04-15 08:08:15.481][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-15 08:08:15.482][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-15 08:08:15.483][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-04-15 08:08:15.484][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-15 08:08:15.485][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-15 08:08:15.486][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-04-15 08:08:15.487][self$setPropertyValue]
biodb.DEBUG[2023-04-15 08:08:15.488][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-04-15 08:08:15.489][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-04-15 08:08:15.490][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-04-15 08:08:15.491][self$setPropertyValue]
biodb.DEBUG[2023-04-15 08:08:15.493][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2023-04-15 08:08:15.494][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-04-15 08:08:15.496][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2023-04-15 08:08:15.497][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-04-15 08:08:15.498][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-04-15 08:08:15.499][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-04-15 08:08:15.500][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-04-15 08:08:15.501][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-04-15 08:08:15.502][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-04-15 08:08:15.504][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2023-04-15 08:08:15.505][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-04-15 08:08:15.506][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-04-15 08:08:15.507][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2023-04-15 08:08:15.508][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-04-15 08:08:15.509][self$setPropertyValue]
biodb.DEBUG[2023-04-15 08:08:15.510][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-04-15 08:08:15.512][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2023-04-15 08:08:15.512][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2023-04-15 08:08:15.512][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2023-04-15 08:08:15.512][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2023-04-15 08:08:15.512][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2023-04-15 08:08:15.513][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-04-15 08:08:15.514][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-15 08:08:15.515][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-15 08:08:15.516][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-04-15 08:08:15.517][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-15 08:08:15.518][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-15 08:08:15.519][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-04-15 08:08:15.520][self$setPropertyValue]
biodb.DEBUG[2023-04-15 08:08:15.522][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-04-15 08:08:15.523][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-04-15 08:08:15.524][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-04-15 08:08:15.525][self$setPropertyValue]
biodb.DEBUG[2023-04-15 08:08:15.526][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2023-04-15 08:08:15.528][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2023-04-15 08:08:15.529][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2023-04-15 08:08:15.530][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-04-15 08:08:15.531][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-04-15 08:08:15.533][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-04-15 08:08:15.534][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-04-15 08:08:15.535][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-04-15 08:08:15.536][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-04-15 08:08:15.537][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2023-04-15 08:08:15.538][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-04-15 08:08:15.539][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2023-04-15 08:08:15.540][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2023-04-15 08:08:15.542][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-04-15 08:08:15.543][self$setPropertyValue]
biodb.DEBUG[2023-04-15 08:08:15.544][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-04-15 08:08:15.545][self$setPropertyValue]
biodb.DEBUG[2023-04-15 08:08:15.546][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-04-15 08:08:15.547][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-15 08:08:15.548][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-15 08:08:15.549][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-04-15 08:08:15.550][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-15 08:08:15.551][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-15 08:08:15.552][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-04-15 08:08:15.554][self$setPropertyValue]
biodb.DEBUG[2023-04-15 08:08:15.555][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-04-15 08:08:15.556][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-04-15 08:08:15.557][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-04-15 08:08:15.558][self$setPropertyValue]
biodb.DEBUG[2023-04-15 08:08:15.559][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2023-04-15 08:08:15.561][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2023-04-15 08:08:15.562][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2023-04-15 08:08:15.563][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-04-15 08:08:15.564][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-04-15 08:08:15.566][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-04-15 08:08:15.567][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-04-15 08:08:15.568][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-04-15 08:08:15.569][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-04-15 08:08:15.570][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2023-04-15 08:08:15.571][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-04-15 08:08:15.572][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2023-04-15 08:08:15.573][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2023-04-15 08:08:15.575][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-04-15 08:08:15.576][self$setPropertyValue]
biodb.DEBUG[2023-04-15 08:08:15.577][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-04-15 08:08:15.578][self$setPropertyValue]
biodb.DEBUG[2023-04-15 08:08:15.579][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-04-15 08:08:15.580][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-15 08:08:15.581][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-15 08:08:15.582][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-04-15 08:08:15.583][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-15 08:08:15.584][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-15 08:08:15.585][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-04-15 08:08:15.587][self$setPropertyValue]
biodb.DEBUG[2023-04-15 08:08:15.588][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-04-15 08:08:15.589][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-04-15 08:08:15.590][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-04-15 08:08:15.591][self$setPropertyValue]
biodb.DEBUG[2023-04-15 08:08:15.594][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-04-15 08:08:15.595][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:08:15.596][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:08:15.597][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:08:15.598][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:08:15.599][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-15 08:08:15.601][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:08:15.602][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:08:15.603][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:08:15.604][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:08:15.605][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-15 08:08:15.606][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:08:15.607][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:08:15.608][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:08:15.609][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:08:15.610][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-15 08:08:15.611][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:08:15.612][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:08:15.613][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:08:15.614][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:08:15.615][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-15 08:08:15.616][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:08:15.617][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:08:15.618][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:08:15.619][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:08:15.620][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-15 08:08:15.621][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:08:15.622][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:08:15.623][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:08:15.624][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:08:15.625][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-15 08:08:15.626][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:08:15.627][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:08:15.628][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:08:15.629][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:08:15.630][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-15 08:08:15.631][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:08:15.632][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:08:15.633][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:08:15.634][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:08:15.635][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-15 08:08:15.637][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:08:15.638][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:08:15.639][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:08:15.640][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:08:15.641][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-15 08:08:15.642][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:08:15.643][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:08:15.644][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:08:15.645][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:08:15.646][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-15 08:08:15.647][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:08:15.648][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:08:15.649][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:08:15.650][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:08:15.651][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-15 08:08:15.652][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:08:15.653][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:08:15.654][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:08:15.655][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:08:15.656][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-15 08:08:15.657][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:08:15.658][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:08:15.659][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:08:15.660][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:08:15.661][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-15 08:08:15.662][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:08:15.663][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:08:15.664][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:08:15.665][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:08:15.666][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-15 08:08:15.667][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:08:15.668][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:08:15.669][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:08:15.670][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:08:15.671][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-15 08:08:15.673][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:08:15.674][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:08:15.675][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:08:15.676][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:08:15.677][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-15 08:08:15.678][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:08:15.679][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:08:15.680][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:08:15.681][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:08:15.682][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-15 08:08:15.683][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:08:15.684][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:08:15.685][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2023-04-15 08:08:15.689][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2023-04-15 08:08:15.690][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2023-04-15 08:08:15.692][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2023-04-15 08:08:15.693][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2023-04-15 08:08:15.695][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2023-04-15 08:08:15.696][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2023-04-15 08:08:15.698][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2023-04-15 08:08:15.699][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2023-04-15 08:08:15.701][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2023-04-15 08:08:15.707][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2023-04-15 08:08:15.708][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2023-04-15 08:08:15.710][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2023-04-15 08:08:15.711][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2023-04-15 08:08:15.713][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2023-04-15 08:08:15.714][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2023-04-15 08:08:15.716][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2023-04-15 08:08:15.717][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2023-04-15 08:08:15.718][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2023-04-15 08:08:15.720][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2023-04-15 08:08:15.721][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2023-04-15 08:08:15.723][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2023-04-15 08:08:15.724][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2023-04-15 08:08:15.726][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2023-04-15 08:08:15.727][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2023-04-15 08:08:15.729][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2023-04-15 08:08:15.730][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2023-04-15 08:08:15.732][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2023-04-15 08:08:15.733][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2023-04-15 08:08:15.734][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2023-04-15 08:08:15.736][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2023-04-15 08:08:15.737][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2023-04-15 08:08:15.739][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2023-04-15 08:08:15.740][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2023-04-15 08:08:15.742][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2023-04-15 08:08:15.743][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2023-04-15 08:08:15.745][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2023-04-15 08:08:15.746][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2023-04-15 08:08:15.748][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2023-04-15 08:08:15.749][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2023-04-15 08:08:15.751][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2023-04-15 08:08:15.752][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2023-04-15 08:08:15.753][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2023-04-15 08:08:15.755][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2023-04-15 08:08:15.756][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2023-04-15 08:08:15.758][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2023-04-15 08:08:15.759][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2023-04-15 08:08:15.761][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2023-04-15 08:08:15.762][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2023-04-15 08:08:15.764][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2023-04-15 08:08:15.765][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2023-04-15 08:08:15.767][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2023-04-15 08:08:15.768][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2023-04-15 08:08:15.770][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2023-04-15 08:08:15.771][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2023-04-15 08:08:15.773][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2023-04-15 08:08:15.774][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2023-04-15 08:08:15.775][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2023-04-15 08:08:15.777][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2023-04-15 08:08:15.778][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2023-04-15 08:08:15.780][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2023-04-15 08:08:15.781][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2023-04-15 08:08:15.783][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2023-04-15 08:08:15.784][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2023-04-15 08:08:15.786][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2023-04-15 08:08:15.787][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2023-04-15 08:08:15.789][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2023-04-15 08:08:15.790][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2023-04-15 08:08:15.791][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2023-04-15 08:08:15.793][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2023-04-15 08:08:15.794][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2023-04-15 08:08:15.796][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2023-04-15 08:08:15.797][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2023-04-15 08:08:15.799][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2023-04-15 08:08:15.800][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2023-04-15 08:08:15.802][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2023-04-15 08:08:15.803][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2023-04-15 08:08:15.805][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2023-04-15 08:08:15.806][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2023-04-15 08:08:15.808][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2023-04-15 08:08:15.809][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2023-04-15 08:08:15.810][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2023-04-15 08:08:15.812][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2023-04-15 08:08:15.839][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2023-04-15 08:08:15.841][initialize] This is biodb version 1.6.1.
