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 nebbiolo2


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: /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD check --test-dir=longtests --no-stop-on-test-error --no-codoc --no-examples --no-manual --ignore-vignettes --check-subdirs=no biodbMirbase_1.2.2.tar.gz
StartedAt: 2023-04-15 08:06:47 -0400 (Sat, 15 Apr 2023)
EndedAt: 2023-04-15 08:07:24 -0400 (Sat, 15 Apr 2023)
EllapsedTime: 37.0 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) -- "Shortstop Beagle"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

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

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

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

> # Script needed to run testthat automatically from ‘R CMD check’. See
> # testthat::test_dir documentation.
> library(testthat)
> library(biodbMirbase)
> Sys.setenv(TESTTHAT_REPORTER="summary")
> Sys.setenv(BIODB_LOG_DST="console")
> test_check("biodbMirbase")
biodb.INFO [2023-04-15 08:07:14.760][biodb::testContext]
biodb.INFO [2023-04-15 08:07:14.762][biodb::testContext] ********************************************************************************
biodb.INFO [2023-04-15 08:07:14.763][biodb::testContext] Test context - Generic long tests
biodb.INFO [2023-04-15 08:07:14.763][biodb::testContext] ********************************************************************************
biodb.INFO [2023-04-15 08:07:14.764][biodb::testContext]
biodb.INFO [2023-04-15 08:07:14.769][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.6.1.
biodb.DEBUG[2023-04-15 08:07:14.771][self$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.16-bioc/R/site-library/biodb/definitions.yml".
biodb.DEBUG[2023-04-15 08:07:14.776][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-04-15 08:07:14.777][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2023-04-15 08:07:14.778][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2023-04-15 08:07:14.778][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:07:14.779][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:07:14.780][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:07:14.781][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2023-04-15 08:07:14.794][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2023-04-15 08:07:14.795][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:07:14.796][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:07:14.796][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:07:14.797][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2023-04-15 08:07:14.798][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2023-04-15 08:07:14.799][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:07:14.799][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:07:14.800][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:07:14.801][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2023-04-15 08:07:14.801][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2023-04-15 08:07:14.802][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2023-04-15 08:07:14.803][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:07:14.804][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:07:14.804][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:07:14.805][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2023-04-15 08:07:14.806][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2023-04-15 08:07:14.806][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2023-04-15 08:07:14.807][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:07:14.808][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:07:14.808][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:07:14.809][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2023-04-15 08:07:14.810][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2023-04-15 08:07:14.811][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:07:14.811][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:07:14.812][FUN] Functions in observer BiodbConfig: [21]: ".__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 08:07:14.813][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2023-04-15 08:07:14.814][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2023-04-15 08:07:14.814][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2023-04-15 08:07:14.815][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:07:14.816][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:07:14.816][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:07:14.817][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2023-04-15 08:07:14.818][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2023-04-15 08:07:14.819][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:07:14.819][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:07:14.820][FUN] Functions in observer BiodbConfig: [21]: ".__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 08:07:14.821][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2023-04-15 08:07:14.821][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2023-04-15 08:07:14.822][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2023-04-15 08:07:14.823][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:07:14.823][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:07:14.824][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:07:14.825][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2023-04-15 08:07:14.826][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2023-04-15 08:07:14.826][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2023-04-15 08:07:14.827][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2023-04-15 08:07:14.828][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2023-04-15 08:07:14.829][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2023-04-15 08:07:14.829][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:07:14.830][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:07:14.831][FUN] Functions in observer BiodbConfig: [21]: ".__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 08:07:14.831][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2023-04-15 08:07:14.832][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2023-04-15 08:07:14.833][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:07:14.834][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:07:14.834][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:07:14.835][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2023-04-15 08:07:14.836][self$set] Set key entries.sep to "|".
biodb.DEBUG[2023-04-15 08:07:14.837][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:07:14.837][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:07:14.838][FUN] Functions in observer BiodbConfig: [21]: ".__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 08:07:14.839][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2023-04-15 08:07:14.839][self$set] Set key offline to FALSE.
biodb.DEBUG[2023-04-15 08:07:14.840][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:07:14.841][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:07:14.841][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:07:14.842][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2023-04-15 08:07:14.843][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2023-04-15 08:07:14.844][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:07:14.844][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:07:14.845][FUN] Functions in observer BiodbConfig: [21]: ".__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 08:07:14.846][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2023-04-15 08:07:14.846][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2023-04-15 08:07:14.847][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:07:14.848][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:07:14.848][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:07:14.849][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2023-04-15 08:07:14.850][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2023-04-15 08:07:14.855][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2023-04-15 08:07:14.856][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:07:14.857][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:07:14.857][FUN] Functions in observer BiodbConfig: [21]: ".__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 08:07:14.858][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2023-04-15 08:07:14.859][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2023-04-15 08:07:14.860][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2023-04-15 08:07:14.861][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:07:14.861][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:07:14.862][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:07:14.865][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2023-04-15 08:07:14.892][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-04-15 08:07:14.904][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2023-04-15 08:07:14.905][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-04-15 08:07:14.905][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-04-15 08:07:14.906][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-04-15 08:07:14.907][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-04-15 08:07:14.908][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-04-15 08:07:14.909][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-04-15 08:07:14.909][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2023-04-15 08:07:14.910][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-04-15 08:07:14.911][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-04-15 08:07:14.912][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2023-04-15 08:07:14.912][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-04-15 08:07:14.913][self$setPropertyValue]
biodb.DEBUG[2023-04-15 08:07:14.914][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-04-15 08:07:14.915][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2023-04-15 08:07:14.915][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2023-04-15 08:07:14.915][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2023-04-15 08:07:14.915][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2023-04-15 08:07:14.915][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2023-04-15 08:07:14.916][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-04-15 08:07:14.916][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-15 08:07:14.917][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-15 08:07:14.918][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-04-15 08:07:14.923][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-15 08:07:14.924][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-15 08:07:14.924][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-04-15 08:07:14.925][self$setPropertyValue]
biodb.DEBUG[2023-04-15 08:07:14.926][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-04-15 08:07:14.926][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-04-15 08:07:14.927][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-04-15 08:07:14.928][self$setPropertyValue]
biodb.DEBUG[2023-04-15 08:07:14.928][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2023-04-15 08:07:14.930][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-04-15 08:07:14.930][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2023-04-15 08:07:14.931][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-04-15 08:07:14.932][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-04-15 08:07:14.932][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-04-15 08:07:14.933][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-04-15 08:07:14.934][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-04-15 08:07:14.934][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-04-15 08:07:14.935][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2023-04-15 08:07:14.936][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-04-15 08:07:14.936][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-04-15 08:07:14.937][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2023-04-15 08:07:14.938][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-04-15 08:07:14.938][self$setPropertyValue]
biodb.DEBUG[2023-04-15 08:07:14.939][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-04-15 08:07:14.940][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2023-04-15 08:07:14.940][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2023-04-15 08:07:14.940][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2023-04-15 08:07:14.940][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2023-04-15 08:07:14.940][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2023-04-15 08:07:14.940][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-04-15 08:07:14.941][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-15 08:07:14.942][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-15 08:07:14.942][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-04-15 08:07:14.943][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-15 08:07:14.944][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-15 08:07:14.944][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-04-15 08:07:14.945][self$setPropertyValue]
biodb.DEBUG[2023-04-15 08:07:14.946][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-04-15 08:07:14.946][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-04-15 08:07:14.947][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-04-15 08:07:14.948][self$setPropertyValue]
biodb.DEBUG[2023-04-15 08:07:14.948][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2023-04-15 08:07:14.949][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2023-04-15 08:07:14.950][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2023-04-15 08:07:14.951][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-04-15 08:07:14.952][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-04-15 08:07:14.952][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-04-15 08:07:14.953][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-04-15 08:07:14.954][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-04-15 08:07:14.954][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-04-15 08:07:14.955][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2023-04-15 08:07:14.956][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-04-15 08:07:14.956][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2023-04-15 08:07:14.957][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2023-04-15 08:07:14.958][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-04-15 08:07:14.958][self$setPropertyValue]
biodb.DEBUG[2023-04-15 08:07:14.959][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-04-15 08:07:14.960][self$setPropertyValue]
biodb.DEBUG[2023-04-15 08:07:14.960][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-04-15 08:07:14.961][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-15 08:07:14.962][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-15 08:07:14.962][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-04-15 08:07:14.963][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-15 08:07:14.964][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-15 08:07:14.964][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-04-15 08:07:14.965][self$setPropertyValue]
biodb.DEBUG[2023-04-15 08:07:14.965][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-04-15 08:07:14.966][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-04-15 08:07:14.967][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-04-15 08:07:14.967][self$setPropertyValue]
biodb.DEBUG[2023-04-15 08:07:14.968][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2023-04-15 08:07:14.969][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2023-04-15 08:07:14.970][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2023-04-15 08:07:14.971][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-04-15 08:07:14.971][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-04-15 08:07:14.972][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-04-15 08:07:14.973][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-04-15 08:07:14.973][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-04-15 08:07:14.974][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-04-15 08:07:14.975][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2023-04-15 08:07:14.975][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-04-15 08:07:14.976][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2023-04-15 08:07:14.977][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2023-04-15 08:07:14.977][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-04-15 08:07:14.978][self$setPropertyValue]
biodb.DEBUG[2023-04-15 08:07:14.979][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-04-15 08:07:14.979][self$setPropertyValue]
biodb.DEBUG[2023-04-15 08:07:14.980][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-04-15 08:07:14.981][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-15 08:07:14.981][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-15 08:07:14.982][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-04-15 08:07:14.983][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-15 08:07:14.983][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-15 08:07:14.984][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-04-15 08:07:14.985][self$setPropertyValue]
biodb.DEBUG[2023-04-15 08:07:14.985][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-04-15 08:07:14.986][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-04-15 08:07:14.987][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-04-15 08:07:14.987][self$setPropertyValue]
