Back to Long Tests report for BioC 3.16

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

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

CHECK results for biodbMirbase on lconway


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: /Library/Frameworks/R.framework/Resources/bin/R CMD check --test-dir=longtests --no-stop-on-test-error --no-codoc --no-examples --no-manual --ignore-vignettes --check-subdirs=no biodbMirbase_1.2.2.tar.gz
StartedAt: 2023-04-15 08:01:34 -0400 (Sat, 15 Apr 2023)
EndedAt: 2023-04-15 08:02:30 -0400 (Sat, 15 Apr 2023)
EllapsedTime: 55.7 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-apple-darwin17.0 (64-bit)

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> # Script needed to run testthat automatically from ‘R CMD check’. See
> # testthat::test_dir documentation.
> library(testthat)
> library(biodbMirbase)
> Sys.setenv(TESTTHAT_REPORTER="summary")
> Sys.setenv(BIODB_LOG_DST="console")
> test_check("biodbMirbase")
biodb.INFO [2023-04-15 08:02:12.592][biodb::testContext]
biodb.INFO [2023-04-15 08:02:12.610][biodb::testContext] ********************************************************************************
biodb.INFO [2023-04-15 08:02:12.611][biodb::testContext] Test context - Generic long tests
biodb.INFO [2023-04-15 08:02:12.612][biodb::testContext] ********************************************************************************
biodb.INFO [2023-04-15 08:02:12.613][biodb::testContext]
biodb.INFO [2023-04-15 08:02:12.619][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.6.1.
biodb.DEBUG[2023-04-15 08:02:12.620][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.2/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2023-04-15 08:02:12.627][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-04-15 08:02:12.628][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2023-04-15 08:02:12.629][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2023-04-15 08:02:12.630][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:02:12.630][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:02:12.631][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:02:12.632][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2023-04-15 08:02:12.647][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2023-04-15 08:02:12.648][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:02:12.648][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:02:12.649][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:02:12.650][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2023-04-15 08:02:12.651][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2023-04-15 08:02:12.652][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:02:12.652][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:02:12.653][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:02:12.654][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2023-04-15 08:02:12.655][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2023-04-15 08:02:12.656][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2023-04-15 08:02:12.657][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:02:12.657][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:02:12.658][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:02:12.659][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2023-04-15 08:02:12.660][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2023-04-15 08:02:12.661][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2023-04-15 08:02:12.662][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:02:12.662][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:02:12.663][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:02:12.664][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2023-04-15 08:02:12.665][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2023-04-15 08:02:12.666][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:02:12.666][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:02:12.667][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:02:12.668][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2023-04-15 08:02:12.669][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2023-04-15 08:02:12.670][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2023-04-15 08:02:12.671][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:02:12.671][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:02:12.672][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:02:12.673][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2023-04-15 08:02:12.674][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2023-04-15 08:02:12.675][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:02:12.675][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:02:12.676][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:02:12.677][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2023-04-15 08:02:12.678][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2023-04-15 08:02:12.679][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2023-04-15 08:02:12.680][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:02:12.680][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:02:12.681][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:02:12.682][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2023-04-15 08:02:12.683][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2023-04-15 08:02:12.684][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2023-04-15 08:02:12.685][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2023-04-15 08:02:12.685][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2023-04-15 08:02:12.686][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2023-04-15 08:02:12.687][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:02:12.688][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:02:12.689][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:02:12.690][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2023-04-15 08:02:12.690][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2023-04-15 08:02:12.691][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:02:12.692][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:02:12.693][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:02:12.694][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2023-04-15 08:02:12.695][self$set] Set key entries.sep to "|".
biodb.DEBUG[2023-04-15 08:02:12.695][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:02:12.696][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:02:12.697][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:02:12.698][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2023-04-15 08:02:12.699][self$set] Set key offline to FALSE.