biodb.DEBUG[2023-04-15 08:08:15.844][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-04-15 08:08:15.845][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:08:15.846][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-15 08:08:15.847][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:08:15.848][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[2023-04-15 08:08:15.853][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:08:15.854][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-15 08:08:15.855][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-15 08:08:15.856][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:08:15.857][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-15 08:08:15.858][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:08:15.859][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[2023-04-15 08:08:15.860][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:08:15.861][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-15 08:08:15.862][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-15 08:08:15.863][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:08:15.864][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-15 08:08:15.865][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:08:15.866][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:08:15.867][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:08:15.868][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-15 08:08:15.869][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-15 08:08:15.870][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:08:15.871][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-15 08:08:15.872][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:08:15.873][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:08:15.874][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:08:15.875][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-15 08:08:15.876][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-15 08:08:15.877][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:08:15.878][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-15 08:08:15.879][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:08:15.880][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:08:15.881][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:08:15.882][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-15 08:08:15.883][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-15 08:08:15.884][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:08:15.885][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-15 08:08:15.886][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:08:15.887][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:08:15.888][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:08:15.889][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-15 08:08:15.890][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-15 08:08:15.891][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:08:15.892][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-15 08:08:15.893][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:08:15.894][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:08:15.895][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:08:15.896][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-15 08:08:15.897][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-15 08:08:15.898][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:08:15.899][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-15 08:08:15.900][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:08:15.901][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:08:15.902][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:08:15.903][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-15 08:08:15.904][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-15 08:08:15.905][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:08:15.906][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-15 08:08:15.907][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:08:15.908][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:08:15.909][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:08:15.910][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-15 08:08:15.911][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-15 08:08:15.912][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:08:15.913][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-15 08:08:15.914][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:08:15.915][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:08:15.916][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:08:15.917][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-15 08:08:15.918][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-15 08:08:15.919][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:08:15.920][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-15 08:08:15.921][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:08:15.922][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:08:15.923][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:08:15.924][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-15 08:08:15.925][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-15 08:08:15.926][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:08:15.927][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-15 08:08:15.928][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:08:15.929][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:08:15.930][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:08:15.931][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-15 08:08:15.932][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-15 08:08:15.933][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:08:15.934][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-15 08:08:15.935][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:08:15.936][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:08:15.937][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:08:15.938][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-15 08:08:15.939][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-15 08:08:15.940][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:08:15.941][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-15 08:08:15.942][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:08:15.943][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:08:15.944][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:08:15.945][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-15 08:08:15.946][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-15 08:08:15.947][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:08:15.948][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-15 08:08:15.949][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:08:15.950][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:08:15.951][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:08:15.952][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-15 08:08:15.953][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-15 08:08:15.954][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:08:15.955][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-15 08:08:15.956][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:08:15.957][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[2023-04-15 08:08:15.958][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:08:15.959][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-15 08:08:15.960][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-15 08:08:15.961][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:08:15.962][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-15 08:08:15.963][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:08:15.964][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[2023-04-15 08:08:15.965][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:08:15.966][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-15 08:08:15.967][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-15 08:08:15.968][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:08:15.969][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-15 08:08:15.970][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:08:15.971][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:08:15.978][biodb$loadDefinitions] Load definitions from file "F:/biocbuild/bbs-3.16-bioc-longtests/meat/biodbMirbase.Rcheck/biodbMirbase/definitions.yml".
biodb.DEBUG[2023-04-15 08:08:15.986][self$getDbsInfo()$define] Define connector mirbase.mature.
biodb.DEBUG[2023-04-15 08:08:15.988][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-04-15 08:08:15.989][self$setPropertyValue] Setting property "description" to "Write here the description of this database.".
biodb.DEBUG[2023-04-15 08:08:15.990][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-04-15 08:08:15.991][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-04-15 08:08:15.993][self$setPropertyValue] Setting property "downloadable" to "TRUE".
biodb.DEBUG[2023-04-15 08:08:15.994][self$setPropertyValue] Setting property "dwnld.ext" to "gz".
biodb.DEBUG[2023-04-15 08:08:15.995][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2023-04-15 08:08:15.996][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-04-15 08:08:15.997][self$setPropertyValue] Setting property "entry.content.type" to "txt".
biodb.DEBUG[2023-04-15 08:08:15.998][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-04-15 08:08:15.999][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-04-15 08:08:16.000][self$setPropertyValue] Setting property "name" to "miRBase mature database".
biodb.DEBUG[2023-04-15 08:08:16.001][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-04-15 08:08:16.002][self$setPropertyValue] Setting property "parsing.expr" to "^>[^ ]+ *(MIMAT[0-9]+) .*$".
biodb.DEBUG[2023-04-15 08:08:16.002][self$setPropertyValue] Setting property "parsing.expr" to "^>[^ ]+ *MIMAT[0-9]+ (.*)$".
biodb.DEBUG[2023-04-15 08:08:16.002][self$setPropertyValue] Setting property "parsing.expr" to "^>([^ ]+) *MIMAT[0-9]+ .*$".
biodb.DEBUG[2023-04-15 08:08:16.002][self$setPropertyValue] Setting property "parsing.expr" to "^([ACGU]+)$".
biodb.DEBUG[2023-04-15 08:08:16.004][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2023-04-15 08:08:16.005][self$setPropertyValue]
biodb.DEBUG[2023-04-15 08:08:16.006][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2023-04-15 08:08:16.007][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-15 08:08:16.008][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-15 08:08:16.009][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-04-15 08:08:16.010][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-15 08:08:16.011][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-15 08:08:16.012][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-04-15 08:08:16.013][self$setPropertyValue] Setting property "urls" to "http://www.mirbase.org/".
biodb.DEBUG[2023-04-15 08:08:16.013][self$setPropertyValue] Setting property "urls" to "https://www.mirbase.org/ftp/CURRENT/mature.fa.gz".
biodb.DEBUG[2023-04-15 08:08:16.014][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-04-15 08:08:16.015][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-04-15 08:08:16.017][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2023-04-15 08:08:16.018][self$setPropertyValue]
biodb.DEBUG[2023-04-15 08:08:16.023][self$getEntryFields()$define] Define field mirbase.mature.id.
biodb.DEBUG[2023-04-15 08:08:16.044][initialize] Initialize connector mirbase.mature.
biodb.DEBUG[2023-04-15 08:08:16.045][initialize] Register connector mirbase.mature with the request scheduler
biodb.DEBUG[2023-04-15 08:08:16.049][private$bdb$getRequestScheduler()$re ...] Register connector mirbase.mature.
biodb.DEBUG[2023-04-15 08:08:16.053][private$addConnectorRules] Create new rule for URL "www.mirbase.org" of connector "mirbase.mature".
biodb.DEBUG[2023-04-15 08:08:16.057][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2023-04-15 08:08:16.058][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2023-04-15 08:08:16.059][rule$addConnector] Connector "mirbase.mature" is already listed in rule "www.mirbase.org".
biodb.DEBUG[2023-04-15 08:08:16.060][biodb$getFactory()$createConn] Creating new connector mirbase.mature for database class mirbase.mature .
biodb.INFO [2023-04-15 08:08:16.069][biodb::testThat]
biodb.INFO [2023-04-15 08:08:16.070][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2023-04-15 08:08:16.071][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-04-15 08:08:16.072][biodb::testThat]
biodb.TRACE[2023-04-15 08:08:16.077][loadFileContents] Loaded 1 files from cache: [1]: "F:/biocbuild/bbs-3.16-bioc-longtests/meat/biodbMirbase.Rcheck/biodbMirbase/testref/entry-mirbase.mature-MIMAT0000433-content.txt".
biodb.DEBUG[2023-04-15 08:08:16.078][biodb$getFactory()$createEntryFromCo ...] Creating miRBase mature database entries from 1 content(s).
biodb.DEBUG[2023-04-15 08:08:16.082][biodb$getFactory()$createEntryFromCo ...] Parsing 1 miRBase mature database entries.
biodb.DEBUG[2023-04-15 08:08:16.089][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-15 08:08:16.090][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-15 08:08:16.091][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-15 08:08:16.107][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:08:16.108][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-15 08:08:16.109][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:08:16.110][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-15 08:08:16.120][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-15 08:08:16.121][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-15 08:08:16.122][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:08:16.123][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:08:16.144][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-04-15 08:08:16.158][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-04-15 08:08:16.160][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:08:16.161][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:08:16.163][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-15 08:08:16.165][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-15 08:08:16.166][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:08:16.168][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:08:16.169][self$getBiodb()$getEntryFields()$get] Asked field names are: sequence.