biodb.DEBUG[2023-04-15 08:07:14.990][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-04-15 08:07:14.991][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:07:14.991][FUN] Functions in observer BiodbConfig: [21]: ".__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 08:07:14.992][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:07:14.992][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:07:14.993][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 08:07:14.994][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:07:14.994][FUN] Functions in observer BiodbConfig: [21]: ".__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 08:07:14.995][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:07:14.996][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:07:14.996][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 08:07:14.997][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:07:14.997][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 08:07:14.998][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:07:14.999][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:07:14.999][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-15 08:07:15.000][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:07:15.001][FUN] Functions in observer BiodbConfig: [21]: ".__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 08:07:15.001][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:07:15.002][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:07:15.002][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 08:07:15.003][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:07:15.004][FUN] Functions in observer BiodbConfig: [21]: ".__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 08:07:15.004][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:07:15.005][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:07:15.005][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-15 08:07:15.006][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:07:15.007][FUN] Functions in observer BiodbConfig: [21]: ".__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 08:07:15.007][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:07:15.008][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:07:15.008][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-15 08:07:15.009][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:07:15.010][FUN] Functions in observer BiodbConfig: [21]: ".__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 08:07:15.010][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:07:15.011][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:07:15.011][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-15 08:07:15.012][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:07:15.013][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:07:15.013][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:07:15.014][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:07:15.014][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-15 08:07:15.015][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:07:15.016][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:07:15.016][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:07:15.017][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:07:15.017][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-15 08:07:15.018][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:07:15.019][FUN] Functions in observer BiodbConfig: [21]: ".__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 08:07:15.019][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:07:15.020][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:07:15.020][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-15 08:07:15.021][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:07:15.022][FUN] Functions in observer BiodbConfig: [21]: ".__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 08:07:15.022][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:07:15.023][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:07:15.023][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-15 08:07:15.024][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:07:15.025][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 08:07:15.025][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:07:15.026][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:07:15.026][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-15 08:07:15.027][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:07:15.028][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:07:15.028][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:07:15.029][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:07:15.029][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 08:07:15.030][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:07:15.031][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:07:15.031][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:07:15.032][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:07:15.032][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 08:07:15.033][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:07:15.034][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 08:07:15.034][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:07:15.035][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:07:15.036][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-15 08:07:15.036][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:07:15.037][FUN] Functions in observer BiodbConfig: [21]: ".__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 08:07:15.037][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:07:15.038][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:07:15.039][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-15 08:07:15.039][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:07:15.040][FUN] Functions in observer BiodbConfig: [21]: ".__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 08:07:15.040][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:07:15.041][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:07:15.042][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 08:07:15.042][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:07:15.043][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:07:15.043][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2023-04-15 08:07:15.047][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2023-04-15 08:07:15.048][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2023-04-15 08:07:15.049][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2023-04-15 08:07:15.050][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2023-04-15 08:07:15.050][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2023-04-15 08:07:15.051][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2023-04-15 08:07:15.052][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2023-04-15 08:07:15.053][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2023-04-15 08:07:15.054][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2023-04-15 08:07:15.055][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2023-04-15 08:07:15.056][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2023-04-15 08:07:15.057][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2023-04-15 08:07:15.058][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2023-04-15 08:07:15.059][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2023-04-15 08:07:15.060][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2023-04-15 08:07:15.061][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2023-04-15 08:07:15.062][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2023-04-15 08:07:15.063][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2023-04-15 08:07:15.064][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2023-04-15 08:07:15.064][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2023-04-15 08:07:15.065][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2023-04-15 08:07:15.066][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2023-04-15 08:07:15.067][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2023-04-15 08:07:15.068][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2023-04-15 08:07:15.069][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2023-04-15 08:07:15.070][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2023-04-15 08:07:15.071][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2023-04-15 08:07:15.072][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2023-04-15 08:07:15.073][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2023-04-15 08:07:15.074][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2023-04-15 08:07:15.075][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2023-04-15 08:07:15.076][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2023-04-15 08:07:15.077][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2023-04-15 08:07:15.077][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2023-04-15 08:07:15.078][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2023-04-15 08:07:15.079][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2023-04-15 08:07:15.080][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2023-04-15 08:07:15.081][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2023-04-15 08:07:15.082][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2023-04-15 08:07:15.083][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2023-04-15 08:07:15.084][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2023-04-15 08:07:15.085][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2023-04-15 08:07:15.086][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2023-04-15 08:07:15.087][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2023-04-15 08:07:15.087][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2023-04-15 08:07:15.088][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2023-04-15 08:07:15.089][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2023-04-15 08:07:15.090][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2023-04-15 08:07:15.091][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2023-04-15 08:07:15.092][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2023-04-15 08:07:15.093][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2023-04-15 08:07:15.094][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2023-04-15 08:07:15.095][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2023-04-15 08:07:15.096][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2023-04-15 08:07:15.097][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2023-04-15 08:07:15.102][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2023-04-15 08:07:15.102][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2023-04-15 08:07:15.103][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2023-04-15 08:07:15.104][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2023-04-15 08:07:15.105][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2023-04-15 08:07:15.106][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2023-04-15 08:07:15.107][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2023-04-15 08:07:15.108][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2023-04-15 08:07:15.109][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2023-04-15 08:07:15.110][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2023-04-15 08:07:15.111][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2023-04-15 08:07:15.112][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2023-04-15 08:07:15.113][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2023-04-15 08:07:15.113][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2023-04-15 08:07:15.114][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2023-04-15 08:07:15.115][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2023-04-15 08:07:15.116][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2023-04-15 08:07:15.117][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2023-04-15 08:07:15.118][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2023-04-15 08:07:15.119][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2023-04-15 08:07:15.120][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2023-04-15 08:07:15.121][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2023-04-15 08:07:15.122][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2023-04-15 08:07:15.123][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2023-04-15 08:07:15.124][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2023-04-15 08:07:15.125][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2023-04-15 08:07:15.125][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2023-04-15 08:07:15.129][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2023-04-15 08:07:15.130][initialize] This is biodb version 1.6.1.
biodb.DEBUG[2023-04-15 08:07:15.133][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-04-15 08:07:15.133][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:07:15.134][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 08:07:15.134][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:07:15.135][FUN] Functions in observer BiodbConfig: [21]: ".__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 08:07:15.138][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:07:15.139][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-15 08:07:15.139][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-15 08:07:15.140][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:07:15.140][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-15 08:07:15.141][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:07:15.142][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:07:15.142][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:07:15.143][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-15 08:07:15.143][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-15 08:07:15.144][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:07:15.145][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-15 08:07:15.145][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:07:15.146][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:07:15.147][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:07:15.147][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-15 08:07:15.148][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-15 08:07:15.148][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:07:15.149][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 08:07:15.149][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:07:15.150][FUN] Functions in observer BiodbConfig: [21]: ".__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 08:07:15.151][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:07:15.151][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-15 08:07:15.152][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-15 08:07:15.152][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:07:15.153][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 08:07:15.154][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:07:15.154][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:07:15.155][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:07:15.155][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-15 08:07:15.156][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-15 08:07:15.157][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:07:15.157][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-15 08:07:15.158][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:07:15.158][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:07:15.159][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:07:15.160][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-15 08:07:15.160][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-15 08:07:15.161][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:07:15.161][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-15 08:07:15.162][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:07:15.163][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:07:15.163][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:07:15.164][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-15 08:07:15.164][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-15 08:07:15.165][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:07:15.166][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-15 08:07:15.166][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:07:15.167][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:07:15.167][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:07:15.168][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-15 08:07:15.169][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-15 08:07:15.169][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:07:15.170][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-15 08:07:15.170][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:07:15.171][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:07:15.172][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:07:15.172][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-15 08:07:15.173][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-15 08:07:15.173][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:07:15.174][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-15 08:07:15.175][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:07:15.175][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:07:15.176][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:07:15.176][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-15 08:07:15.177][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-15 08:07:15.178][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:07:15.178][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-15 08:07:15.179][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:07:15.179][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:07:15.180][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:07:15.181][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-15 08:07:15.181][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-15 08:07:15.182][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:07:15.182][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-15 08:07:15.183][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:07:15.184][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:07:15.184][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:07:15.185][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-15 08:07:15.185][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-15 08:07:15.186][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:07:15.187][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-15 08:07:15.187][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:07:15.188][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:07:15.188][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:07:15.189][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-15 08:07:15.190][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-15 08:07:15.190][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:07:15.191][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 08:07:15.191][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:07:15.192][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:07:15.193][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:07:15.193][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-15 08:07:15.194][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-15 08:07:15.194][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:07:15.195][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 08:07:15.196][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:07:15.196][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:07:15.197][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:07:15.198][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-15 08:07:15.198][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-15 08:07:15.199][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:07:15.199][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-15 08:07:15.200][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:07:15.201][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:07:15.201][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:07:15.202][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-15 08:07:15.202][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-15 08:07:15.203][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:07:15.204][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-15 08:07:15.204][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:07:15.205][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:07:15.205][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:07:15.206][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-15 08:07:15.207][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-15 08:07:15.207][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:07:15.208][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 08:07:15.208][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:07:15.209][FUN] Functions in observer BiodbConfig: [21]: ".__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 08:07:15.210][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.16-bioc-longtests/meat/biodbMirbase.Rcheck/biodbMirbase/definitions.yml".
biodb.DEBUG[2023-04-15 08:07:15.216][self$getDbsInfo()$define] Define connector mirbase.mature.
biodb.DEBUG[2023-04-15 08:07:15.233][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-04-15 08:07:15.234][self$setPropertyValue] Setting property "description" to "Write here the description of this database.".
biodb.DEBUG[2023-04-15 08:07:15.235][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-04-15 08:07:15.235][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-04-15 08:07:15.236][self$setPropertyValue] Setting property "downloadable" to "TRUE".
biodb.DEBUG[2023-04-15 08:07:15.237][self$setPropertyValue] Setting property "dwnld.ext" to "gz".
biodb.DEBUG[2023-04-15 08:07:15.237][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2023-04-15 08:07:15.238][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-04-15 08:07:15.239][self$setPropertyValue] Setting property "entry.content.type" to "txt".
biodb.DEBUG[2023-04-15 08:07:15.239][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-04-15 08:07:15.240][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-04-15 08:07:15.241][self$setPropertyValue] Setting property "name" to "miRBase mature database".
biodb.DEBUG[2023-04-15 08:07:15.241][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-04-15 08:07:15.242][self$setPropertyValue] Setting property "parsing.expr" to "^>[^ ]+ *(MIMAT[0-9]+) .*$".