biodb.DEBUG[2023-04-15 08:02:12.699][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:02:12.700][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:02:12.701][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:02:12.702][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2023-04-15 08:02:12.703][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2023-04-15 08:02:12.703][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:02:12.704][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:02:12.705][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:02:12.706][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2023-04-15 08:02:12.707][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2023-04-15 08:02:12.708][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:02:12.709][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:02:12.709][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:02:12.710][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2023-04-15 08:02:12.711][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2023-04-15 08:02:12.733][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2023-04-15 08:02:12.734][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:02:12.735][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:02:12.735][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:02:12.736][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2023-04-15 08:02:12.737][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2023-04-15 08:02:12.738][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2023-04-15 08:02:12.739][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:02:12.739][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:02:12.740][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:02:12.743][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2023-04-15 08:02:12.778][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-04-15 08:02:12.790][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2023-04-15 08:02:12.791][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-04-15 08:02:12.791][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-04-15 08:02:12.792][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-04-15 08:02:12.793][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-04-15 08:02:12.794][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-04-15 08:02:12.795][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-04-15 08:02:12.795][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2023-04-15 08:02:12.796][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-04-15 08:02:12.797][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-04-15 08:02:12.798][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2023-04-15 08:02:12.799][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-04-15 08:02:12.799][self$setPropertyValue]
biodb.DEBUG[2023-04-15 08:02:12.800][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-04-15 08:02:12.801][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2023-04-15 08:02:12.801][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2023-04-15 08:02:12.801][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2023-04-15 08:02:12.801][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2023-04-15 08:02:12.801][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2023-04-15 08:02:12.802][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-04-15 08:02:12.803][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-15 08:02:12.803][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-15 08:02:12.804][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-04-15 08:02:12.805][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-15 08:02:12.805][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-15 08:02:12.806][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-04-15 08:02:12.807][self$setPropertyValue]
biodb.DEBUG[2023-04-15 08:02:12.808][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-04-15 08:02:12.808][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-04-15 08:02:12.809][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-04-15 08:02:12.810][self$setPropertyValue]
biodb.DEBUG[2023-04-15 08:02:12.811][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2023-04-15 08:02:12.812][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-04-15 08:02:12.813][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2023-04-15 08:02:12.814][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-04-15 08:02:12.814][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-04-15 08:02:12.815][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-04-15 08:02:12.816][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-04-15 08:02:12.817][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-04-15 08:02:12.818][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-04-15 08:02:12.818][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2023-04-15 08:02:12.819][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-04-15 08:02:12.820][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-04-15 08:02:12.821][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2023-04-15 08:02:12.822][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-04-15 08:02:12.823][self$setPropertyValue]
biodb.DEBUG[2023-04-15 08:02:12.823][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-04-15 08:02:12.824][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2023-04-15 08:02:12.824][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2023-04-15 08:02:12.824][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2023-04-15 08:02:12.824][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2023-04-15 08:02:12.824][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2023-04-15 08:02:12.825][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-04-15 08:02:12.826][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-15 08:02:12.826][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-15 08:02:12.827][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-04-15 08:02:12.828][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-15 08:02:12.829][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-15 08:02:12.829][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-04-15 08:02:12.830][self$setPropertyValue]
biodb.DEBUG[2023-04-15 08:02:12.831][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-04-15 08:02:12.832][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-04-15 08:02:12.832][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-04-15 08:02:12.833][self$setPropertyValue]
biodb.DEBUG[2023-04-15 08:02:12.834][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2023-04-15 08:02:12.835][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2023-04-15 08:02:12.836][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2023-04-15 08:02:12.837][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-04-15 08:02:12.837][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-04-15 08:02:12.838][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-04-15 08:02:12.839][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-04-15 08:02:12.840][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-04-15 08:02:12.840][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-04-15 08:02:12.841][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2023-04-15 08:02:12.842][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-04-15 08:02:12.842][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2023-04-15 08:02:12.843][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2023-04-15 08:02:12.844][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-04-15 08:02:12.845][self$setPropertyValue]
biodb.DEBUG[2023-04-15 08:02:12.846][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-04-15 08:02:12.846][self$setPropertyValue]
biodb.DEBUG[2023-04-15 08:02:12.847][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-04-15 08:02:12.848][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-15 08:02:12.849][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-15 08:02:12.849][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-04-15 08:02:12.850][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-15 08:02:12.851][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-15 08:02:12.852][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-04-15 08:02:12.853][self$setPropertyValue]
biodb.DEBUG[2023-04-15 08:02:12.853][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-04-15 08:02:12.854][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-04-15 08:02:12.855][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-04-15 08:02:12.856][self$setPropertyValue]
biodb.DEBUG[2023-04-15 08:02:12.856][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2023-04-15 08:02:12.858][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2023-04-15 08:02:12.859][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2023-04-15 08:02:12.860][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-04-15 08:02:12.860][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-04-15 08:02:12.861][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-04-15 08:02:12.862][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-04-15 08:02:12.863][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-04-15 08:02:12.864][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-04-15 08:02:12.864][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2023-04-15 08:02:12.865][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-04-15 08:02:12.866][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2023-04-15 08:02:12.867][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2023-04-15 08:02:12.868][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-04-15 08:02:12.868][self$setPropertyValue]
biodb.DEBUG[2023-04-15 08:02:12.869][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-04-15 08:02:12.870][self$setPropertyValue]
biodb.DEBUG[2023-04-15 08:02:12.871][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-04-15 08:02:12.871][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-15 08:02:12.872][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-15 08:02:12.873][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-04-15 08:02:12.874][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-15 08:02:12.874][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-15 08:02:12.875][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-04-15 08:02:12.876][self$setPropertyValue]