biodb.TRACE[2023-04-15 08:08:16.171][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2023-04-15 08:08:16.173][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:08:16.174][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:08:16.176][self$getBiodb()$getEntryFields()$get] Asked field names are: mirbase.mature.id.
biodb.TRACE[2023-04-15 08:08:16.177][self$getBiodb()$getEntryFields()$get] Realnames of fields are: mirbase.mature.id.
biodb.TRACE[2023-04-15 08:08:16.179][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:08:16.180][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:08:16.182][self$getBiodb()$getEntryFields()$get] Asked field names are: mirbase.mature.id.
biodb.TRACE[2023-04-15 08:08:16.183][self$getBiodb()$getEntryFields()$get] Realnames of fields are: mirbase.mature.id.
biodb.TRACE[2023-04-15 08:08:16.185][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:08:16.186][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:08:16.188][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-15 08:08:16.189][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-15 08:08:16.191][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:08:16.192][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:08:16.194][self$getBiodb()$getEntryFields()$get] Asked field names are: mirbase.mature.id.
biodb.TRACE[2023-04-15 08:08:16.196][self$getBiodb()$getEntryFields()$get] Realnames of fields are: mirbase.mature.id.
biodb.TRACE[2023-04-15 08:08:16.197][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:08:16.198][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:08:16.200][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-15 08:08:16.201][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-15 08:08:16.203][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:08:16.204][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:08:16.206][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-15 08:08:16.207][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-15 08:08:16.209][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:08:16.210][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:08:16.212][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-15 08:08:16.213][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-15 08:08:16.215][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:08:16.216][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:08:16.277][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-15 08:08:16.279][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-15 08:08:16.280][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:08:16.282][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:08:16.283][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-15 08:08:16.285][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-15 08:08:16.286][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:08:16.288][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:08:16.289][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-15 08:08:16.291][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-15 08:08:16.292][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:08:16.293][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-15 08:08:16.295][biodb$getFactory()$createEntryFromCo ...] Accession numbers: MIMAT0000433.
biodb.TRACE[2023-04-15 08:08:16.298][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2023-04-15 08:08:16.299][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2023-04-15 08:08:16.300][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:08:16.301][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:08:16.303][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2023-04-15 08:08:16.304][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2023-04-15 08:08:16.305][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:08:16.306][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:08:16.307][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2023-04-15 08:08:16.309][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2023-04-15 08:08:16.310][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:08:16.311][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:08:16.312][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2023-04-15 08:08:16.313][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2023-04-15 08:08:16.314][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:08:16.315][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:08:16.335][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-15 08:08:16.337][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-15 08:08:16.338][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:08:16.339][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:08:16.353][self$getBiodb()$getEntryFields()$get] Asked field names are: mirbase.mature.id.
biodb.TRACE[2023-04-15 08:08:16.354][self$getBiodb()$getEntryFields()$get] Realnames of fields are: mirbase.mature.id.
biodb.TRACE[2023-04-15 08:08:16.355][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:08:16.357][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:08:16.363][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-15 08:08:16.364][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-15 08:08:16.366][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:08:16.367][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:08:16.368][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-15 08:08:16.369][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-15 08:08:16.370][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:08:16.371][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:08:16.372][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-15 08:08:16.374][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-15 08:08:16.375][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:08:16.376][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:08:16.378][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-15 08:08:16.379][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-15 08:08:16.380][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:08:16.381][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:08:16.383][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-15 08:08:16.384][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-15 08:08:16.385][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:08:16.386][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:08:16.387][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-15 08:08:16.388][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-15 08:08:16.389][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:08:16.390][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:08:16.392][self$getBiodb()$getEntryFields()$get] Asked field names are: mirbase.mature.id.
biodb.TRACE[2023-04-15 08:08:16.393][self$getBiodb()$getEntryFields()$get] Realnames of fields are: mirbase.mature.id.
biodb.TRACE[2023-04-15 08:08:16.394][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:08:16.395][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:08:16.397][self$getBiodb()$getEntryFields()$get] Asked field names are: mirbase.mature.id.
biodb.TRACE[2023-04-15 08:08:16.398][self$getBiodb()$getEntryFields()$get] Realnames of fields are: mirbase.mature.id.
biodb.TRACE[2023-04-15 08:08:16.400][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:08:16.401][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:08:16.402][self$getBiodb()$getEntryFields()$get] Asked field names are: mirbase.mature.id.
biodb.TRACE[2023-04-15 08:08:16.403][self$getBiodb()$getEntryFields()$get] Realnames of fields are: mirbase.mature.id.
biodb.TRACE[2023-04-15 08:08:16.404][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:08:16.406][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:08:16.415][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-15 08:08:16.416][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-15 08:08:16.418][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:08:16.419][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:08:16.420][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-15 08:08:16.421][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-15 08:08:16.422][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:08:16.423][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:08:16.424][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-15 08:08:16.426][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-15 08:08:16.427][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:08:16.428][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:08:16.429][ef$get] Asked field names are: accession.
biodb.TRACE[2023-04-15 08:08:16.430][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-15 08:08:16.431][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:08:16.432][ef$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:08:16.433][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-15 08:08:16.435][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-15 08:08:16.436][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:08:16.438][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:08:16.447][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-15 08:08:16.448][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-15 08:08:16.449][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:08:16.450][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:08:16.452][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-15 08:08:16.453][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-15 08:08:16.454][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:08:16.455][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:08:16.456][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-15 08:08:16.457][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-15 08:08:16.458][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:08:16.459][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:08:16.461][ef$get] Asked field names are: name.
biodb.TRACE[2023-04-15 08:08:16.462][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-04-15 08:08:16.463][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:08:16.464][ef$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:08:16.465][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-15 08:08:16.466][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-15 08:08:16.467][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:08:16.468][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:08:16.477][self$getBiodb()$getEntryFields()$get] Asked field names are: sequence.
biodb.TRACE[2023-04-15 08:08:16.479][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2023-04-15 08:08:16.480][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:08:16.481][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:08:16.482][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2023-04-15 08:08:16.484][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2023-04-15 08:08:16.485][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:08:16.486][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:08:16.487][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2023-04-15 08:08:16.488][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2023-04-15 08:08:16.490][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:08:16.491][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:08:16.492][ef$get] Asked field names are: sequence.
biodb.TRACE[2023-04-15 08:08:16.493][ef$get] Realnames of fields are: aa.seq.
biodb.TRACE[2023-04-15 08:08:16.494][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:08:16.495][ef$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:08:16.501][self$getBiodb()$getEntryFields()$get] Asked field names are: sequence.
biodb.TRACE[2023-04-15 08:08:16.502][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2023-04-15 08:08:16.503][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:08:16.504][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:08:16.513][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-04-15 08:08:16.514][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-04-15 08:08:16.516][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:08:16.517][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:08:16.518][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-04-15 08:08:16.519][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-04-15 08:08:16.520][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:08:16.521][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:08:16.522][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-04-15 08:08:16.523][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-04-15 08:08:16.525][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:08:16.526][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:08:16.527][ef$get] Asked field names are: description.
biodb.TRACE[2023-04-15 08:08:16.528][ef$get] Realnames of fields are: description.
biodb.TRACE[2023-04-15 08:08:16.529][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:08:16.530][ef$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:08:16.531][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-04-15 08:08:16.532][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-04-15 08:08:16.534][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:08:16.535][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:08:16.543][ef$get] Asked field names are: aa.seq.
biodb.TRACE[2023-04-15 08:08:16.545][ef$get] Realnames of fields are: aa.seq.
biodb.TRACE[2023-04-15 08:08:16.546][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:08:16.547][ef$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:08:16.553][ef$get] Asked field names are: accession.
biodb.TRACE[2023-04-15 08:08:16.555][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-15 08:08:16.556][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:08:16.557][ef$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:08:16.563][ef$get] Asked field names are: description.
biodb.TRACE[2023-04-15 08:08:16.565][ef$get] Realnames of fields are: description.
biodb.TRACE[2023-04-15 08:08:16.566][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:08:16.567][ef$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:08:16.573][ef$get] Asked field names are: name.
biodb.TRACE[2023-04-15 08:08:16.574][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-04-15 08:08:16.576][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:08:16.577][ef$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:08:16.594][loadFileContents] Loaded 1 files from cache: [1]: "F:/biocbuild/bbs-3.16-bioc-longtests/meat/biodbMirbase.Rcheck/biodbMirbase/testref/entry-mirbase.mature-MIMAT0000434-content.txt".
biodb.DEBUG[2023-04-15 08:08:16.621][biodb$getFactory()$createEntryFromCo ...] Creating miRBase mature database entries from 1 content(s).
biodb.DEBUG[2023-04-15 08:08:16.623][biodb$getFactory()$createEntryFromCo ...] Parsing 1 miRBase mature database entries.
biodb.DEBUG[2023-04-15 08:08:16.624][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-15 08:08:16.625][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-15 08:08:16.627][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-15 08:08:16.633][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:08:16.634][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-15 08:08:16.635][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:08:16.636][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-15 08:08:16.638][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-15 08:08:16.640][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-15 08:08:16.641][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:08:16.642][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:08:16.656][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-04-15 08:08:16.657][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-04-15 08:08:16.658][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:08:16.659][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:08:16.661][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-15 08:08:16.662][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-15 08:08:16.663][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:08:16.664][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:08:16.666][self$getBiodb()$getEntryFields()$get] Asked field names are: sequence.