biodb.DEBUG[2023-04-15 08:07:15.242][self$setPropertyValue] Setting property "parsing.expr" to "^>[^ ]+ *MIMAT[0-9]+ (.*)$".
biodb.DEBUG[2023-04-15 08:07:15.242][self$setPropertyValue] Setting property "parsing.expr" to "^>([^ ]+) *MIMAT[0-9]+ .*$".
biodb.DEBUG[2023-04-15 08:07:15.242][self$setPropertyValue] Setting property "parsing.expr" to "^([ACGU]+)$".
biodb.DEBUG[2023-04-15 08:07:15.243][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2023-04-15 08:07:15.243][self$setPropertyValue]
biodb.DEBUG[2023-04-15 08:07:15.244][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2023-04-15 08:07:15.245][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-15 08:07:15.245][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-15 08:07:15.246][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-04-15 08:07:15.247][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-15 08:07:15.247][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-15 08:07:15.248][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-04-15 08:07:15.248][self$setPropertyValue] Setting property "urls" to "http://www.mirbase.org/".
biodb.DEBUG[2023-04-15 08:07:15.248][self$setPropertyValue] Setting property "urls" to "https://www.mirbase.org/ftp/CURRENT/mature.fa.gz".
biodb.DEBUG[2023-04-15 08:07:15.249][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-04-15 08:07:15.250][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-04-15 08:07:15.250][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2023-04-15 08:07:15.251][self$setPropertyValue]
biodb.DEBUG[2023-04-15 08:07:15.254][self$getEntryFields()$define] Define field mirbase.mature.id.
biodb.DEBUG[2023-04-15 08:07:15.274][initialize] Initialize connector mirbase.mature.
biodb.DEBUG[2023-04-15 08:07:15.275][initialize] Register connector mirbase.mature with the request scheduler
biodb.DEBUG[2023-04-15 08:07:15.278][private$bdb$getRequestScheduler()$re ...] Register connector mirbase.mature.
biodb.DEBUG[2023-04-15 08:07:15.280][private$addConnectorRules] Create new rule for URL "www.mirbase.org" of connector "mirbase.mature".
biodb.DEBUG[2023-04-15 08:07:15.283][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2023-04-15 08:07:15.284][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2023-04-15 08:07:15.285][rule$addConnector] Connector "mirbase.mature" is already listed in rule "www.mirbase.org".
biodb.DEBUG[2023-04-15 08:07:15.285][biodb$getFactory()$createConn] Creating new connector mirbase.mature for database class mirbase.mature .
biodb.INFO [2023-04-15 08:07:15.291][biodb::testThat]
biodb.INFO [2023-04-15 08:07:15.292][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2023-04-15 08:07:15.292][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-04-15 08:07:15.293][biodb::testThat]
biodb.TRACE[2023-04-15 08:07:15.295][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/bbs-3.16-bioc-longtests/meat/biodbMirbase.Rcheck/biodbMirbase/testref/entry-mirbase.mature-MIMAT0000433-content.txt".
biodb.DEBUG[2023-04-15 08:07:15.296][biodb$getFactory()$createEntryFromCo ...] Creating miRBase mature database entries from 1 content(s).
biodb.DEBUG[2023-04-15 08:07:15.299][biodb$getFactory()$createEntryFromCo ...] Parsing 1 miRBase mature database entries.
biodb.DEBUG[2023-04-15 08:07:15.305][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-15 08:07:15.306][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-15 08:07:15.306][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-15 08:07:15.315][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:07:15.316][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 08:07:15.316][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:07:15.317][FUN] Functions in observer BiodbConfig: [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 08:07:15.324][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-15 08:07:15.325][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-15 08:07:15.326][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:07:15.327][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:07:15.343][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-04-15 08:07:15.351][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-04-15 08:07:15.351][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:07:15.352][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:07:15.353][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-15 08:07:15.354][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-15 08:07:15.354][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:07:15.355][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:07:15.356][self$getBiodb()$getEntryFields()$get] Asked field names are: sequence.
biodb.TRACE[2023-04-15 08:07:15.357][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2023-04-15 08:07:15.357][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:07:15.358][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:07:15.359][self$getBiodb()$getEntryFields()$get] Asked field names are: mirbase.mature.id.
biodb.TRACE[2023-04-15 08:07:15.359][self$getBiodb()$getEntryFields()$get] Realnames of fields are: mirbase.mature.id.
biodb.TRACE[2023-04-15 08:07:15.360][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:07:15.361][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:07:15.361][self$getBiodb()$getEntryFields()$get] Asked field names are: mirbase.mature.id.
biodb.TRACE[2023-04-15 08:07:15.362][self$getBiodb()$getEntryFields()$get] Realnames of fields are: mirbase.mature.id.
biodb.TRACE[2023-04-15 08:07:15.363][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:07:15.363][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:07:15.364][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-15 08:07:15.365][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-15 08:07:15.366][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:07:15.366][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:07:15.367][self$getBiodb()$getEntryFields()$get] Asked field names are: mirbase.mature.id.
biodb.TRACE[2023-04-15 08:07:15.368][self$getBiodb()$getEntryFields()$get] Realnames of fields are: mirbase.mature.id.
biodb.TRACE[2023-04-15 08:07:15.368][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:07:15.369][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:07:15.370][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-15 08:07:15.370][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-15 08:07:15.371][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:07:15.372][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:07:15.372][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-15 08:07:15.373][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-15 08:07:15.374][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:07:15.374][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:07:15.375][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-15 08:07:15.376][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-15 08:07:15.376][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:07:15.377][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:07:15.398][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-15 08:07:15.399][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-15 08:07:15.400][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:07:15.401][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:07:15.401][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-15 08:07:15.402][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-15 08:07:15.403][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:07:15.403][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:07:15.404][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-15 08:07:15.405][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-15 08:07:15.405][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:07:15.406][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-15 08:07:15.407][biodb$getFactory()$createEntryFromCo ...] Accession numbers: MIMAT0000433.
biodb.TRACE[2023-04-15 08:07:15.413][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2023-04-15 08:07:15.414][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2023-04-15 08:07:15.414][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:07:15.415][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:07:15.416][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2023-04-15 08:07:15.417][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2023-04-15 08:07:15.417][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:07:15.418][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:07:15.419][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2023-04-15 08:07:15.419][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2023-04-15 08:07:15.420][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:07:15.421][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:07:15.422][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2023-04-15 08:07:15.422][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2023-04-15 08:07:15.423][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:07:15.424][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:07:15.435][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-15 08:07:15.436][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-15 08:07:15.436][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:07:15.437][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:07:15.459][self$getBiodb()$getEntryFields()$get] Asked field names are: mirbase.mature.id.
biodb.TRACE[2023-04-15 08:07:15.460][self$getBiodb()$getEntryFields()$get] Realnames of fields are: mirbase.mature.id.
biodb.TRACE[2023-04-15 08:07:15.461][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:07:15.461][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:07:15.465][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-15 08:07:15.466][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-15 08:07:15.466][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:07:15.467][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:07:15.468][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-15 08:07:15.469][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-15 08:07:15.469][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:07:15.470][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:07:15.471][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-15 08:07:15.471][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-15 08:07:15.472][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:07:15.473][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:07:15.474][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-15 08:07:15.475][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-15 08:07:15.476][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:07:15.476][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:07:15.477][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-15 08:07:15.478][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-15 08:07:15.479][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:07:15.479][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:07:15.480][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-15 08:07:15.481][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-15 08:07:15.481][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:07:15.482][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:07:15.483][self$getBiodb()$getEntryFields()$get] Asked field names are: mirbase.mature.id.
biodb.TRACE[2023-04-15 08:07:15.484][self$getBiodb()$getEntryFields()$get] Realnames of fields are: mirbase.mature.id.
biodb.TRACE[2023-04-15 08:07:15.484][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:07:15.485][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:07:15.485][self$getBiodb()$getEntryFields()$get] Asked field names are: mirbase.mature.id.
biodb.TRACE[2023-04-15 08:07:15.486][self$getBiodb()$getEntryFields()$get] Realnames of fields are: mirbase.mature.id.
biodb.TRACE[2023-04-15 08:07:15.487][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:07:15.487][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:07:15.488][self$getBiodb()$getEntryFields()$get] Asked field names are: mirbase.mature.id.
biodb.TRACE[2023-04-15 08:07:15.489][self$getBiodb()$getEntryFields()$get] Realnames of fields are: mirbase.mature.id.
biodb.TRACE[2023-04-15 08:07:15.490][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:07:15.490][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:07:15.495][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-15 08:07:15.496][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-15 08:07:15.497][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:07:15.497][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:07:15.498][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-15 08:07:15.499][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-15 08:07:15.499][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:07:15.500][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:07:15.501][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-15 08:07:15.502][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-15 08:07:15.502][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:07:15.503][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:07:15.504][ef$get] Asked field names are: accession.
biodb.TRACE[2023-04-15 08:07:15.504][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-15 08:07:15.505][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:07:15.506][ef$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:07:15.506][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-15 08:07:15.507][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-15 08:07:15.508][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:07:15.508][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:07:15.513][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-15 08:07:15.514][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-15 08:07:15.515][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:07:15.515][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:07:15.516][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-15 08:07:15.517][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-15 08:07:15.518][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:07:15.518][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:07:15.519][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-15 08:07:15.520][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-15 08:07:15.520][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:07:15.521][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:07:15.522][ef$get] Asked field names are: name.
biodb.TRACE[2023-04-15 08:07:15.522][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-04-15 08:07:15.523][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:07:15.524][ef$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:07:15.524][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-15 08:07:15.525][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-15 08:07:15.526][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:07:15.526][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:07:15.531][self$getBiodb()$getEntryFields()$get] Asked field names are: sequence.
biodb.TRACE[2023-04-15 08:07:15.532][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2023-04-15 08:07:15.532][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:07:15.533][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:07:15.534][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2023-04-15 08:07:15.535][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2023-04-15 08:07:15.535][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:07:15.536][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:07:15.537][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2023-04-15 08:07:15.537][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2023-04-15 08:07:15.538][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:07:15.539][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:07:15.539][ef$get] Asked field names are: sequence.