biodb.DEBUG[2023-04-15 08:02:12.877][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-04-15 08:02:12.877][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-04-15 08:02:12.878][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-04-15 08:02:12.879][self$setPropertyValue]
biodb.DEBUG[2023-04-15 08:02:12.882][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-04-15 08:02:12.883][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:02:12.883][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:02:12.884][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:02:12.885][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:02:12.886][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-15 08:02:12.886][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:02:12.887][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:02:12.888][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:02:12.889][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:02:12.889][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-15 08:02:12.890][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:02:12.891][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:02:12.892][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:02:12.892][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:02:12.893][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-15 08:02:12.894][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:02:12.894][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:02:12.895][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:02:12.896][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:02:12.897][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-15 08:02:12.897][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:02:12.898][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:02:12.899][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:02:12.899][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:02:12.900][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-15 08:02:12.901][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:02:12.901][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:02:12.902][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:02:12.903][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:02:12.904][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-15 08:02:12.904][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:02:12.905][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:02:12.906][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:02:12.906][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:02:12.907][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-15 08:02:12.908][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:02:12.909][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:02:12.909][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:02:12.910][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:02:12.911][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-15 08:02:12.911][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:02:12.912][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:02:12.913][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:02:12.913][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:02:12.914][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-15 08:02:12.915][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:02:12.915][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:02:12.916][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:02:12.917][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:02:12.918][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-15 08:02:12.918][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:02:12.919][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:02:12.920][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:02:12.920][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:02:12.921][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-15 08:02:12.922][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:02:12.923][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 08:02:12.923][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:02:12.924][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:02:12.925][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-15 08:02:12.925][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:02:12.926][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:02:12.927][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:02:12.927][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:02:12.928][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-15 08:02:12.929][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:02:12.929][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:02:12.930][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:02:12.931][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:02:12.932][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-15 08:02:12.932][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:02:12.933][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:02:12.934][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:02:12.935][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:02:12.935][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-15 08:02:12.936][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:02:12.937][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:02:12.938][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:02:12.938][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:02:12.939][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-15 08:02:12.940][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:02:12.940][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:02:12.941][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:02:12.942][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:02:12.943][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-15 08:02:12.943][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:02:12.944][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:02:12.945][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2023-04-15 08:02:12.948][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2023-04-15 08:02:12.949][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2023-04-15 08:02:12.951][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2023-04-15 08:02:12.952][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2023-04-15 08:02:12.953][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2023-04-15 08:02:12.954][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2023-04-15 08:02:12.955][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2023-04-15 08:02:12.956][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2023-04-15 08:02:12.957][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2023-04-15 08:02:12.958][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2023-04-15 08:02:12.959][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2023-04-15 08:02:12.960][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2023-04-15 08:02:12.962][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2023-04-15 08:02:12.967][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2023-04-15 08:02:12.968][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2023-04-15 08:02:12.969][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2023-04-15 08:02:12.970][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2023-04-15 08:02:12.971][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2023-04-15 08:02:12.972][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2023-04-15 08:02:12.973][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2023-04-15 08:02:12.974][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2023-04-15 08:02:12.975][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2023-04-15 08:02:12.976][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2023-04-15 08:02:12.977][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2023-04-15 08:02:12.978][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2023-04-15 08:02:12.979][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2023-04-15 08:02:12.980][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2023-04-15 08:02:12.981][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2023-04-15 08:02:12.982][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2023-04-15 08:02:12.983][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2023-04-15 08:02:12.984][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2023-04-15 08:02:12.985][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2023-04-15 08:02:12.986][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2023-04-15 08:02:12.987][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2023-04-15 08:02:12.988][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2023-04-15 08:02:12.989][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2023-04-15 08:02:12.990][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2023-04-15 08:02:12.991][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2023-04-15 08:02:12.992][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2023-04-15 08:02:12.993][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2023-04-15 08:02:12.994][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2023-04-15 08:02:12.995][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2023-04-15 08:02:12.996][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2023-04-15 08:02:12.997][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2023-04-15 08:02:12.998][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2023-04-15 08:02:12.999][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2023-04-15 08:02:13.000][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2023-04-15 08:02:13.001][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2023-04-15 08:02:13.002][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2023-04-15 08:02:13.003][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2023-04-15 08:02:13.004][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2023-04-15 08:02:13.005][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2023-04-15 08:02:13.006][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2023-04-15 08:02:13.007][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2023-04-15 08:02:13.008][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2023-04-15 08:02:13.009][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2023-04-15 08:02:13.010][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2023-04-15 08:02:13.011][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2023-04-15 