biodb.TRACE[2023-04-15 08:08:16.667][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2023-04-15 08:08:16.668][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:08:16.669][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:08:16.670][self$getBiodb()$getEntryFields()$get] Asked field names are: mirbase.mature.id.
biodb.TRACE[2023-04-15 08:08:16.672][self$getBiodb()$getEntryFields()$get] Realnames of fields are: mirbase.mature.id.
biodb.TRACE[2023-04-15 08:08:16.673][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:08:16.674][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:08:16.675][self$getBiodb()$getEntryFields()$get] Asked field names are: mirbase.mature.id.
biodb.TRACE[2023-04-15 08:08:16.676][self$getBiodb()$getEntryFields()$get] Realnames of fields are: mirbase.mature.id.
biodb.TRACE[2023-04-15 08:08:16.677][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:08:16.678][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:08:16.680][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-15 08:08:16.681][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-15 08:08:16.682][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:08:16.683][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:08:16.684][self$getBiodb()$getEntryFields()$get] Asked field names are: mirbase.mature.id.
biodb.TRACE[2023-04-15 08:08:16.686][self$getBiodb()$getEntryFields()$get] Realnames of fields are: mirbase.mature.id.
biodb.TRACE[2023-04-15 08:08:16.687][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:08:16.688][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:08:16.689][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-15 08:08:16.694][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-15 08:08:16.695][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:08:16.696][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:08:16.698][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-15 08:08:16.699][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-15 08:08:16.700][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:08:16.701][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:08:16.702][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-15 08:08:16.704][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-15 08:08:16.705][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:08:16.706][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:08:16.707][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-15 08:08:16.708][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-15 08:08:16.709][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:08:16.710][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:08:16.712][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-15 08:08:16.713][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-15 08:08:16.714][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:08:16.715][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:08:16.716][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-15 08:08:16.717][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-15 08:08:16.718][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:08:16.719][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-15 08:08:16.721][biodb$getFactory()$createEntryFromCo ...] Accession numbers: MIMAT0000434.
biodb.TRACE[2023-04-15 08:08:16.738][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2023-04-15 08:08:16.739][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2023-04-15 08:08:16.740][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:08:16.741][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:08:16.742][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2023-04-15 08:08:16.744][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2023-04-15 08:08:16.745][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:08:16.746][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:08:16.747][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2023-04-15 08:08:16.748][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2023-04-15 08:08:16.749][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:08:16.750][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:08:16.751][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2023-04-15 08:08:16.753][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2023-04-15 08:08:16.754][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:08:16.755][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:08:16.757][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-15 08:08:16.758][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-15 08:08:16.759][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:08:16.760][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:08:16.767][self$getBiodb()$getEntryFields()$get] Asked field names are: mirbase.mature.id.
biodb.TRACE[2023-04-15 08:08:16.768][self$getBiodb()$getEntryFields()$get] Realnames of fields are: mirbase.mature.id.
biodb.TRACE[2023-04-15 08:08:16.769][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:08:16.771][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:08:16.777][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-15 08:08:16.778][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-15 08:08:16.779][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:08:16.781][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:08:16.782][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-15 08:08:16.783][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-15 08:08:16.784][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:08:16.785][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:08:16.786][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-15 08:08:16.788][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-15 08:08:16.789][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:08:16.790][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:08:16.792][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-15 08:08:16.793][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-15 08:08:16.794][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:08:16.795][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:08:16.797][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-15 08:08:16.798][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-15 08:08:16.799][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:08:16.800][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:08:16.801][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-15 08:08:16.802][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-15 08:08:16.803][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:08:16.804][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:08:16.806][self$getBiodb()$getEntryFields()$get] Asked field names are: mirbase.mature.id.
biodb.TRACE[2023-04-15 08:08:16.807][self$getBiodb()$getEntryFields()$get] Realnames of fields are: mirbase.mature.id.
biodb.TRACE[2023-04-15 08:08:16.808][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:08:16.809][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:08:16.810][self$getBiodb()$getEntryFields()$get] Asked field names are: mirbase.mature.id.
biodb.TRACE[2023-04-15 08:08:16.812][self$getBiodb()$getEntryFields()$get] Realnames of fields are: mirbase.mature.id.
biodb.TRACE[2023-04-15 08:08:16.813][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:08:16.814][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:08:16.815][self$getBiodb()$getEntryFields()$get] Asked field names are: mirbase.mature.id.
biodb.TRACE[2023-04-15 08:08:16.816][self$getBiodb()$getEntryFields()$get] Realnames of fields are: mirbase.mature.id.
biodb.TRACE[2023-04-15 08:08:16.817][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:08:16.818][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:08:16.835][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-15 08:08:16.836][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-15 08:08:16.837][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:08:16.838][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:08:16.840][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-15 08:08:16.841][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-15 08:08:16.842][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:08:16.843][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:08:16.844][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-15 08:08:16.845][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-15 08:08:16.846][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:08:16.848][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:08:16.849][ef$get] Asked field names are: accession.
biodb.TRACE[2023-04-15 08:08:16.850][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-15 08:08:16.851][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:08:16.852][ef$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:08:16.854][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-15 08:08:16.855][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-15 08:08:16.856][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:08:16.857][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:08:16.866][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-15 08:08:16.867][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-15 08:08:16.868][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:08:16.869][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:08:16.870][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-15 08:08:16.872][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-15 08:08:16.873][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:08:16.874][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:08:16.875][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-15 08:08:16.876][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-15 08:08:16.878][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:08:16.879][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:08:16.880][ef$get] Asked field names are: name.
biodb.TRACE[2023-04-15 08:08:16.881][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-04-15 08:08:16.882][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:08:16.884][ef$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:08:16.885][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-15 08:08:16.886][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-15 08:08:16.887][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:08:16.888][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:08:16.897][self$getBiodb()$getEntryFields()$get] Asked field names are: sequence.
biodb.TRACE[2023-04-15 08:08:16.899][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2023-04-15 08:08:16.900][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:08:16.901][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:08:16.902][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2023-04-15 08:08:16.903][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2023-04-15 08:08:16.904][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:08:16.905][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:08:16.906][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2023-04-15 08:08:16.908][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2023-04-15 08:08:16.912][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:08:16.914][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:08:16.915][ef$get] Asked field names are: sequence.
biodb.TRACE[2023-04-15 08:08:16.916][ef$get] Realnames of fields are: aa.seq.
biodb.TRACE[2023-04-15 08:08:16.917][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:08:16.918][ef$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:08:16.919][self$getBiodb()$getEntryFields()$get] Asked field names are: sequence.
biodb.TRACE[2023-04-15 08:08:16.921][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2023-04-15 08:08:16.922][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:08:16.923][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:08:16.932][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-04-15 08:08:16.933][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-04-15 08:08:16.934][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:08:16.935][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:08:16.936][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-04-15 08:08:16.937][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-04-15 08:08:16.938][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:08:16.939][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:08:16.941][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-04-15 08:08:16.942][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-04-15 08:08:16.943][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:08:16.944][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:08:16.945][ef$get] Asked field names are: description.
biodb.TRACE[2023-04-15 08:08:16.947][ef$get] Realnames of fields are: description.
biodb.TRACE[2023-04-15 08:08:16.948][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:08:16.949][ef$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:08:16.950][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-04-15 08:08:16.951][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-04-15 08:08:16.952][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:08:16.953][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:08:16.962][ef$get] Asked field names are: aa.seq.
biodb.TRACE[2023-04-15 08:08:16.964][ef$get] Realnames of fields are: aa.seq.
biodb.TRACE[2023-04-15 08:08:16.965][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:08:16.966][ef$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:08:16.972][ef$get] Asked field names are: accession.
biodb.TRACE[2023-04-15 08:08:16.973][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-15 08:08:16.975][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:08:16.976][ef$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:08:16.982][ef$get] Asked field names are: description.
biodb.TRACE[2023-04-15 08:08:16.984][ef$get] Realnames of fields are: description.
biodb.TRACE[2023-04-15 08:08:16.985][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:08:16.986][ef$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:08:16.992][ef$get] Asked field names are: name.
biodb.TRACE[2023-04-15 08:08:16.994][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-04-15 08:08:16.995][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:08:16.996][ef$get] fields variable is a list.
biodb.INFO [2023-04-15 08:08:17.004][biodb::testThat]
biodb.INFO [2023-04-15 08:08:17.005][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2023-04-15 08:08:17.006][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-04-15 08:08:17.007][biodb::testThat]
biodb.DEBUG[2023-04-15 08:08:17.010][private$loadEntries] Creating entries from ids [2]: "MIMAT0000433, MIMAT0000434".
biodb.DEBUG[2023-04-15 08:08:17.016][conn$getEntryContent] Get miRBase mature database entry content(s) for 2 id(s)...
biodb.INFO [2023-04-15 08:08:17.021][self$getFolderPath] Create cache folder "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/mirbase.mature-ecbae556d51779d9d48125ba5a617e19" for "mirbase.mature-ecbae556d51779d9d48125ba5a617e19".