biodb.TRACE[2023-04-15 08:07:15.540][ef$get] Realnames of fields are: aa.seq.
biodb.TRACE[2023-04-15 08:07:15.541][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:07:15.541][ef$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:07:15.542][self$getBiodb()$getEntryFields()$get] Asked field names are: sequence.
biodb.TRACE[2023-04-15 08:07:15.543][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2023-04-15 08:07:15.543][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:07:15.544][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:07:15.549][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-04-15 08:07:15.549][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-04-15 08:07:15.550][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:07:15.551][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:07:15.551][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-04-15 08:07:15.552][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-04-15 08:07:15.553][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:07:15.553][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:07:15.554][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-04-15 08:07:15.558][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-04-15 08:07:15.559][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:07:15.560][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:07:15.561][ef$get] Asked field names are: description.
biodb.TRACE[2023-04-15 08:07:15.562][ef$get] Realnames of fields are: description.
biodb.TRACE[2023-04-15 08:07:15.563][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:07:15.563][ef$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:07:15.564][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-04-15 08:07:15.565][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-04-15 08:07:15.566][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:07:15.566][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:07:15.573][ef$get] Asked field names are: aa.seq.
biodb.TRACE[2023-04-15 08:07:15.574][ef$get] Realnames of fields are: aa.seq.
biodb.TRACE[2023-04-15 08:07:15.574][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:07:15.575][ef$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:07:15.579][ef$get] Asked field names are: accession.
biodb.TRACE[2023-04-15 08:07:15.579][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-15 08:07:15.580][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:07:15.581][ef$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:07:15.585][ef$get] Asked field names are: description.
biodb.TRACE[2023-04-15 08:07:15.585][ef$get] Realnames of fields are: description.
biodb.TRACE[2023-04-15 08:07:15.586][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:07:15.587][ef$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:07:15.590][ef$get] Asked field names are: name.
biodb.TRACE[2023-04-15 08:07:15.591][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-04-15 08:07:15.592][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:07:15.593][ef$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:07:15.606][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/bbs-3.16-bioc-longtests/meat/biodbMirbase.Rcheck/biodbMirbase/testref/entry-mirbase.mature-MIMAT0000434-content.txt".
biodb.DEBUG[2023-04-15 08:07:15.639][biodb$getFactory()$createEntryFromCo ...] Creating miRBase mature database entries from 1 content(s).
biodb.DEBUG[2023-04-15 08:07:15.640][biodb$getFactory()$createEntryFromCo ...] Parsing 1 miRBase mature database entries.
biodb.DEBUG[2023-04-15 08:07:15.641][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-15 08:07:15.642][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-15 08:07:15.643][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-15 08:07:15.646][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:07:15.647][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 08:07:15.648][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:07:15.648][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.TRACE[2023-04-15 08:07:15.650][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-15 08:07:15.651][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-15 08:07:15.651][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:07:15.652][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:07:15.664][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-04-15 08:07:15.665][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-04-15 08:07:15.666][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:07:15.666][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:07:15.667][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-15 08:07:15.668][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-15 08:07:15.669][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:07:15.669][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:07:15.670][self$getBiodb()$getEntryFields()$get] Asked field names are: sequence.
biodb.TRACE[2023-04-15 08:07:15.671][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2023-04-15 08:07:15.672][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:07:15.672][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:07:15.673][self$getBiodb()$getEntryFields()$get] Asked field names are: mirbase.mature.id.
biodb.TRACE[2023-04-15 08:07:15.674][self$getBiodb()$getEntryFields()$get] Realnames of fields are: mirbase.mature.id.
biodb.TRACE[2023-04-15 08:07:15.675][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:07:15.675][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:07:15.676][self$getBiodb()$getEntryFields()$get] Asked field names are: mirbase.mature.id.
biodb.TRACE[2023-04-15 08:07:15.677][self$getBiodb()$getEntryFields()$get] Realnames of fields are: mirbase.mature.id.
biodb.TRACE[2023-04-15 08:07:15.678][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:07:15.678][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:07:15.679][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-15 08:07:15.680][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-15 08:07:15.681][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:07:15.681][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:07:15.682][self$getBiodb()$getEntryFields()$get] Asked field names are: mirbase.mature.id.
biodb.TRACE[2023-04-15 08:07:15.683][self$getBiodb()$getEntryFields()$get] Realnames of fields are: mirbase.mature.id.
biodb.TRACE[2023-04-15 08:07:15.683][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:07:15.684][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:07:15.685][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-15 08:07:15.686][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-15 08:07:15.686][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:07:15.687][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:07:15.688][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-15 08:07:15.689][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-15 08:07:15.689][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:07:15.690][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:07:15.691][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-15 08:07:15.691][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-15 08:07:15.692][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:07:15.693][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:07:15.694][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-15 08:07:15.694][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-15 08:07:15.695][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:07:15.696][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:07:15.697][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-15 08:07:15.697][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-15 08:07:15.698][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:07:15.699][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:07:15.700][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-15 08:07:15.700][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-15 08:07:15.701][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:07:15.702][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-15 08:07:15.703][biodb$getFactory()$createEntryFromCo ...] Accession numbers: MIMAT0000434.
biodb.TRACE[2023-04-15 08:07:15.716][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2023-04-15 08:07:15.717][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2023-04-15 08:07:15.718][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:07:15.718][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:07:15.719][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2023-04-15 08:07:15.720][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2023-04-15 08:07:15.720][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:07:15.721][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:07:15.722][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2023-04-15 08:07:15.723][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2023-04-15 08:07:15.723][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:07:15.724][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:07:15.725][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2023-04-15 08:07:15.725][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2023-04-15 08:07:15.726][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:07:15.727][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:07:15.728][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-15 08:07:15.728][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-15 08:07:15.729][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:07:15.730][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:07:15.733][self$getBiodb()$getEntryFields()$get] Asked field names are: mirbase.mature.id.
biodb.TRACE[2023-04-15 08:07:15.734][self$getBiodb()$getEntryFields()$get] Realnames of fields are: mirbase.mature.id.
biodb.TRACE[2023-04-15 08:07:15.734][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:07:15.735][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:07:15.738][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-15 08:07:15.739][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-15 08:07:15.740][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:07:15.740][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:07:15.741][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-15 08:07:15.742][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-15 08:07:15.742][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:07:15.743][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:07:15.744][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-15 08:07:15.744][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-15 08:07:15.745][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:07:15.746][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:07:15.747][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-15 08:07:15.748][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-15 08:07:15.748][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:07:15.749][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:07:15.749][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-15 08:07:15.750][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-15 08:07:15.751][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:07:15.752][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:07:15.752][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-15 08:07:15.753][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-15 08:07:15.754][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:07:15.754][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:07:15.755][self$getBiodb()$getEntryFields()$get] Asked field names are: mirbase.mature.id.
biodb.TRACE[2023-04-15 08:07:15.756][self$getBiodb()$getEntryFields()$get] Realnames of fields are: mirbase.mature.id.
biodb.TRACE[2023-04-15 08:07:15.756][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:07:15.757][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:07:15.758][self$getBiodb()$getEntryFields()$get] Asked field names are: mirbase.mature.id.
biodb.TRACE[2023-04-15 08:07:15.758][self$getBiodb()$getEntryFields()$get] Realnames of fields are: mirbase.mature.id.
biodb.TRACE[2023-04-15 08:07:15.759][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:07:15.760][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:07:15.760][self$getBiodb()$getEntryFields()$get] Asked field names are: mirbase.mature.id.
biodb.TRACE[2023-04-15 08:07:15.761][self$getBiodb()$getEntryFields()$get] Realnames of fields are: mirbase.mature.id.
biodb.TRACE[2023-04-15 08:07:15.762][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:07:15.762][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:07:15.775][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-15 08:07:15.776][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-15 08:07:15.777][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:07:15.777][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:07:15.778][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-15 08:07:15.779][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-15 08:07:15.779][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:07:15.780][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:07:15.781][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-15 08:07:15.781][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-15 08:07:15.782][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:07:15.783][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:07:15.783][ef$get] Asked field names are: accession.
biodb.TRACE[2023-04-15 08:07:15.784][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-15 08:07:15.785][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:07:15.785][ef$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:07:15.786][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-15 08:07:15.787][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-15 08:07:15.787][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:07:15.788][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:07:15.793][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-15 08:07:15.794][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-15 08:07:15.794][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:07:15.795][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:07:15.796][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-15 08:07:15.796][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-15 08:07:15.797][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:07:15.798][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:07:15.798][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-15 08:07:15.799][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-15 08:07:15.800][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:07:15.800][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:07:15.801][ef$get] Asked field names are: name.
biodb.TRACE[2023-04-15 08:07:15.802][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-04-15 08:07:15.803][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:07:15.803][ef$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:07:15.804][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-15 08:07:15.805][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-15 08:07:15.805][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:07:15.806][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:07:15.811][self$getBiodb()$getEntryFields()$get] Asked field names are: sequence.
biodb.TRACE[2023-04-15 08:07:15.812][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2023-04-15 08:07:15.812][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:07:15.813][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:07:15.813][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2023-04-15 08:07:15.814][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2023-04-15 08:07:15.815][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:07:15.815][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:07:15.816][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2023-04-15 08:07:15.817][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2023-04-15 08:07:15.818][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:07:15.818][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:07:15.819][ef$get] Asked field names are: sequence.
biodb.TRACE[2023-04-15 08:07:15.820][ef$get] Realnames of fields are: aa.seq.
biodb.TRACE[2023-04-15 08:07:15.820][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:07:15.821][ef$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:07:15.822][self$getBiodb()$getEntryFields()$get] Asked field names are: sequence.
biodb.TRACE[2023-04-15 08:07:15.822][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2023-04-15 08:07:15.823][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:07:15.824][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:07:15.828][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-04-15 08:07:15.829][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-04-15 08:07:15.830][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:07:15.830][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:07:15.831][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-04-15 08:07:15.832][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-04-15 08:07:15.832][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:07:15.833][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:07:15.834][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-04-15 08:07:15.834][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-04-15 08:07:15.835][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:07:15.836][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:07:15.836][ef$get] Asked field names are: description.