08:02:13.012][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2023-04-15 08:02:13.013][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2023-04-15 08:02:13.014][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2023-04-15 08:02:13.015][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2023-04-15 08:02:13.016][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2023-04-15 08:02:13.017][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2023-04-15 08:02:13.018][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2023-04-15 08:02:13.019][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2023-04-15 08:02:13.020][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2023-04-15 08:02:13.021][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2023-04-15 08:02:13.022][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2023-04-15 08:02:13.023][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2023-04-15 08:02:13.024][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2023-04-15 08:02:13.025][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2023-04-15 08:02:13.026][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2023-04-15 08:02:13.027][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2023-04-15 08:02:13.028][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2023-04-15 08:02:13.029][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2023-04-15 08:02:13.030][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2023-04-15 08:02:13.031][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2023-04-15 08:02:13.032][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2023-04-15 08:02:13.033][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2023-04-15 08:02:13.034][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2023-04-15 08:02:13.035][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2023-04-15 08:02:13.040][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2023-04-15 08:02:13.041][initialize] This is biodb version 1.6.1.
biodb.DEBUG[2023-04-15 08:02:13.043][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-04-15 08:02:13.044][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:02:13.045][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-15 08:02:13.045][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:02:13.046][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:02:13.049][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:02:13.050][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-15 08:02:13.051][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-15 08:02:13.051][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:02:13.052][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-15 08:02:13.053][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:02:13.053][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:02:13.054][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:02:13.055][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-15 08:02:13.055][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-15 08:02:13.056][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:02:13.057][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 08:02:13.057][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:02:13.058][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 08:02:13.059][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:02:13.059][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-15 08:02:13.060][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-15 08:02:13.060][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:02:13.061][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-15 08:02:13.062][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:02:13.062][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:02:13.063][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:02:13.064][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-15 08:02:13.064][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-15 08:02:13.065][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:02:13.066][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 08:02:13.066][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:02:13.067][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:02:13.068][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:02:13.068][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-15 08:02:13.069][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-15 08:02:13.070][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:02:13.070][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 08:02:13.071][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:02:13.072][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:02:13.073][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:02:13.073][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-15 08:02:13.074][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-15 08:02:13.074][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:02:13.075][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-15 08:02:13.076][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:02:13.076][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:02:13.077][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:02:13.078][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-15 08:02:13.078][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-15 08:02:13.079][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:02:13.080][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-15 08:02:13.080][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:02:13.081][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:02:13.082][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:02:13.082][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-15 08:02:13.083][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-15 08:02:13.083][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:02:13.084][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-15 08:02:13.085][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:02:13.085][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:02:13.086][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:02:13.087][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-15 08:02:13.087][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-15 08:02:13.088][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:02:13.088][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 08:02:13.089][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:02:13.090][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:02:13.090][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:02:13.091][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-15 08:02:13.092][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-15 08:02:13.092][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:02:13.093][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-15 08:02:13.093][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:02:13.094][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:02:13.095][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:02:13.095][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-15 08:02:13.096][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-15 08:02:13.097][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:02:13.097][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-15 08:02:13.098][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:02:13.098][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:02:13.099][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:02:13.100][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-15 08:02:13.100][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-15 08:02:13.101][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:02:13.102][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-15 08:02:13.102][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:02:13.103][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:02:13.103][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:02:13.104][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-15 08:02:13.105][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-15 08:02:13.105][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:02:13.106][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-15 08:02:13.107][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:02:13.107][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:02:13.108][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:02:13.108][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-15 08:02:13.109][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-15 08:02:13.110][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:02:13.110][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 08:02:13.111][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:02:13.112][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.DEBUG[2023-04-15 08:02:13.112][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:02:13.113][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-15 08:02:13.114][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-15 08:02:13.114][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:02:13.115][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-15 08:02:13.115][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:02:13.116][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:02:13.117][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:02:13.117][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-15 08:02:13.118][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-15 08:02:13.119][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:02:13.119][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-15 08:02:13.120][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:02:13.121][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:02:13.121][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:02:13.122][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-15 08:02:13.123][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-15 08:02:13.123][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:02:13.124][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-15 08:02:13.125][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:02:13.125][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:02:13.127][biodb$loadDefinitions] Load definitions from file "/Users/biocbuild/bbs-3.16-bioc-longtests/meat/biodbMirbase.Rcheck/biodbMirbase/definitions.yml".