biodb.DEBUG[2023-04-15 08:08:17.023][self$isDownloaded] Database mirbase.mature has not yet been downloaded.
biodb.INFO [2023-04-15 08:08:17.024][self$download] Downloading whole database of mirbase.mature.
biodb.DEBUG[2023-04-15 08:08:17.027][self$getDownloadPath] Download path of mirbase.mature is "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/mirbase.mature-ecbae556d51779d9d48125ba5a617e19/download.gz".
biodb.DEBUG[2023-04-15 08:08:17.028][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[2023-04-15 08:08:19.465][self$getDownloadPath] Download path of mirbase.mature is "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/mirbase.mature-ecbae556d51779d9d48125ba5a617e19/download.gz".
biodb.DEBUG[2023-04-15 08:08:19.467][self$download] Downloading of mirbase.mature completed.
biodb.TRACE[2023-04-15 08:08:19.470][self$addFilesToCache] Moving files to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/tmp\marker7f02ae46188marker".
biodb.TRACE[2023-04-15 08:08:19.472][private$doAddFilesToCache] Destination files are [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/mirbase.mature-ecbae556d51779d9d48125ba5a617e19/downloaded.marker".
biodb.DEBUG[2023-04-15 08:08:19.510][self$addFilesToCache] Done adding files.
biodb.DEBUG[2023-04-15 08:08:19.512][self$isDownloaded] Database mirbase.mature has already been downloaded.
biodb.INFO [2023-04-15 08:08:19.514][self$download] Extract whole database of mirbase.mature.
biodb.DEBUG[2023-04-15 08:08:19.516][self$getDownloadPath] Download path of mirbase.mature is "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/mirbase.mature-ecbae556d51779d9d48125ba5a617e19/download.gz".
biodb.DEBUG[2023-04-15 08:08:19.787][self$getDownloadPath] Download path of mirbase.mature is "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/mirbase.mature-ecbae556d51779d9d48125ba5a617e19/download.gz".
biodb.DEBUG[2023-04-15 08:08:19.788][private$doExtractDownload] Found 48885 entries in file "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/mirbase.mature-ecbae556d51779d9d48125ba5a617e19/download.gz".
biodb.TRACE[2023-04-15 08:08:20.033][private$doSaveContentToFile] Saving to cache [48885]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/mirbase.mature-ecbae556d51779d9d48125ba5a617e19/MIMAT0000001.txt, C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/mirbase.mature-ecbae556d51779d9d48125ba5a617e19/MIMAT0015091.txt, C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/mirbase.mature-ecbae556d51779d9d48125ba5a617e19/MIMAT0000002.txt, C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/mirbase.mature-ecbae556d51779d9d48125ba5a617e19/MIMAT0015092.txt, C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/mirbase.mature-ecbae556d51779d9d48125ba5a617e19/MIMAT0020301.txt, C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/mirbase.mature-ecbae556d51779d9d48125ba5a617e19/MIMAT0000003.txt, C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/mirbase.mature-ecbae556d51779d9d48125ba5a617e19/MIMAT0020302.txt, C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/mirbase.mature-ecbae556d51779d9d48125ba5a617e19/MIMAT0000004.txt, C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/mirbase.mature-ecbae556d51779d9d48125ba5a617e19/MIMAT0000005.txt, C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/mirbase.mature-ecbae556d51779d9d48125ba5a617e19/MIMAT0015093.txt, ..."
biodb.TRACE[2023-04-15 08:14:04.464][self$addFilesToCache] Moving files to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/tmp\marker7f01f74d45marker".
biodb.TRACE[2023-04-15 08:14:04.466][private$doAddFilesToCache] Destination files are [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/mirbase.mature-ecbae556d51779d9d48125ba5a617e19/extracted.marker".
biodb.DEBUG[2023-04-15 08:14:04.478][self$addFilesToCache] Done adding files.
biodb.TRACE[2023-04-15 08:14:04.481][cch$loadFileContent] Trying to load 2 files from cache: [2]: "MIMAT0000433, MIMAT0000434".
biodb.TRACE[2023-04-15 08:14:04.482][cch$loadFileContent] file.exist = [2]: "TRUE, TRUE".
biodb.TRACE[2023-04-15 08:14:04.546][loadFileContents] Loaded 2 files from cache: [2]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/mirbase.mature-ecbae556d51779d9d48125ba5a617e19/MIMAT0000433.txt, C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/mirbase.mature-ecbae556d51779d9d48125ba5a617e19/MIMAT0000434.txt".
biodb.DEBUG[2023-04-15 08:14:04.548][conn$getEntryContent] 2 miRBase mature database entry content(s) loaded from cache.
biodb.DEBUG[2023-04-15 08:14:04.549][self$createEntryFromContent] Creating miRBase mature database entries from 2 content(s).
biodb.DEBUG[2023-04-15 08:14:04.551][self$createEntryFromContent] Parsing 2 miRBase mature database entries.
biodb.DEBUG[2023-04-15 08:14:04.553][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-15 08:14:04.554][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-15 08:14:04.555][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-15 08:14:04.563][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:14:04.564][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-15 08:14:04.565][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:14:04.566][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-15 08:14:04.591][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-15 08:14:04.592][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-15 08:14:04.593][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:14:04.595][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:14:04.596][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-04-15 08:14:04.597][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-04-15 08:14:04.599][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:14:04.600][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:14:04.601][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-15 08:14:04.602][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-15 08:14:04.604][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:14:04.605][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:14:04.606][self$getBiodb()$getEntryFields()$get] Asked field names are: sequence.
biodb.TRACE[2023-04-15 08:14:04.607][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2023-04-15 08:14:04.608][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:14:04.610][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:14:04.611][self$getBiodb()$getEntryFields()$get] Asked field names are: mirbase.mature.id.
biodb.TRACE[2023-04-15 08:14:04.612][self$getBiodb()$getEntryFields()$get] Realnames of fields are: mirbase.mature.id.
biodb.TRACE[2023-04-15 08:14:04.613][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:14:04.614][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:14:04.616][self$getBiodb()$getEntryFields()$get] Asked field names are: mirbase.mature.id.
biodb.TRACE[2023-04-15 08:14:04.617][self$getBiodb()$getEntryFields()$get] Realnames of fields are: mirbase.mature.id.
biodb.TRACE[2023-04-15 08:14:04.618][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:14:04.619][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:14:04.620][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-15 08:14:04.622][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-15 08:14:04.623][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:14:04.624][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:14:04.625][self$getBiodb()$getEntryFields()$get] Asked field names are: mirbase.mature.id.
biodb.TRACE[2023-04-15 08:14:04.626][self$getBiodb()$getEntryFields()$get] Realnames of fields are: mirbase.mature.id.
biodb.TRACE[2023-04-15 08:14:04.628][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:14:04.629][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:14:04.630][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-15 08:14:04.631][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-15 08:14:04.632][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:14:04.634][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:14:04.635][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-15 08:14:04.636][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-15 08:14:04.637][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:14:04.638][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:14:04.640][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-15 08:14:04.641][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-15 08:14:04.642][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:14:04.643][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-15 08:14:04.645][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-15 08:14:04.646][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-15 08:14:04.647][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-15 08:14:04.654][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:14:04.655][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-15 08:14:04.656][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:14:04.657][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-15 08:14:04.659][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-15 08:14:04.661][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-15 08:14:04.662][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:14:04.663][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:14:04.664][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-04-15 08:14:04.666][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-04-15 08:14:04.667][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:14:04.668][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:14:04.669][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-15 08:14:04.671][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-15 08:14:04.672][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:14:04.673][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:14:04.675][self$getBiodb()$getEntryFields()$get] Asked field names are: sequence.
biodb.TRACE[2023-04-15 08:14:04.676][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2023-04-15 08:14:04.677][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:14:04.678][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:14:04.679][self$getBiodb()$getEntryFields()$get] Asked field names are: mirbase.mature.id.
biodb.TRACE[2023-04-15 08:14:04.681][self$getBiodb()$getEntryFields()$get] Realnames of fields are: mirbase.mature.id.
biodb.TRACE[2023-04-15 08:14:04.682][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:14:04.683][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:14:04.684][self$getBiodb()$getEntryFields()$get] Asked field names are: mirbase.mature.id.
biodb.TRACE[2023-04-15 08:14:04.685][self$getBiodb()$getEntryFields()$get] Realnames of fields are: mirbase.mature.id.
biodb.TRACE[2023-04-15 08:14:04.687][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:14:04.688][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:14:04.689][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-15 08:14:04.690][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-15 08:14:04.691][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:14:04.693][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:14:04.694][self$getBiodb()$getEntryFields()$get] Asked field names are: mirbase.mature.id.
biodb.TRACE[2023-04-15 08:14:04.695][self$getBiodb()$getEntryFields()$get] Realnames of fields are: mirbase.mature.id.