biodb.TRACE[2023-04-15 08:07:15.837][ef$get] Realnames of fields are: description.
biodb.TRACE[2023-04-15 08:07:15.838][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:07:15.838][ef$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:07:15.839][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-04-15 08:07:15.840][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-04-15 08:07:15.840][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:07:15.841][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:07:15.846][ef$get] Asked field names are: aa.seq.
biodb.TRACE[2023-04-15 08:07:15.847][ef$get] Realnames of fields are: aa.seq.
biodb.TRACE[2023-04-15 08:07:15.847][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:07:15.848][ef$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:07:15.851][ef$get] Asked field names are: accession.
biodb.TRACE[2023-04-15 08:07:15.852][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-15 08:07:15.853][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:07:15.853][ef$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:07:15.856][ef$get] Asked field names are: description.
biodb.TRACE[2023-04-15 08:07:15.857][ef$get] Realnames of fields are: description.
biodb.TRACE[2023-04-15 08:07:15.858][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:07:15.858][ef$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:07:15.862][ef$get] Asked field names are: name.
biodb.TRACE[2023-04-15 08:07:15.862][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-04-15 08:07:15.863][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:07:15.864][ef$get] fields variable is a list.
biodb.INFO [2023-04-15 08:07:15.868][biodb::testThat]
biodb.INFO [2023-04-15 08:07:15.868][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2023-04-15 08:07:15.869][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-04-15 08:07:15.870][biodb::testThat]
biodb.DEBUG[2023-04-15 08:07:15.871][private$loadEntries] Creating entries from ids [2]: "MIMAT0000433, MIMAT0000434".
biodb.DEBUG[2023-04-15 08:07:15.876][conn$getEntryContent] Get miRBase mature database entry content(s) for 2 id(s)...
biodb.INFO [2023-04-15 08:07:15.879][self$getFolderPath] Create cache folder "/home/biocbuild/.cache/R/biodb/mirbase.mature-ecbae556d51779d9d48125ba5a617e19" for "mirbase.mature-ecbae556d51779d9d48125ba5a617e19".
biodb.DEBUG[2023-04-15 08:07:15.879][self$isDownloaded] Database mirbase.mature has not yet been downloaded.
biodb.INFO [2023-04-15 08:07:15.880][self$download] Downloading whole database of mirbase.mature.
biodb.DEBUG[2023-04-15 08:07:15.881][self$getDownloadPath] Download path of mirbase.mature is "/home/biocbuild/.cache/R/biodb/mirbase.mature-ecbae556d51779d9d48125ba5a617e19/download.gz".
biodb.DEBUG[2023-04-15 08:07:15.882][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 08:07:18.900][self$getDownloadPath] Download path of mirbase.mature is "/home/biocbuild/.cache/R/biodb/mirbase.mature-ecbae556d51779d9d48125ba5a617e19/download.gz".
biodb.DEBUG[2023-04-15 08:07:18.902][self$download] Downloading of mirbase.mature completed.
biodb.TRACE[2023-04-15 08:07:18.906][self$addFilesToCache] Moving files to cache [1]: "/home/biocbuild/.cache/R/biodb/tmp/marker1cfb8a3c1b3a14marker".
biodb.TRACE[2023-04-15 08:07:18.908][private$doAddFilesToCache] Destination files are [1]: "/home/biocbuild/.cache/R/biodb/mirbase.mature-ecbae556d51779d9d48125ba5a617e19/downloaded.marker".
biodb.DEBUG[2023-04-15 08:07:18.908][self$addFilesToCache] Done adding files.
biodb.DEBUG[2023-04-15 08:07:18.909][self$isDownloaded] Database mirbase.mature has already been downloaded.
biodb.INFO [2023-04-15 08:07:18.910][self$download] Extract whole database of mirbase.mature.
biodb.DEBUG[2023-04-15 08:07:18.911][self$getDownloadPath] Download path of mirbase.mature is "/home/biocbuild/.cache/R/biodb/mirbase.mature-ecbae556d51779d9d48125ba5a617e19/download.gz".
biodb.DEBUG[2023-04-15 08:07:19.082][self$getDownloadPath] Download path of mirbase.mature is "/home/biocbuild/.cache/R/biodb/mirbase.mature-ecbae556d51779d9d48125ba5a617e19/download.gz".
biodb.DEBUG[2023-04-15 08:07:19.083][private$doExtractDownload] Found 48885 entries in file "/home/biocbuild/.cache/R/biodb/mirbase.mature-ecbae556d51779d9d48125ba5a617e19/download.gz".
biodb.TRACE[2023-04-15 08:07:19.240][private$doSaveContentToFile] Saving to cache [48885]: "/home/biocbuild/.cache/R/biodb/mirbase.mature-ecbae556d51779d9d48125ba5a617e19/MIMAT0000001.txt, /home/biocbuild/.cache/R/biodb/mirbase.mature-ecbae556d51779d9d48125ba5a617e19/MIMAT0015091.txt, /home/biocbuild/.cache/R/biodb/mirbase.mature-ecbae556d51779d9d48125ba5a617e19/MIMAT0000002.txt, /home/biocbuild/.cache/R/biodb/mirbase.mature-ecbae556d51779d9d48125ba5a617e19/MIMAT0015092.txt, /home/biocbuild/.cache/R/biodb/mirbase.mature-ecbae556d51779d9d48125ba5a617e19/MIMAT0020301.txt, /home/biocbuild/.cache/R/biodb/mirbase.mature-ecbae556d51779d9d48125ba5a617e19/MIMAT0000003.txt, /home/biocbuild/.cache/R/biodb/mirbase.mature-ecbae556d51779d9d48125ba5a617e19/MIMAT0020302.txt, /home/biocbuild/.cache/R/biodb/mirbase.mature-ecbae556d51779d9d48125ba5a617e19/MIMAT0000004.txt, /home/biocbuild/.cache/R/biodb/mirbase.mature-ecbae556d51779d9d48125ba5a617e19/MIMAT0000005.txt, /home/biocbuild/.cache/R/biodb/mirbase.mature-ecbae556d51779d9d48125ba5a617e19/MIMAT0015093.txt, ..."
biodb.TRACE[2023-04-15 08:07:21.055][self$addFilesToCache] Moving files to cache [1]: "/home/biocbuild/.cache/R/biodb/tmp/marker1cfb8a76c8184amarker".
biodb.TRACE[2023-04-15 08:07:21.056][private$doAddFilesToCache] Destination files are [1]: "/home/biocbuild/.cache/R/biodb/mirbase.mature-ecbae556d51779d9d48125ba5a617e19/extracted.marker".
biodb.DEBUG[2023-04-15 08:07:21.057][self$addFilesToCache] Done adding files.
biodb.TRACE[2023-04-15 08:07:21.058][cch$loadFileContent] Trying to load 2 files from cache: [2]: "MIMAT0000433, MIMAT0000434".
biodb.TRACE[2023-04-15 08:07:21.059][cch$loadFileContent] file.exist = [2]: "TRUE, TRUE".
biodb.TRACE[2023-04-15 08:07:21.060][loadFileContents] Loaded 2 files from cache: [2]: "/home/biocbuild/.cache/R/biodb/mirbase.mature-ecbae556d51779d9d48125ba5a617e19/MIMAT0000433.txt, /home/biocbuild/.cache/R/biodb/mirbase.mature-ecbae556d51779d9d48125ba5a617e19/MIMAT0000434.txt".
biodb.DEBUG[2023-04-15 08:07:21.061][conn$getEntryContent] 2 miRBase mature database entry content(s) loaded from cache.
biodb.DEBUG[2023-04-15 08:07:21.062][self$createEntryFromContent] Creating miRBase mature database entries from 2 content(s).
biodb.DEBUG[2023-04-15 08:07:21.063][self$createEntryFromContent] Parsing 2 miRBase mature database entries.
biodb.DEBUG[2023-04-15 08:07:21.064][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-15 08:07:21.065][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-15 08:07:21.065][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-15 08:07:21.069][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:07:21.070][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-15 08:07:21.071][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:07:21.071][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-15 08:07:21.073][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-15 08:07:21.074][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-15 08:07:21.075][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:07:21.075][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:07:21.076][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-04-15 08:07:21.077][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-04-15 08:07:21.078][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:07:21.078][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:07:21.079][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-15 08:07:21.080][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-15 08:07:21.081][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:07:21.082][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:07:21.082][self$getBiodb()$getEntryFields()$get] Asked field names are: sequence.
biodb.TRACE[2023-04-15 08:07:21.083][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2023-04-15 08:07:21.084][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:07:21.085][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:07:21.085][self$getBiodb()$getEntryFields()$get] Asked field names are: mirbase.mature.id.
biodb.TRACE[2023-04-15 08:07:21.086][self$getBiodb()$getEntryFields()$get] Realnames of fields are: mirbase.mature.id.
biodb.TRACE[2023-04-15 08:07:21.087][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:07:21.087][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:07:21.088][self$getBiodb()$getEntryFields()$get] Asked field names are: mirbase.mature.id.
biodb.TRACE[2023-04-15 08:07:21.089][self$getBiodb()$getEntryFields()$get] Realnames of fields are: mirbase.mature.id.
biodb.TRACE[2023-04-15 08:07:21.090][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:07:21.090][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:07:21.091][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-15 08:07:21.092][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-15 08:07:21.092][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:07:21.093][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:07:21.094][self$getBiodb()$getEntryFields()$get] Asked field names are: mirbase.mature.id.
biodb.TRACE[2023-04-15 08:07:21.094][self$getBiodb()$getEntryFields()$get] Realnames of fields are: mirbase.mature.id.
biodb.TRACE[2023-04-15 08:07:21.095][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:07:21.096][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:07:21.096][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-15 08:07:21.097][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-15 08:07:21.098][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:07:21.099][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:07:21.099][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-15 08:07:21.100][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-15 08:07:21.101][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:07:21.101][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:07:21.102][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-15 08:07:21.103][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-15 08:07:21.103][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:07:21.104][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-15 08:07:21.105][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-15 08:07:21.106][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-15 08:07:21.106][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-15 08:07:21.110][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:07:21.110][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-15 08:07:21.111][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:07:21.112][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-15 08:07:21.113][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-15 08:07:21.114][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-15 08:07:21.114][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:07:21.115][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:07:21.116][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-04-15 08:07:21.117][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-04-15 08:07:21.117][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:07:21.118][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:07:21.119][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-15 08:07:21.120][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-15 08:07:21.120][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:07:21.121][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:07:21.122][self$getBiodb()$getEntryFields()$get] Asked field names are: sequence.