biodb.DEBUG[2023-04-15 08:02:13.133][self$getDbsInfo()$define] Define connector mirbase.mature.
biodb.DEBUG[2023-04-15 08:02:13.139][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-04-15 08:02:13.140][self$setPropertyValue] Setting property "description" to "Write here the description of this database.".
biodb.DEBUG[2023-04-15 08:02:13.141][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-04-15 08:02:13.142][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-04-15 08:02:13.142][self$setPropertyValue] Setting property "downloadable" to "TRUE".
biodb.DEBUG[2023-04-15 08:02:13.143][self$setPropertyValue] Setting property "dwnld.ext" to "gz".
biodb.DEBUG[2023-04-15 08:02:13.144][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2023-04-15 08:02:13.145][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-04-15 08:02:13.145][self$setPropertyValue] Setting property "entry.content.type" to "txt".
biodb.DEBUG[2023-04-15 08:02:13.146][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-04-15 08:02:13.147][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-04-15 08:02:13.147][self$setPropertyValue] Setting property "name" to "miRBase mature database".
biodb.DEBUG[2023-04-15 08:02:13.148][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-04-15 08:02:13.149][self$setPropertyValue] Setting property "parsing.expr" to "^>[^ ]+ *(MIMAT[0-9]+) .*$".
biodb.DEBUG[2023-04-15 08:02:13.149][self$setPropertyValue] Setting property "parsing.expr" to "^>[^ ]+ *MIMAT[0-9]+ (.*)$".
biodb.DEBUG[2023-04-15 08:02:13.149][self$setPropertyValue] Setting property "parsing.expr" to "^>([^ ]+) *MIMAT[0-9]+ .*$".
biodb.DEBUG[2023-04-15 08:02:13.149][self$setPropertyValue] Setting property "parsing.expr" to "^([ACGU]+)$".
biodb.DEBUG[2023-04-15 08:02:13.150][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2023-04-15 08:02:13.150][self$setPropertyValue]
biodb.DEBUG[2023-04-15 08:02:13.151][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2023-04-15 08:02:13.152][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-15 08:02:13.152][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-15 08:02:13.153][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-04-15 08:02:13.154][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-15 08:02:13.154][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-15 08:02:13.155][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-04-15 08:02:13.156][self$setPropertyValue] Setting property "urls" to "http://www.mirbase.org/".
biodb.DEBUG[2023-04-15 08:02:13.156][self$setPropertyValue] Setting property "urls" to "https://www.mirbase.org/ftp/CURRENT/mature.fa.gz".
biodb.DEBUG[2023-04-15 08:02:13.156][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-04-15 08:02:13.157][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-04-15 08:02:13.158][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2023-04-15 08:02:13.158][self$setPropertyValue]
biodb.DEBUG[2023-04-15 08:02:13.162][self$getEntryFields()$define] Define field mirbase.mature.id.
biodb.DEBUG[2023-04-15 08:02:13.181][initialize] Initialize connector mirbase.mature.