biodb.TRACE[2023-04-15 08:14:04.696][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:14:04.697][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:14:04.699][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-15 08:14:04.700][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-15 08:14:04.701][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:14:04.702][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:14:04.703][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-15 08:14:04.705][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-15 08:14:04.706][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:14:04.707][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:14:04.708][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-15 08:14:04.710][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-15 08:14:04.711][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:14:04.712][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:14:04.713][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-15 08:14:04.715][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-15 08:14:04.716][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:14:04.717][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:14:04.718][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-15 08:14:04.719][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-15 08:14:04.720][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:14:04.722][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:14:04.723][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-15 08:14:04.724][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-15 08:14:04.725][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:14:04.726][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:14:04.745][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-15 08:14:04.747][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-15 08:14:04.748][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:14:04.749][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:14:04.750][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-15 08:14:04.752][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-15 08:14:04.753][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:14:04.754][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:14:04.755][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-15 08:14:04.757][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-15 08:14:04.758][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:14:04.759][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-15 08:14:04.760][self$createEntryFromContent] Accession numbers: MIMAT0000433, MIMAT0000434.
biodb.TRACE[2023-04-15 08:14:04.761][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2023-04-15 08:14:04.763][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2023-04-15 08:14:04.764][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:14:04.765][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:14:04.766][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2023-04-15 08:14:04.767][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2023-04-15 08:14:04.768][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:14:04.770][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:14:04.771][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2023-04-15 08:14:04.772][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2023-04-15 08:14:04.773][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:14:04.774][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:14:04.781][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2023-04-15 08:14:04.783][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2023-04-15 08:14:04.784][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:14:04.785][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:14:04.786][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2023-04-15 08:14:04.788][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2023-04-15 08:14:04.789][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:14:04.790][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:14:04.791][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2023-04-15 08:14:04.792][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2023-04-15 08:14:04.794][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:14:04.795][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2023-04-15 08:14:04.803][biodb::testThat]
biodb.INFO [2023-04-15 08:14:04.804][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2023-04-15 08:14:04.806][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-04-15 08:14:04.807][biodb::testThat]
biodb.INFO [2023-04-15 08:14:04.811][biodb::testThat]
biodb.INFO [2023-04-15 08:14:04.812][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2023-04-15 08:14:04.813][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-04-15 08:14:04.814][biodb::testThat]
biodb.WARN [2023-04-15 08:14:04.839][self$searchForEntries] This database is not searchable by field "name".
biodb.WARN [2023-04-15 08:14:04.859][self$searchForEntries] This database is not searchable by field "name".
biodb.INFO [2023-04-15 08:14:04.867][biodb::testThat]
biodb.INFO [2023-04-15 08:14:04.869][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2023-04-15 08:14:04.870][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-04-15 08:14:04.890][biodb::testThat]
biodb.TRACE[2023-04-15 08:14:04.913][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2023-04-15 08:14:04.915][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2023-04-15 08:14:04.916][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:14:04.917][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:14:04.918][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2023-04-15 08:14:04.919][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2023-04-15 08:14:04.921][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:14:04.922][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:14:04.923][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2023-04-15 08:14:04.924][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2023-04-15 08:14:04.925][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:14:04.926][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:14:04.928][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2023-04-15 08:14:04.929][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2023-04-15 08:14:04.930][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:14:04.931][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:14:04.959][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2023-04-15 08:14:04.960][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2023-04-15 08:14:04.962][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:14:04.963][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:14:04.964][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2023-04-15 08:14:04.965][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2023-04-15 08:14:04.966][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:14:04.967][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:14:04.969][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2023-04-15 08:14:04.970][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2023-04-15 08:14:04.971][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:14:04.972][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:14:04.973][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2023-04-15 08:14:04.975][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2023-04-15 08:14:04.976][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:14:04.977][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2023-04-15 08:14:04.981][biodb::testThat]
biodb.INFO [2023-04-15 08:14:04.982][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2023-04-15 08:14:04.984][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-04-15 08:14:04.985][biodb::testThat]
biodb.INFO [2023-04-15 08:14:04.991][biodb::testThat]
biodb.INFO [2023-04-15 08:14:04.993][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2023-04-15 08:14:05.012][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-04-15 08:14:05.014][biodb::testThat]
biodb.INFO [2023-04-15 08:14:05.019][biodb::testThat]
biodb.INFO [2023-04-15 08:14:05.021][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2023-04-15 08:14:05.022][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-04-15 08:14:05.023][biodb::testThat]
biodb.DEBUG[2023-04-15 08:14:05.027][function(conn, opt)] Trying to download "http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000433".
biodb.DEBUG[2023-04-15 08:14:12.192][getUrlContent] Use base::url() for downloading content of URL http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000433.
biodb.INFO [2023-04-15 08:14:13.734][biodb::testThat]
biodb.INFO [2023-04-15 08:14:13.735][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2023-04-15 08:14:13.736][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-04-15 08:14:13.738][biodb::testThat]
biodb.INFO [2023-04-15 08:14:13.742][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2023-04-15 08:14:13.744][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector mirbase.mature from the request scheduler
biodb.INFO [2023-04-15 08:14:13.745][self$deleteConn] Connector "mirbase.mature" deleted.
biodb.DEBUG[2023-04-15 08:14:13.746][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2023-04-15 08:14:13.747][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-15 08:14:13.749][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-15 08:14:13.750][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:14:13.751][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-15 08:14:13.752][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:14:13.753][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2023-04-15 08:14:13.815][biodb::testContext]
biodb.INFO [2023-04-15 08:14:13.816][biodb::testContext] ********************************************************************************
biodb.INFO [2023-04-15 08:14:13.817][biodb::testContext] Test context - Example long tests
biodb.INFO [2023-04-15 08:14:13.819][biodb::testContext] ********************************************************************************
biodb.INFO [2023-04-15 08:14:13.820][biodb::testContext]
biodb.INFO [2023-04-15 08:14:13.822][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.6.1.
biodb.DEBUG[2023-04-15 08:14:13.825][self$loadDefinitions] Load definitions from file "F:/biocbuild/bbs-3.16-bioc/R/library/biodb/definitions.yml".
biodb.DEBUG[2023-04-15 08:14:13.830][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-04-15 08:14:13.831][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2023-04-15 08:14:13.832][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2023-04-15 08:14:13.833][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:14:13.834][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:14:13.836][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:14:13.837][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2023-04-15 08:14:13.838][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2023-04-15 08:14:13.839][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:14:13.840][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:14:13.841][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:14:13.842][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2023-04-15 08:14:13.843][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2023-04-15 08:14:13.844][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:14:13.845][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:14:13.847][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:14:13.848][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2023-04-15 08:14:13.849][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2023-04-15 08:14:13.850][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2023-04-15 08:14:13.851][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:14:13.852][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:14:13.853][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:14:13.854][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2023-04-15 08:14:13.855][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2023-04-15 08:14:13.857][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2023-04-15 08:14:13.858][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:14:13.859][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:14:13.860][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:14:13.861][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2023-04-15 08:14:13.862][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2023-04-15 08:14:13.863][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:14:13.864][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:14:13.865][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:14:13.866][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2023-04-15 08:14:13.964][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2023-04-15 08:14:13.966][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2023-04-15 08:14:13.968][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:14:13.969][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:14:13.971][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:14:13.973][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2023-04-15 08:14:13.974][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2023-04-15 08:14:13.976][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:14:13.977][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:14:13.979][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:14:13.981][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2023-04-15 08:14:13.982][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2023-04-15 08:14:13.984][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2023-04-15 08:14:13.985][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:14:13.986][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:14:13.987][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:14:13.988][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2023-04-15 08:14:13.989][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2023-04-15 08:14:13.990][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2023-04-15 08:14:13.991][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2023-04-15 08:14:13.993][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2023-04-15 08:14:13.994][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2023-04-15 08:14:13.995][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:14:13.996][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:14:13.997][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:14:13.998][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2023-04-15 08:14:14.000][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2023-04-15 08:14:14.001][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:14:14.002][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:14:14.003][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:14:14.004][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2023-04-15 08:14:14.005][self$set] Set key entries.sep to "|".
biodb.DEBUG[2023-04-15 08:14:14.006][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:14:14.007][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:14:14.008][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:14:14.009][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2023-04-15 08:14:14.011][self$set] Set key offline to FALSE.