biodb.TRACE[2023-04-15 08:07:21.123][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2023-04-15 08:07:21.123][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:07:21.124][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:07:21.125][self$getBiodb()$getEntryFields()$get] Asked field names are: mirbase.mature.id.
biodb.TRACE[2023-04-15 08:07:21.126][self$getBiodb()$getEntryFields()$get] Realnames of fields are: mirbase.mature.id.
biodb.TRACE[2023-04-15 08:07:21.126][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:07:21.127][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:07:21.128][self$getBiodb()$getEntryFields()$get] Asked field names are: mirbase.mature.id.
biodb.TRACE[2023-04-15 08:07:21.128][self$getBiodb()$getEntryFields()$get] Realnames of fields are: mirbase.mature.id.
biodb.TRACE[2023-04-15 08:07:21.129][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:07:21.130][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:07:21.131][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-15 08:07:21.131][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-15 08:07:21.132][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:07:21.133][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:07:21.133][self$getBiodb()$getEntryFields()$get] Asked field names are: mirbase.mature.id.
biodb.TRACE[2023-04-15 08:07:21.134][self$getBiodb()$getEntryFields()$get] Realnames of fields are: mirbase.mature.id.
biodb.TRACE[2023-04-15 08:07:21.135][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:07:21.136][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:07:21.136][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-15 08:07:21.137][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-15 08:07:21.138][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:07:21.138][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:07:21.139][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-15 08:07:21.140][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-15 08:07:21.141][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:07:21.141][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:07:21.142][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-15 08:07:21.143][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-15 08:07:21.144][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:07:21.158][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:07:21.159][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-15 08:07:21.159][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-15 08:07:21.160][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:07:21.161][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:07:21.161][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-15 08:07:21.162][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-15 08:07:21.163][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:07:21.163][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:07:21.164][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-15 08:07:21.165][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-15 08:07:21.166][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:07:21.166][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:07:21.167][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-15 08:07:21.168][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-15 08:07:21.168][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:07:21.169][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:07:21.170][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-15 08:07:21.170][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-15 08:07:21.171][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:07:21.172][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:07:21.172][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-15 08:07:21.173][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-15 08:07:21.174][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:07:21.174][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-15 08:07:21.175][self$createEntryFromContent] Accession numbers: MIMAT0000433, MIMAT0000434.
biodb.TRACE[2023-04-15 08:07:21.176][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2023-04-15 08:07:21.177][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2023-04-15 08:07:21.177][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:07:21.178][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:07:21.179][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2023-04-15 08:07:21.179][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2023-04-15 08:07:21.180][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:07:21.181][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:07:21.181][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2023-04-15 08:07:21.182][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2023-04-15 08:07:21.183][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:07:21.184][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:07:21.187][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2023-04-15 08:07:21.188][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2023-04-15 08:07:21.189][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:07:21.189][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:07:21.190][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2023-04-15 08:07:21.191][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2023-04-15 08:07:21.192][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:07:21.192][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:07:21.193][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2023-04-15 08:07:21.194][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2023-04-15 08:07:21.194][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:07:21.195][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2023-04-15 08:07:21.199][biodb::testThat]
biodb.INFO [2023-04-15 08:07:21.200][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2023-04-15 08:07:21.201][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-04-15 08:07:21.201][biodb::testThat]
biodb.INFO [2023-04-15 08:07:21.204][biodb::testThat]
biodb.INFO [2023-04-15 08:07:21.204][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2023-04-15 08:07:21.205][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-04-15 08:07:21.206][biodb::testThat]
biodb.WARN [2023-04-15 08:07:21.223][self$searchForEntries] This database is not searchable by field "name".
biodb.WARN [2023-04-15 08:07:21.237][self$searchForEntries] This database is not searchable by field "name".
biodb.INFO [2023-04-15 08:07:21.242][biodb::testThat]
biodb.INFO [2023-04-15 08:07:21.243][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2023-04-15 08:07:21.243][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-04-15 08:07:21.244][biodb::testThat]
biodb.TRACE[2023-04-15 08:07:21.272][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2023-04-15 08:07:21.273][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2023-04-15 08:07:21.274][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:07:21.274][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:07:21.275][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2023-04-15 08:07:21.276][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2023-04-15 08:07:21.277][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:07:21.277][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:07:21.278][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2023-04-15 08:07:21.279][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2023-04-15 08:07:21.279][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:07:21.280][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:07:21.281][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2023-04-15 08:07:21.281][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2023-04-15 08:07:21.282][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:07:21.283][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:07:21.304][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2023-04-15 08:07:21.305][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2023-04-15 08:07:21.305][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:07:21.306][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:07:21.307][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2023-04-15 08:07:21.307][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2023-04-15 08:07:21.308][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:07:21.309][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:07:21.309][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2023-04-15 08:07:21.310][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2023-04-15 08:07:21.311][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:07:21.311][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:07:21.312][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2023-04-15 08:07:21.313][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2023-04-15 08:07:21.314][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:07:21.314][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2023-04-15 08:07:21.316][biodb::testThat]
biodb.INFO [2023-04-15 08:07:21.317][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2023-04-15 08:07:21.318][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-04-15 08:07:21.318][biodb::testThat]
biodb.INFO [2023-04-15 08:07:21.322][biodb::testThat]
biodb.INFO [2023-04-15 08:07:21.323][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2023-04-15 08:07:21.323][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-04-15 08:07:21.324][biodb::testThat]
biodb.INFO [2023-04-15 08:07:21.327][biodb::testThat]
biodb.INFO [2023-04-15 08:07:21.328][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2023-04-15 08:07:21.328][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-04-15 08:07:21.329][biodb::testThat]
biodb.DEBUG[2023-04-15 08:07:21.331][function(conn, opt)] Trying to download "http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000433".
biodb.DEBUG[2023-04-15 08:07:23.607][getUrlContent] Use RCurl for downloading content of URL http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000433.
biodb.INFO [2023-04-15 08:07:23.827][biodb::testThat]
biodb.INFO [2023-04-15 08:07:23.828][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2023-04-15 08:07:23.829][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-04-15 08:07:23.830][biodb::testThat]
biodb.INFO [2023-04-15 08:07:23.832][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2023-04-15 08:07:23.833][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector mirbase.mature from the request scheduler
biodb.INFO [2023-04-15 08:07:23.834][self$deleteConn] Connector "mirbase.mature" deleted.
biodb.DEBUG[2023-04-15 08:07:23.834][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2023-04-15 08:07:23.835][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-15 08:07:23.836][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-15 08:07:23.836][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:07:23.837][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 08:07:23.838][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:07:23.838][FUN] Functions in observer BiodbConfig: [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 08:07:23.845][biodb::testContext]
biodb.INFO [2023-04-15 08:07:23.845][biodb::testContext] ********************************************************************************
biodb.INFO [2023-04-15 08:07:23.846][biodb::testContext] Test context - Example long tests
biodb.INFO [2023-04-15 08:07:23.847][biodb::testContext] ********************************************************************************
biodb.INFO [2023-04-15 08:07:23.848][biodb::testContext]
biodb.INFO [2023-04-15 08:07:23.849][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.6.1.
biodb.DEBUG[2023-04-15 08:07:23.850][self$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.16-bioc/R/site-library/biodb/definitions.yml".
biodb.DEBUG[2023-04-15 08:07:23.868][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-04-15 08:07:23.869][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2023-04-15 08:07:23.870][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2023-04-15 08:07:23.870][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:07:23.871][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:07:23.871][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:07:23.872][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2023-04-15 08:07:23.873][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2023-04-15 08:07:23.873][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:07:23.874][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:07:23.875][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:07:23.875][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2023-04-15 08:07:23.876][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2023-04-15 08:07:23.877][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:07:23.877][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:07:23.878][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:07:23.879][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2023-04-15 08:07:23.879][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2023-04-15 08:07:23.880][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2023-04-15 08:07:23.881][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:07:23.881][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:07:23.882][FUN] Functions in observer BiodbConfig: [21]: ".__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 08:07:23.883][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2023-04-15 08:07:23.883][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2023-04-15 08:07:23.884][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2023-04-15 08:07:23.885][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:07:23.885][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:07:23.886][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:07:23.887][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2023-04-15 08:07:23.887][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2023-04-15 08:07:23.888][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:07:23.889][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:07:23.889][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:07:23.890][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2023-04-15 08:07:23.891][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2023-04-15 08:07:23.891][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2023-04-15 08:07:23.892][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:07:23.893][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:07:23.893][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:07:23.894][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2023-04-15 08:07:23.895][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2023-04-15 08:07:23.895][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:07:23.896][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:07:23.897][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:07:23.897][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2023-04-15 08:07:23.898][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2023-04-15 08:07:23.899][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2023-04-15 08:07:23.899][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:07:23.900][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:07:23.900][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:07:23.901][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2023-04-15 08:07:23.902][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2023-04-15 08:07:23.903][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2023-04-15 08:07:23.903][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2023-04-15 08:07:23.904][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2023-04-15 08:07:23.905][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2023-04-15 08:07:23.905][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:07:23.906][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:07:23.907][FUN] Functions in observer BiodbConfig: [21]: ".__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 08:07:23.907][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2023-04-15 08:07:23.908][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2023-04-15 08:07:23.909][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:07:23.909][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:07:23.910][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:07:23.910][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2023-04-15 08:07:23.911][self$set] Set key entries.sep to "|".
biodb.DEBUG[2023-04-15 08:07:23.912][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:07:23.912][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:07:23.913][FUN] Functions in observer BiodbConfig: [21]: ".__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 08:07:23.914][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2023-04-15 08:07:23.914][self$set] Set key offline to FALSE.