biodb.DEBUG[2023-04-15 08:02:13.181][initialize] Register connector mirbase.mature with the request scheduler
biodb.DEBUG[2023-04-15 08:02:13.185][private$bdb$getRequestScheduler()$re ...] Register connector mirbase.mature.
biodb.DEBUG[2023-04-15 08:02:13.188][private$addConnectorRules] Create new rule for URL "www.mirbase.org" of connector "mirbase.mature".
biodb.DEBUG[2023-04-15 08:02:13.191][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2023-04-15 08:02:13.192][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2023-04-15 08:02:13.193][rule$addConnector] Connector "mirbase.mature" is already listed in rule "www.mirbase.org".
biodb.DEBUG[2023-04-15 08:02:13.194][biodb$getFactory()$createConn] Creating new connector mirbase.mature for database class mirbase.mature .
biodb.INFO [2023-04-15 08:02:13.201][biodb::testThat]
biodb.INFO [2023-04-15 08:02:13.201][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2023-04-15 08:02:13.202][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-04-15 08:02:13.203][biodb::testThat]
biodb.TRACE[2023-04-15 08:02:13.205][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/bbs-3.16-bioc-longtests/meat/biodbMirbase.Rcheck/biodbMirbase/testref/entry-mirbase.mature-MIMAT0000433-content.txt".
biodb.DEBUG[2023-04-15 08:02:13.207][biodb$getFactory()$createEntryFromCo ...] Creating miRBase mature database entries from 1 content(s).
biodb.DEBUG[2023-04-15 08:02:13.209][biodb$getFactory()$createEntryFromCo ...] Parsing 1 miRBase mature database entries.
biodb.DEBUG[2023-04-15 08:02:13.216][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-15 08:02:13.216][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-15 08:02:13.217][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-15 08:02:13.228][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:02:13.228][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-15 08:02:13.229][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:02:13.230][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-15 08:02:13.238][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-15 08:02:13.239][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-15 08:02:13.239][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:13.240][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:13.257][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-04-15 08:02:13.266][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-04-15 08:02:13.267][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:13.267][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:13.268][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-15 08:02:13.269][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-15 08:02:13.270][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:13.271][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:13.271][self$getBiodb()$getEntryFields()$get] Asked field names are: sequence.
biodb.TRACE[2023-04-15 08:02:13.272][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2023-04-15 08:02:13.273][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:13.274][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:13.275][self$getBiodb()$getEntryFields()$get] Asked field names are: mirbase.mature.id.
biodb.TRACE[2023-04-15 08:02:13.275][self$getBiodb()$getEntryFields()$get] Realnames of fields are: mirbase.mature.id.
biodb.TRACE[2023-04-15 08:02:13.276][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:13.277][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:13.277][self$getBiodb()$getEntryFields()$get] Asked field names are: mirbase.mature.id.
biodb.TRACE[2023-04-15 08:02:13.278][self$getBiodb()$getEntryFields()$get] Realnames of fields are: mirbase.mature.id.
biodb.TRACE[2023-04-15 08:02:13.279][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:13.280][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:13.280][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-15 08:02:13.281][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-15 08:02:13.282][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:13.282][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:13.283][self$getBiodb()$getEntryFields()$get] Asked field names are: mirbase.mature.id.
biodb.TRACE[2023-04-15 08:02:13.284][self$getBiodb()$getEntryFields()$get] Realnames of fields are: mirbase.mature.id.
biodb.TRACE[2023-04-15 08:02:13.285][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:13.285][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:13.286][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-15 08:02:13.287][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-15 08:02:13.288][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:13.289][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:13.289][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-15 08:02:13.290][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-15 08:02:13.291][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:13.292][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:13.292][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-15 08:02:13.293][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-15 08:02:13.294][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:13.295][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:13.338][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-15 08:02:13.339][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-15 08:02:13.339][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:13.340][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:13.341][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-15 08:02:13.341][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-15 08:02:13.342][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:13.343][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:13.344][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-15 08:02:13.344][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-15 08:02:13.345][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:13.346][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-15 08:02:13.347][biodb$getFactory()$createEntryFromCo ...] Accession numbers: MIMAT0000433.