biodb.DEBUG[2023-04-15 08:14:14.012][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:14:14.013][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:14:14.014][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:14:14.015][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2023-04-15 08:14:14.016][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2023-04-15 08:14:14.017][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:14:14.018][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:14:14.020][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:14:14.021][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2023-04-15 08:14:14.022][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2023-04-15 08:14:14.023][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:14:14.024][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:14:14.025][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:14:14.026][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2023-04-15 08:14:14.027][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2023-04-15 08:14:14.031][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2023-04-15 08:14:14.032][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:14:14.033][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:14:14.034][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:14:14.036][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2023-04-15 08:14:14.037][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2023-04-15 08:14:14.038][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2023-04-15 08:14:14.039][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:14:14.040][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:14:14.041][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:14:14.043][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2023-04-15 08:14:14.045][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-04-15 08:14:14.060][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2023-04-15 08:14:14.061][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-04-15 08:14:14.062][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-04-15 08:14:14.064][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-04-15 08:14:14.065][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-04-15 08:14:14.066][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-04-15 08:14:14.067][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-04-15 08:14:14.068][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2023-04-15 08:14:14.070][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-04-15 08:14:14.071][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-04-15 08:14:14.072][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2023-04-15 08:14:14.073][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-04-15 08:14:14.074][self$setPropertyValue]
biodb.DEBUG[2023-04-15 08:14:14.076][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-04-15 08:14:14.077][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2023-04-15 08:14:14.077][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2023-04-15 08:14:14.077][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2023-04-15 08:14:14.077][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2023-04-15 08:14:14.077][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2023-04-15 08:14:14.078][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-04-15 08:14:14.079][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-15 08:14:14.080][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-15 08:14:14.082][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-04-15 08:14:14.083][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-15 08:14:14.084][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-15 08:14:14.085][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-04-15 08:14:14.086][self$setPropertyValue]
biodb.DEBUG[2023-04-15 08:14:14.087][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-04-15 08:14:14.088][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-04-15 08:14:14.090][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-04-15 08:14:14.091][self$setPropertyValue]
biodb.DEBUG[2023-04-15 08:14:14.092][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2023-04-15 08:14:14.094][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-04-15 08:14:14.095][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2023-04-15 08:14:14.096][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-04-15 08:14:14.098][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-04-15 08:14:14.099][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-04-15 08:14:14.100][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-04-15 08:14:14.101][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-04-15 08:14:14.102][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-04-15 08:14:14.104][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2023-04-15 08:14:14.105][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-04-15 08:14:14.106][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-04-15 08:14:14.108][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2023-04-15 08:14:14.109][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-04-15 08:14:14.110][self$setPropertyValue]
biodb.DEBUG[2023-04-15 08:14:14.111][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-04-15 08:14:14.113][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2023-04-15 08:14:14.113][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2023-04-15 08:14:14.113][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2023-04-15 08:14:14.113][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2023-04-15 08:14:14.113][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2023-04-15 08:14:14.114][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-04-15 08:14:14.115][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-15 08:14:14.116][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-15 08:14:14.117][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-04-15 08:14:14.118][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-15 08:14:14.119][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-15 08:14:14.121][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-04-15 08:14:14.122][self$setPropertyValue]
biodb.DEBUG[2023-04-15 08:14:14.123][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-04-15 08:14:14.124][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-04-15 08:14:14.125][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-04-15 08:14:14.126][self$setPropertyValue]
biodb.DEBUG[2023-04-15 08:14:14.128][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2023-04-15 08:14:14.129][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2023-04-15 08:14:14.131][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2023-04-15 08:14:14.132][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-04-15 08:14:14.133][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-04-15 08:14:14.134][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-04-15 08:14:14.135][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-04-15 08:14:14.136][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-04-15 08:14:14.137][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-04-15 08:14:14.139][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2023-04-15 08:14:14.140][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-04-15 08:14:14.141][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2023-04-15 08:14:14.142][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2023-04-15 08:14:14.143][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-04-15 08:14:14.144][self$setPropertyValue]
biodb.DEBUG[2023-04-15 08:14:14.146][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-04-15 08:14:14.147][self$setPropertyValue]
biodb.DEBUG[2023-04-15 08:14:14.148][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-04-15 08:14:14.149][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-15 08:14:14.159][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-15 08:14:14.161][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-04-15 08:14:14.162][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-15 08:14:14.164][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-15 08:14:14.165][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-04-15 08:14:14.167][self$setPropertyValue]
biodb.DEBUG[2023-04-15 08:14:14.169][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-04-15 08:14:14.170][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-04-15 08:14:14.172][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-04-15 08:14:14.173][self$setPropertyValue]
biodb.DEBUG[2023-04-15 08:14:14.175][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2023-04-15 08:14:14.178][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2023-04-15 08:14:14.179][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2023-04-15 08:14:14.180][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-04-15 08:14:14.181][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-04-15 08:14:14.182][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-04-15 08:14:14.184][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-04-15 08:14:14.185][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-04-15 08:14:14.186][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-04-15 08:14:14.187][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2023-04-15 08:14:14.188][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-04-15 08:14:14.190][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2023-04-15 08:14:14.191][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2023-04-15 08:14:14.192][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-04-15 08:14:14.193][self$setPropertyValue]
biodb.DEBUG[2023-04-15 08:14:14.194][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-04-15 08:14:14.196][self$setPropertyValue]
biodb.DEBUG[2023-04-15 08:14:14.197][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-04-15 08:14:14.198][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-15 08:14:14.199][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-15 08:14:14.200][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-04-15 08:14:14.201][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-15 08:14:14.202][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-15 08:14:14.203][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-04-15 08:14:14.205][self$setPropertyValue]
biodb.DEBUG[2023-04-15 08:14:14.206][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-04-15 08:14:14.207][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-04-15 08:14:14.208][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-04-15 08:14:14.209][self$setPropertyValue]
biodb.DEBUG[2023-04-15 08:14:14.211][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-04-15 08:14:14.212][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:14:14.213][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:14:14.214][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:14:14.215][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:14:14.216][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-15 08:14:14.217][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:14:14.219][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:14:14.220][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:14:14.221][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:14:14.222][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-15 08:14:14.223][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:14:14.224][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[2023-04-15 08:14:14.225][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:14:14.226][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:14:14.227][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-15 08:14:14.228][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:14:14.229][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[2023-04-15 08:14:14.231][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:14:14.232][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:14:14.233][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-15 08:14:14.234][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:14:14.235][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:14:14.236][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:14:14.237][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:14:14.238][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-15 08:14:14.239][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:14:14.240][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:14:14.241][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:14:14.242][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:14:14.243][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-15 08:14:14.244][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:14:14.245][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[2023-04-15 08:14:14.247][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:14:14.248][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:14:14.249][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-15 08:14:14.250][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:14:14.251][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:14:14.252][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:14:14.253][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:14:14.254][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-15 08:14:14.255][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:14:14.256][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".
biodb.DEBUG[2023-04-15 08:14:14.257][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:14:14.258][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:14:14.259][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-15 08:14:14.260][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:14:14.262][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:14:14.263][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:14:14.264][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:14:14.265][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-15 08:14:14.266][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:14:14.267][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:14:14.268][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:14:14.269][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:14:14.270][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-15 08:14:14.271][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:14:14.272][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[2023-04-15 08:14:14.273][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:14:14.275][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:14:14.276][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-15 08:14:14.277][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:14:14.278][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:14:14.279][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:14:14.281][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:14:14.282][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-15 08:14:14.283][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:14:14.284][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:14:14.285][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:14:14.286][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:14:14.287][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-15 08:14:14.288][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:14:14.289][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:14:14.290][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:14:14.291][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:14:14.293][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-15 08:14:14.294][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:14:14.295][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:14:14.296][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:14:14.297][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:14:14.298][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-15 08:14:14.299][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:14:14.300][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:14:14.301][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:14:14.302][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:14:14.303][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-15 08:14:14.304][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:14:14.305][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:14:14.307][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2023-04-15 08:14:14.308][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2023-04-15 08:14:14.310][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2023-04-15 08:14:14.311][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2023-04-15 08:14:14.313][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2023-04-15 08:14:14.315][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2023-04-15 08:14:14.316][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2023-04-15 08:14:14.318][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2023-04-15 08:14:14.319][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2023-04-15 08:14:14.321][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2023-04-15 08:14:14.322][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2023-04-15 08:14:14.324][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2023-04-15 08:14:14.325][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2023-04-15 08:14:14.327][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2023-04-15 08:14:14.328][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2023-04-15 08:14:14.330][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2023-04-15 08:14:14.331][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2023-04-15 08:14:14.333][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2023-04-15 08:14:14.334][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2023-04-15 08:14:14.336][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2023-04-15 08:14:14.337][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2023-04-15 08:14:14.339][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2023-04-15 08:14:14.340][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2023-04-15 08:14:14.342][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2023-04-15 08:14:14.343][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2023-04-15 08:14:14.345][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2023-04-15 08:14:14.355][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2023-04-15 08:14:14.358][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2023-04-15 08:14:14.360][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2023-04-15 08:14:14.363][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2023-04-15 08:14:14.365][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2023-04-15 08:14:14.367][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2023-04-15 08:14:14.370][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2023-04-15 08:14:14.372][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2023-04-15 08:14:14.374][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2023-04-15 08:14:14.375][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2023-04-15 08:14:14.377][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2023-04-15 08:14:14.378][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2023-04-15 08:14:14.380][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2023-04-15 08:14:14.382][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2023-04-15 08:14:14.383][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2023-04-15 08:14:14.385][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2023-04-15 08:14:14.386][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2023-04-15 08:14:14.388][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2023-04-15 08:14:14.389][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2023-04-15 08:14:14.391][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2023-04-15 08:14:14.392][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2023-04-15 08:14:14.394][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2023-04-15 08:14:14.396][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2023-04-15 08:14:14.397][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2023-04-15 08:14:14.399][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2023-04-15 08:14:14.400][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2023-04-15 08:14:14.402][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2023-04-15 08:14:14.403][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2023-04-15 08:14:14.405][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2023-04-15 08:14:14.406][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2023-04-15 08:14:14.408][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2023-04-15 08:14:14.409][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2023-04-15 08:14:14.411][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2023-04-15 08:14:14.412][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2023-04-15 08:14:14.414][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2023-04-15 08:14:14.415][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2023-04-15 08:14:14.417][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2023-04-15 08:14:14.419][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2023-04-15 08:14:14.420][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2023-04-15 08:14:14.422][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2023-04-15 08:14:14.423][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2023-04-15 08:14:14.425][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2023-04-15 08:14:14.426][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2023-04-15 08:14:14.428][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2023-04-15 08:14:14.429][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2023-04-15 08:14:14.431][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2023-04-15 08:14:14.432][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2023-04-15 08:14:14.434][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2023-04-15 08:14:14.436][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2023-04-15 08:14:14.437][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2023-04-15 08:14:14.439][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2023-04-15 08:14:14.440][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2023-04-15 08:14:14.442][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2023-04-15 08:14:14.443][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2023-04-15 08:14:14.445][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2023-04-15 08:14:14.446][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2023-04-15 08:14:14.448][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2023-04-15 08:14:14.450][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2023-04-15 08:14:14.452][initialize] This is biodb version 1.6.1.