biodb.DEBUG[2023-04-15 08:07:23.915][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:07:23.916][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:07:23.916][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:07:23.917][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2023-04-15 08:07:23.918][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2023-04-15 08:07:23.918][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:07:23.919][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:07:23.920][FUN] Functions in observer BiodbConfig: [21]: ".__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 08:07:23.920][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2023-04-15 08:07:23.921][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2023-04-15 08:07:23.922][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:07:23.922][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:07:23.923][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:07:23.924][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2023-04-15 08:07:23.924][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2023-04-15 08:07:23.929][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2023-04-15 08:07:23.930][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:07:23.930][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:07:23.931][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:07:23.932][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2023-04-15 08:07:23.933][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2023-04-15 08:07:23.933][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2023-04-15 08:07:23.934][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:07:23.935][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:07:23.935][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:07:23.936][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2023-04-15 08:07:23.938][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-04-15 08:07:23.938][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2023-04-15 08:07:23.939][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-04-15 08:07:23.940][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-04-15 08:07:23.941][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-04-15 08:07:23.941][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-04-15 08:07:23.942][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-04-15 08:07:23.943][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-04-15 08:07:23.944][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2023-04-15 08:07:23.944][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-04-15 08:07:23.945][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-04-15 08:07:23.946][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2023-04-15 08:07:23.947][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-04-15 08:07:23.947][self$setPropertyValue]
biodb.DEBUG[2023-04-15 08:07:23.948][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-04-15 08:07:23.949][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2023-04-15 08:07:23.949][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2023-04-15 08:07:23.949][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2023-04-15 08:07:23.949][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2023-04-15 08:07:23.949][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2023-04-15 08:07:23.949][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-04-15 08:07:23.962][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-15 08:07:23.963][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-15 08:07:23.964][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-04-15 08:07:23.964][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-15 08:07:23.965][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-15 08:07:23.966][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-04-15 08:07:23.966][self$setPropertyValue]
biodb.DEBUG[2023-04-15 08:07:23.967][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-04-15 08:07:23.968][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-04-15 08:07:23.968][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-04-15 08:07:23.969][self$setPropertyValue]
biodb.DEBUG[2023-04-15 08:07:23.970][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2023-04-15 08:07:23.971][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-04-15 08:07:23.972][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2023-04-15 08:07:23.973][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-04-15 08:07:23.973][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-04-15 08:07:23.974][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-04-15 08:07:23.975][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-04-15 08:07:23.976][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-04-15 08:07:23.976][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-04-15 08:07:23.977][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2023-04-15 08:07:23.978][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-04-15 08:07:23.978][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-04-15 08:07:23.979][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2023-04-15 08:07:23.980][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-04-15 08:07:23.981][self$setPropertyValue]
biodb.DEBUG[2023-04-15 08:07:23.981][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-04-15 08:07:23.982][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2023-04-15 08:07:23.982][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2023-04-15 08:07:23.982][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2023-04-15 08:07:23.982][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2023-04-15 08:07:23.982][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2023-04-15 08:07:23.983][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-04-15 08:07:23.983][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-15 08:07:23.984][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-15 08:07:23.985][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-04-15 08:07:23.985][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-15 08:07:23.986][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-15 08:07:23.987][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-04-15 08:07:23.987][self$setPropertyValue]
biodb.DEBUG[2023-04-15 08:07:23.988][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-04-15 08:07:23.989][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-04-15 08:07:23.989][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-04-15 08:07:23.990][self$setPropertyValue]
biodb.DEBUG[2023-04-15 08:07:23.991][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2023-04-15 08:07:23.992][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2023-04-15 08:07:23.993][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2023-04-15 08:07:23.994][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-04-15 08:07:23.994][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-04-15 08:07:23.995][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-04-15 08:07:23.996][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-04-15 08:07:23.996][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-04-15 08:07:23.997][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-04-15 08:07:23.998][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2023-04-15 08:07:23.999][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-04-15 08:07:23.999][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2023-04-15 08:07:24.000][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2023-04-15 08:07:24.001][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-04-15 08:07:24.001][self$setPropertyValue]
biodb.DEBUG[2023-04-15 08:07:24.002][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-04-15 08:07:24.003][self$setPropertyValue]
biodb.DEBUG[2023-04-15 08:07:24.004][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-04-15 08:07:24.004][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-15 08:07:24.005][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-15 08:07:24.006][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-04-15 08:07:24.006][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-15 08:07:24.007][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-15 08:07:24.008][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-04-15 08:07:24.008][self$setPropertyValue]
biodb.DEBUG[2023-04-15 08:07:24.009][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-04-15 08:07:24.010][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-04-15 08:07:24.010][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-04-15 08:07:24.011][self$setPropertyValue]
biodb.DEBUG[2023-04-15 08:07:24.012][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2023-04-15 08:07:24.013][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2023-04-15 08:07:24.014][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2023-04-15 08:07:24.014][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-04-15 08:07:24.015][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-04-15 08:07:24.016][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-04-15 08:07:24.017][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-04-15 08:07:24.017][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-04-15 08:07:24.018][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-04-15 08:07:24.019][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2023-04-15 08:07:24.019][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-04-15 08:07:24.020][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2023-04-15 08:07:24.021][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2023-04-15 08:07:24.021][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-04-15 08:07:24.022][self$setPropertyValue]
biodb.DEBUG[2023-04-15 08:07:24.023][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-04-15 08:07:24.024][self$setPropertyValue]
biodb.DEBUG[2023-04-15 08:07:24.024][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-04-15 08:07:24.025][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-15 08:07:24.026][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-15 08:07:24.026][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-04-15 08:07:24.027][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-15 08:07:24.028][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-15 08:07:24.028][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-04-15 08:07:24.029][self$setPropertyValue]
biodb.DEBUG[2023-04-15 08:07:24.030][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-04-15 08:07:24.030][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-04-15 08:07:24.031][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-04-15 08:07:24.032][self$setPropertyValue]
biodb.DEBUG[2023-04-15 08:07:24.033][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-04-15 08:07:24.033][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:07:24.034][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 08:07:24.034][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:07:24.035][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:07:24.036][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-15 08:07:24.036][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:07:24.037][FUN] Functions in observer BiodbConfig: [21]: ".__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 08:07:24.038][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:07:24.038][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:07:24.039][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-15 08:07:24.039][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:07:24.040][FUN] Functions in observer BiodbConfig: [21]: ".__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 08:07:24.053][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:07:24.053][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:07:24.054][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 08:07:24.054][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:07:24.055][FUN] Functions in observer BiodbConfig: [21]: ".__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 08:07:24.056][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:07:24.056][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:07:24.057][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 08:07:24.058][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:07:24.058][FUN] Functions in observer BiodbConfig: [21]: ".__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 08:07:24.059][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:07:24.060][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:07:24.060][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 08:07:24.061][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:07:24.061][FUN] Functions in observer BiodbConfig: [21]: ".__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 08:07:24.062][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:07:24.063][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:07:24.063][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 08:07:24.064][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:07:24.065][FUN] Functions in observer BiodbConfig: [21]: ".__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 08:07:24.065][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:07:24.066][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:07:24.066][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 08:07:24.067][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:07:24.068][FUN] Functions in observer BiodbConfig: [21]: ".__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 08:07:24.068][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:07:24.069][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:07:24.070][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 08:07:24.070][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:07:24.071][FUN] Functions in observer BiodbConfig: [21]: ".__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 08:07:24.071][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:07:24.072][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:07:24.073][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 08:07:24.073][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:07:24.074][FUN] Functions in observer BiodbConfig: [21]: ".__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 08:07:24.075][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:07:24.075][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:07:24.076][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 08:07:24.076][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:07:24.077][FUN] Functions in observer BiodbConfig: [21]: ".__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 08:07:24.078][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:07:24.078][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:07:24.079][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 08:07:24.079][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:07:24.080][FUN] Functions in observer BiodbConfig: [21]: ".__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 08:07:24.081][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:07:24.081][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:07:24.082][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 08:07:24.083][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:07:24.083][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:07:24.084][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:07:24.085][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:07:24.085][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 08:07:24.086][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:07:24.086][FUN] Functions in observer BiodbConfig: [21]: ".__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 08:07:24.087][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:07:24.088][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:07:24.088][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 08:07:24.089][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:07:24.089][FUN] Functions in observer BiodbConfig: [21]: ".__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 08:07:24.090][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:07:24.091][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:07:24.091][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 08:07:24.092][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:07:24.093][FUN] Functions in observer BiodbConfig: [21]: ".__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 08:07:24.093][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:07:24.094][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:07:24.094][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 08:07:24.095][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:07:24.096][FUN] Functions in observer BiodbConfig: [21]: ".__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 08:07:24.096][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:07:24.097][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:07:24.098][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 08:07:24.098][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:07:24.099][FUN] Functions in observer BiodbConfig: [21]: ".__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 08:07:24.100][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2023-04-15 08:07:24.101][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2023-04-15 08:07:24.102][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2023-04-15 08:07:24.103][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2023-04-15 08:07:24.104][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2023-04-15 08:07:24.105][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2023-04-15 08:07:24.106][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2023-04-15 08:07:24.106][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2023-04-15 08:07:24.107][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2023-04-15 08:07:24.108][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2023-04-15 08:07:24.109][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2023-04-15 08:07:24.110][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2023-04-15 08:07:24.111][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2023-04-15 08:07:24.112][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2023-04-15 08:07:24.113][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2023-04-15 08:07:24.114][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2023-04-15 08:07:24.115][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2023-04-15 08:07:24.116][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2023-04-15 08:07:24.117][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2023-04-15 08:07:24.118][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2023-04-15 08:07:24.119][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2023-04-15 08:07:24.120][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2023-04-15 08:07:24.121][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2023-04-15 08:07:24.122][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2023-04-15 08:07:24.123][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2023-04-15 08:07:24.124][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2023-04-15 08:07:24.125][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2023-04-15 08:07:24.126][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2023-04-15 08:07:24.127][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2023-04-15 08:07:24.128][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2023-04-15 08:07:24.141][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2023-04-15 08:07:24.142][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2023-04-15 08:07:24.143][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2023-04-15 08:07:24.143][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2023-04-15 08:07:24.144][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2023-04-15 08:07:24.145][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2023-04-15 08:07:24.146][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2023-04-15 08:07:24.147][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2023-04-15 08:07:24.148][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2023-04-15 08:07:24.149][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2023-04-15 08:07:24.150][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2023-04-15 08:07:24.151][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2023-04-15 08:07:24.152][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2023-04-15 08:07:24.153][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2023-04-15 08:07:24.154][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2023-04-15 08:07:24.155][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2023-04-15 08:07:24.156][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2023-04-15 08:07:24.157][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2023-04-15 08:07:24.158][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2023-04-15 08:07:24.159][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2023-04-15 08:07:24.160][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2023-04-15 08:07:24.161][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2023-04-15 08:07:24.162][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2023-04-15 08:07:24.163][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2023-04-15 08:07:24.164][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2023-04-15 08:07:24.165][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2023-04-15 08:07:24.166][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2023-04-15 08:07:24.167][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2023-04-15 08:07:24.168][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2023-04-15 08:07:24.168][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2023-04-15 08:07:24.169][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2023-04-15 08:07:24.170][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2023-04-15 08:07:24.171][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2023-04-15 08:07:24.172][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2023-04-15 08:07:24.173][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2023-04-15 08:07:24.174][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2023-04-15 08:07:24.175][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2023-04-15 08:07:24.176][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2023-04-15 08:07:24.177][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2023-04-15 08:07:24.178][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2023-04-15 08:07:24.179][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2023-04-15 08:07:24.180][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2023-04-15 08:07:24.181][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2023-04-15 08:07:24.182][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2023-04-15 08:07:24.183][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2023-04-15 08:07:24.184][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2023-04-15 08:07:24.185][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2023-04-15 08:07:24.186][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2023-04-15 08:07:24.187][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2023-04-15 08:07:24.188][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2023-04-15 08:07:24.189][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2023-04-15 08:07:24.190][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2023-04-15 08:07:24.191][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2023-04-15 08:07:24.192][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2023-04-15 08:07:24.193][initialize] This is biodb version 1.6.1.