biodb.TRACE[2023-04-15 08:02:13.349][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2023-04-15 08:02:13.349][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2023-04-15 08:02:13.350][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:13.351][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:13.352][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2023-04-15 08:02:13.352][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2023-04-15 08:02:13.353][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:13.354][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:13.354][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2023-04-15 08:02:13.355][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2023-04-15 08:02:13.356][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:13.356][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:13.357][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2023-04-15 08:02:13.358][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2023-04-15 08:02:13.359][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:13.359][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:13.384][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-15 08:02:13.385][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-15 08:02:13.385][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:13.386][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:13.396][self$getBiodb()$getEntryFields()$get] Asked field names are: mirbase.mature.id.
biodb.TRACE[2023-04-15 08:02:13.397][self$getBiodb()$getEntryFields()$get] Realnames of fields are: mirbase.mature.id.
biodb.TRACE[2023-04-15 08:02:13.398][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:13.398][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:13.402][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-15 08:02:13.403][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-15 08:02:13.404][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:13.405][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:13.405][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-15 08:02:13.406][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-15 08:02:13.407][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:13.407][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:13.408][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-15 08:02:13.409][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-15 08:02:13.410][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:13.410][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:13.412][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-15 08:02:13.413][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-15 08:02:13.414][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:13.415][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:13.415][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-15 08:02:13.416][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-15 08:02:13.417][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:13.418][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:13.418][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-15 08:02:13.419][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-15 08:02:13.420][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:13.421][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:13.422][self$getBiodb()$getEntryFields()$get] Asked field names are: mirbase.mature.id.
biodb.TRACE[2023-04-15 08:02:13.422][self$getBiodb()$getEntryFields()$get] Realnames of fields are: mirbase.mature.id.
biodb.TRACE[2023-04-15 08:02:13.423][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:13.424][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:13.424][self$getBiodb()$getEntryFields()$get] Asked field names are: mirbase.mature.id.
biodb.TRACE[2023-04-15 08:02:13.425][self$getBiodb()$getEntryFields()$get] Realnames of fields are: mirbase.mature.id.
biodb.TRACE[2023-04-15 08:02:13.426][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:13.427][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:13.427][self$getBiodb()$getEntryFields()$get] Asked field names are: mirbase.mature.id.
biodb.TRACE[2023-04-15 08:02:13.428][self$getBiodb()$getEntryFields()$get] Realnames of fields are: mirbase.mature.id.
biodb.TRACE[2023-04-15 08:02:13.429][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:13.430][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:13.436][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-15 08:02:13.436][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-15 08:02:13.437][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:13.438][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:13.439][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-15 08:02:13.439][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-15 08:02:13.440][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:13.441][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:13.442][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-15 08:02:13.442][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-15 08:02:13.443][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:13.444][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:13.445][ef$get] Asked field names are: accession.
biodb.TRACE[2023-04-15 08:02:13.445][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-15 08:02:13.446][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:13.447][ef$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:13.448][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-15 08:02:13.449][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-15 08:02:13.449][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:13.450][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:13.457][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-15 08:02:13.457][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-15 08:02:13.458][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:13.459][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:13.460][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-15 08:02:13.460][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-15 08:02:13.461][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:13.462][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:13.463][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-15 08:02:13.464][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-15 08:02:13.464][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:13.465][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:13.466][ef$get] Asked field names are: name.
biodb.TRACE[2023-04-15 08:02:13.467][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-04-15 08:02:13.468][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:13.468][ef$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:13.469][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-15 08:02:13.470][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-15 08:02:13.471][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:13.471][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:13.477][self$getBiodb()$getEntryFields()$get] Asked field names are: sequence.
biodb.TRACE[2023-04-15 08:02:13.478][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2023-04-15 08:02:13.479][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:13.480][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:13.481][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2023-04-15 08:02:13.481][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2023-04-15 08:02:13.482][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:13.483][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:13.484][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2023-04-15 08:02:13.485][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2023-04-15 08:02:13.486][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:13.486][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:13.487][ef$get] Asked field names are: sequence.
biodb.TRACE[2023-04-15 08:02:13.488][ef$get] Realnames of fields are: aa.seq.
biodb.TRACE[2023-04-15 08:02:13.489][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:13.489][ef$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:13.490][self$getBiodb()$getEntryFields()$get] Asked field names are: sequence.