biodb.DEBUG[2023-04-15 08:14:14.453][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-04-15 08:14:14.454][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:14:14.455][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-15 08:14:14.456][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:14:14.457][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:14:14.458][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:14:14.460][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-15 08:14:14.461][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-15 08:14:14.462][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:14:14.463][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-15 08:14:14.464][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:14:14.465][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:14:14.466][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:14:14.467][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-15 08:14:14.468][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-15 08:14:14.469][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:14:14.470][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-15 08:14:14.471][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:14:14.472][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:14:14.474][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:14:14.475][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-15 08:14:14.476][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-15 08:14:14.477][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:14:14.478][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-15 08:14:14.479][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:14:14.480][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:14:14.481][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:14:14.482][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-15 08:14:14.483][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-15 08:14:14.484][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:14:14.485][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-15 08:14:14.486][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:14:14.487][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:14:14.488][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:14:14.490][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-15 08:14:14.491][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-15 08:14:14.492][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:14:14.493][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-15 08:14:14.494][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:14:14.495][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:14:14.496][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:14:14.497][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-15 08:14:14.499][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-15 08:14:14.500][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:14:14.501][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-15 08:14:14.502][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:14:14.503][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:14:14.504][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:14:14.505][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-15 08:14:14.506][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-15 08:14:14.507][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:14:14.508][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-15 08:14:14.509][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:14:14.510][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:14:14.511][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:14:14.512][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-15 08:14:14.513][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-15 08:14:14.514][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:14:14.515][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-15 08:14:14.516][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:14:14.517][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:14:14.518][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:14:14.519][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-15 08:14:14.520][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-15 08:14:14.521][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:14:14.522][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-15 08:14:14.523][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:14:14.524][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:14:14.525][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:14:14.526][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-15 08:14:14.527][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-15 08:14:14.528][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:14:14.529][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-15 08:14:14.530][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:14:14.531][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:14:14.533][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:14:14.534][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-15 08:14:14.535][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-15 08:14:14.536][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:14:14.546][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-15 08:14:14.548][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:14:14.549][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:14:14.551][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:14:14.552][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-15 08:14:14.554][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-15 08:14:14.555][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:14:14.557][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-15 08:14:14.558][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:14:14.560][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:14:14.561][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:14:14.562][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-15 08:14:14.564][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-15 08:14:14.565][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:14:14.566][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-15 08:14:14.567][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:14:14.568][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:14:14.569][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:14:14.570][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-15 08:14:14.571][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-15 08:14:14.572][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:14:14.573][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-15 08:14:14.574][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:14:14.575][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:14:14.577][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:14:14.578][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-15 08:14:14.579][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-15 08:14:14.580][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:14:14.581][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-15 08:14:14.582][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:14:14.583][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:14:14.584][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:14:14.585][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-15 08:14:14.587][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-15 08:14:14.588][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:14:14.589][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-15 08:14:14.590][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:14:14.591][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:14:14.592][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:14:14.593][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-15 08:14:14.594][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-15 08:14:14.595][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:14:14.596][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-15 08:14:14.597][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:14:14.598][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:14:14.789][biodb$loadDefinitions] Load definitions from file "F:/biocbuild/bbs-3.16-bioc-longtests/meat/biodbMirbase.Rcheck/biodbMirbase/definitions.yml".
biodb.DEBUG[2023-04-15 08:14:14.823][self$getDbsInfo()$define] Define connector mirbase.mature.
biodb.DEBUG[2023-04-15 08:14:14.825][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-04-15 08:14:14.827][self$setPropertyValue] Setting property "description" to "Write here the description of this database.".
biodb.DEBUG[2023-04-15 08:14:14.828][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-04-15 08:14:14.829][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-04-15 08:14:14.830][self$setPropertyValue] Setting property "downloadable" to "TRUE".
biodb.DEBUG[2023-04-15 08:14:14.832][self$setPropertyValue] Setting property "dwnld.ext" to "gz".
biodb.DEBUG[2023-04-15 08:14:14.833][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2023-04-15 08:14:14.834][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-04-15 08:14:14.835][self$setPropertyValue] Setting property "entry.content.type" to "txt".
biodb.DEBUG[2023-04-15 08:14:14.836][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-04-15 08:14:14.838][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-04-15 08:14:14.839][self$setPropertyValue] Setting property "name" to "miRBase mature database".
biodb.DEBUG[2023-04-15 08:14:14.840][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-04-15 08:14:14.841][self$setPropertyValue] Setting property "parsing.expr" to "^>[^ ]+ *(MIMAT[0-9]+) .*$".
biodb.DEBUG[2023-04-15 08:14:14.841][self$setPropertyValue] Setting property "parsing.expr" to "^>[^ ]+ *MIMAT[0-9]+ (.*)$".
biodb.DEBUG[2023-04-15 08:14:14.841][self$setPropertyValue] Setting property "parsing.expr" to "^>([^ ]+) *MIMAT[0-9]+ .*$".
biodb.DEBUG[2023-04-15 08:14:14.841][self$setPropertyValue] Setting property "parsing.expr" to "^([ACGU]+)$".
biodb.DEBUG[2023-04-15 08:14:14.842][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2023-04-15 08:14:14.844][self$setPropertyValue]
biodb.DEBUG[2023-04-15 08:14:14.845][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2023-04-15 08:14:14.846][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-15 08:14:14.847][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-15 08:14:14.848][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-04-15 08:14:14.850][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-15 08:14:14.851][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-15 08:14:14.852][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-04-15 08:14:14.853][self$setPropertyValue] Setting property "urls" to "http://www.mirbase.org/".
biodb.DEBUG[2023-04-15 08:14:14.853][self$setPropertyValue] Setting property "urls" to "https://www.mirbase.org/ftp/CURRENT/mature.fa.gz".
biodb.DEBUG[2023-04-15 08:14:14.854][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-04-15 08:14:14.855][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-04-15 08:14:14.857][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2023-04-15 08:14:14.858][self$setPropertyValue]
biodb.DEBUG[2023-04-15 08:14:14.863][self$getEntryFields()$define] Define field mirbase.mature.id.
biodb.DEBUG[2023-04-15 08:14:14.867][initialize] Initialize connector mirbase.mature.
biodb.DEBUG[2023-04-15 08:14:14.868][initialize] Register connector mirbase.mature with the request scheduler
biodb.DEBUG[2023-04-15 08:14:14.869][private$bdb$getRequestScheduler()$re ...] Register connector mirbase.mature.
biodb.DEBUG[2023-04-15 08:14:14.871][private$addConnectorRules] Create new rule for URL "www.mirbase.org" of connector "mirbase.mature".
biodb.DEBUG[2023-04-15 08:14:14.872][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2023-04-15 08:14:14.873][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2023-04-15 08:14:14.875][rule$addConnector] Connector "mirbase.mature" is already listed in rule "www.mirbase.org".
biodb.DEBUG[2023-04-15 08:14:14.876][biodb$getFactory()$createConn] Creating new connector mirbase.mature for database class mirbase.mature .
biodb.INFO [2023-04-15 08:14:14.877][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2023-04-15 08:14:14.879][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector mirbase.mature from the request scheduler
biodb.INFO [2023-04-15 08:14:14.880][self$deleteConn] Connector "mirbase.mature" deleted.
biodb.DEBUG[2023-04-15 08:14:14.881][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2023-04-15 08:14:14.882][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-15 08:14:14.883][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-15 08:14:14.884][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:14:14.885][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-15 08:14:14.886][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:14:14.887][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 75 ]
> 
> proc.time()
   user  system elapsed 
  10.39   30.10  361.54

'R CMD check' output

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD check --no-multiarch --test-dir=longtests --no-stop-on-test-error --no-codoc --no-examples --no-manual --ignore-vignettes --check-subdirs=no biodbMirbase_1.2.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.16-bioc-longtests/meat/biodbMirbase.Rcheck'
* using R version 4.2.3 (2023-03-15 ucrt)
* using platform: x86_64-w64-mingw32 (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 '1.2.2'
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking whether package '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)