biodb.DEBUG[2023-04-15 08:07:24.194][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-04-15 08:07:24.194][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:07:24.195][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 08:07:24.195][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:07:24.196][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:07:24.197][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:07:24.197][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-15 08:07:24.198][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-15 08:07:24.199][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:07:24.199][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-15 08:07:24.200][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:07:24.200][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:07:24.201][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:07:24.202][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-15 08:07:24.202][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-15 08:07:24.203][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:07:24.204][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-15 08:07:24.204][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:07:24.205][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:07:24.205][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:07:24.206][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-15 08:07:24.207][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-15 08:07:24.207][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:07:24.208][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 08:07:24.209][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:07:24.209][FUN] Functions in observer BiodbConfig: [21]: ".__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 08:07:24.210][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:07:24.210][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-15 08:07:24.211][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-15 08:07:24.212][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:07:24.212][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 08:07:24.213][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:07:24.214][FUN] Functions in observer BiodbConfig: [21]: ".__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 08:07:24.214][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:07:24.215][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-15 08:07:24.216][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-15 08:07:24.279][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:07:24.280][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 08:07:24.281][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:07:24.282][FUN] Functions in observer BiodbConfig: [21]: ".__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 08:07:24.283][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:07:24.284][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-15 08:07:24.285][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-15 08:07:24.285][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:07:24.286][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 08:07:24.287][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:07:24.288][FUN] Functions in observer BiodbConfig: [21]: ".__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 08:07:24.289][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:07:24.289][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-15 08:07:24.290][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-15 08:07:24.291][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:07:24.291][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 08:07:24.292][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:07:24.293][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:07:24.293][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:07:24.294][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-15 08:07:24.295][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-15 08:07:24.295][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:07:24.296][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-15 08:07:24.297][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:07:24.297][FUN] Functions in observer BiodbConfig: [21]: ".__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 08:07:24.298][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:07:24.298][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-15 08:07:24.299][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-15 08:07:24.300][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:07:24.300][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-15 08:07:24.301][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:07:24.302][FUN] Functions in observer BiodbConfig: [21]: ".__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 08:07:24.302][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:07:24.303][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-15 08:07:24.304][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-15 08:07:24.304][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:07:24.305][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-15 08:07:24.305][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:07:24.306][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:07:24.307][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:07:24.307][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-15 08:07:24.308][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-15 08:07:24.309][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:07:24.309][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 08:07:24.310][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:07:24.310][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:07:24.311][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:07:24.312][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-15 08:07:24.312][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-15 08:07:24.313][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:07:24.314][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-15 08:07:24.314][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:07:24.315][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:07:24.315][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:07:24.316][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-15 08:07:24.317][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-15 08:07:24.317][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:07:24.318][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 08:07:24.319][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:07:24.319][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:07:24.320][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:07:24.320][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-15 08:07:24.321][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-15 08:07:24.322][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:07:24.322][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 08:07:24.323][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:07:24.324][FUN] Functions in observer BiodbConfig: [21]: ".__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 08:07:24.324][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:07:24.325][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-15 08:07:24.326][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-15 08:07:24.326][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:07:24.327][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-15 08:07:24.327][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:07:24.328][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:07:24.329][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:07:24.329][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-15 08:07:24.330][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-15 08:07:24.331][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:07:24.331][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 08:07:24.332][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:07:24.333][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 08:07:24.333][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:07:24.334][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-15 08:07:24.334][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-15 08:07:24.335][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:07:24.336][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-15 08:07:24.336][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:07:24.337][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:07:24.338][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.16-bioc-longtests/meat/biodbMirbase.Rcheck/biodbMirbase/definitions.yml".
biodb.DEBUG[2023-04-15 08:07:24.345][self$getDbsInfo()$define] Define connector mirbase.mature.
biodb.DEBUG[2023-04-15 08:07:24.364][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-04-15 08:07:24.365][self$setPropertyValue] Setting property "description" to "Write here the description of this database.".
biodb.DEBUG[2023-04-15 08:07:24.365][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-04-15 08:07:24.366][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-04-15 08:07:24.367][self$setPropertyValue] Setting property "downloadable" to "TRUE".
biodb.DEBUG[2023-04-15 08:07:24.368][self$setPropertyValue] Setting property "dwnld.ext" to "gz".
biodb.DEBUG[2023-04-15 08:07:24.368][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2023-04-15 08:07:24.369][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-04-15 08:07:24.370][self$setPropertyValue] Setting property "entry.content.type" to "txt".
biodb.DEBUG[2023-04-15 08:07:24.370][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-04-15 08:07:24.371][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-04-15 08:07:24.372][self$setPropertyValue] Setting property "name" to "miRBase mature database".
biodb.DEBUG[2023-04-15 08:07:24.372][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-04-15 08:07:24.373][self$setPropertyValue] Setting property "parsing.expr" to "^>[^ ]+ *(MIMAT[0-9]+) .*$".
biodb.DEBUG[2023-04-15 08:07:24.373][self$setPropertyValue] Setting property "parsing.expr" to "^>[^ ]+ *MIMAT[0-9]+ (.*)$".
biodb.DEBUG[2023-04-15 08:07:24.373][self$setPropertyValue] Setting property "parsing.expr" to "^>([^ ]+) *MIMAT[0-9]+ .*$".
biodb.DEBUG[2023-04-15 08:07:24.373][self$setPropertyValue] Setting property "parsing.expr" to "^([ACGU]+)$".
biodb.DEBUG[2023-04-15 08:07:24.374][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2023-04-15 08:07:24.374][self$setPropertyValue]
biodb.DEBUG[2023-04-15 08:07:24.375][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2023-04-15 08:07:24.376][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-15 08:07:24.377][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-15 08:07:24.377][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-04-15 08:07:24.378][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-15 08:07:24.378][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-15 08:07:24.379][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-04-15 08:07:24.380][self$setPropertyValue] Setting property "urls" to "http://www.mirbase.org/".
biodb.DEBUG[2023-04-15 08:07:24.380][self$setPropertyValue] Setting property "urls" to "https://www.mirbase.org/ftp/CURRENT/mature.fa.gz".
biodb.DEBUG[2023-04-15 08:07:24.380][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-04-15 08:07:24.381][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-04-15 08:07:24.382][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2023-04-15 08:07:24.382][self$setPropertyValue]
biodb.DEBUG[2023-04-15 08:07:24.383][self$getEntryFields()$define] Define field mirbase.mature.id.
biodb.DEBUG[2023-04-15 08:07:24.385][initialize] Initialize connector mirbase.mature.
biodb.DEBUG[2023-04-15 08:07:24.386][initialize] Register connector mirbase.mature with the request scheduler
biodb.DEBUG[2023-04-15 08:07:24.387][private$bdb$getRequestScheduler()$re ...] Register connector mirbase.mature.
biodb.DEBUG[2023-04-15 08:07:24.388][private$addConnectorRules] Create new rule for URL "www.mirbase.org" of connector "mirbase.mature".
biodb.DEBUG[2023-04-15 08:07:24.389][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2023-04-15 08:07:24.389][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2023-04-15 08:07:24.390][rule$addConnector] Connector "mirbase.mature" is already listed in rule "www.mirbase.org".
biodb.DEBUG[2023-04-15 08:07:24.391][biodb$getFactory()$createConn] Creating new connector mirbase.mature for database class mirbase.mature .
biodb.INFO [2023-04-15 08:07:24.392][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2023-04-15 08:07:24.393][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector mirbase.mature from the request scheduler
biodb.INFO [2023-04-15 08:07:24.393][self$deleteConn] Connector "mirbase.mature" deleted.
biodb.DEBUG[2023-04-15 08:07:24.394][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2023-04-15 08:07:24.394][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-15 08:07:24.395][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-15 08:07:24.396][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:07:24.396][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 08:07:24.397][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:07:24.398][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".
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 75 ]
> 
> proc.time()
   user  system elapsed 
  4.551   0.938  10.873

'R CMD check' output

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


* using log directory ‘/home/biocbuild/bbs-3.16-bioc-longtests/meat/biodbMirbase.Rcheck’
* using R version 4.2.3 (2023-03-15)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using options ‘--no-codoc --no-examples --no-manual --ignore-vignettes --no-stop-on-test-error’
* checking for file ‘biodbMirbase/DESCRIPTION’ ... OK
* this is package ‘biodbMirbase’ version ‘1.2.2’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘biodbMirbase’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... 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)