biodb.TRACE[2023-04-15 08:02:13.491][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2023-04-15 08:02:13.492][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:13.492][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:13.498][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-04-15 08:02:13.499][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-04-15 08:02:13.500][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:13.501][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:13.502][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-04-15 08:02:13.503][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-04-15 08:02:13.503][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:13.504][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:13.505][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-04-15 08:02:13.506][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-04-15 08:02:13.506][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:13.507][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:13.508][ef$get] Asked field names are: description.
biodb.TRACE[2023-04-15 08:02:13.509][ef$get] Realnames of fields are: description.
biodb.TRACE[2023-04-15 08:02:13.510][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:13.515][ef$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:13.516][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-04-15 08:02:13.517][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-04-15 08:02:13.518][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:13.518][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:13.524][ef$get] Asked field names are: aa.seq.
biodb.TRACE[2023-04-15 08:02:13.525][ef$get] Realnames of fields are: aa.seq.
biodb.TRACE[2023-04-15 08:02:13.526][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:13.526][ef$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:13.530][ef$get] Asked field names are: accession.
biodb.TRACE[2023-04-15 08:02:13.531][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-15 08:02:13.532][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:13.532][ef$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:13.536][ef$get] Asked field names are: description.
biodb.TRACE[2023-04-15 08:02:13.537][ef$get] Realnames of fields are: description.
biodb.TRACE[2023-04-15 08:02:13.538][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:13.538][ef$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:13.542][ef$get] Asked field names are: name.
biodb.TRACE[2023-04-15 08:02:13.543][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-04-15 08:02:13.544][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:13.544][ef$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:13.557][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/bbs-3.16-bioc-longtests/meat/biodbMirbase.Rcheck/biodbMirbase/testref/entry-mirbase.mature-MIMAT0000434-content.txt".
biodb.DEBUG[2023-04-15 08:02:13.581][biodb$getFactory()$createEntryFromCo ...] Creating miRBase mature database entries from 1 content(s).
biodb.DEBUG[2023-04-15 08:02:13.582][biodb$getFactory()$createEntryFromCo ...] Parsing 1 miRBase mature database entries.
biodb.DEBUG[2023-04-15 08:02:13.583][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-15 08:02:13.584][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-15 08:02:13.585][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-15 08:02:13.589][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:02:13.589][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-15 08:02:13.590][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:02:13.591][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-15 08:02:13.592][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-15 08:02:13.593][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-15 08:02:13.594][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:13.595][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:13.607][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-04-15 08:02:13.608][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-04-15 08:02:13.609][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:13.610][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:13.611][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-15 08:02:13.612][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-15 08:02:13.612][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:13.613][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:13.614][self$getBiodb()$getEntryFields()$get] Asked field names are: sequence.
biodb.TRACE[2023-04-15 08:02:13.615][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2023-04-15 08:02:13.616][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:13.616][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:13.617][self$getBiodb()$getEntryFields()$get] Asked field names are: mirbase.mature.id.
biodb.TRACE[2023-04-15 08:02:13.618][self$getBiodb()$getEntryFields()$get] Realnames of fields are: mirbase.mature.id.
biodb.TRACE[2023-04-15 08:02:13.619][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:13.619][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:13.620][self$getBiodb()$getEntryFields()$get] Asked field names are: mirbase.mature.id.
biodb.TRACE[2023-04-15 08:02:13.621][self$getBiodb()$getEntryFields()$get] Realnames of fields are: mirbase.mature.id.
biodb.TRACE[2023-04-15 08:02:13.622][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:13.622][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:13.623][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-15 08:02:13.624][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-15 08:02:13.625][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:13.625][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:13.626][self$getBiodb()$getEntryFields()$get] Asked field names are: mirbase.mature.id.
biodb.TRACE[2023-04-15 08:02:13.627][self$getBiodb()$getEntryFields()$get] Realnames of fields are: mirbase.mature.id.
biodb.TRACE[2023-04-15 08:02:13.628][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:13.628][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:13.629][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-15 08:02:13.630][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-15 08:02:13.631][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:13.631][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:13.632][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-15 08:02:13.633][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-15 08:02:13.633][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:13.634][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:13.635][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-15 08:02:13.636][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-15 08:02:13.636][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:13.637][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:13.638][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-15 08:02:13.639][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-15 08:02:13.639][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:13.640][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:13.641][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-15 08:02:13.642][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-15 08:02:13.642][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:13.643][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:13.644][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-15 08:02:13.645][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-15 08:02:13.645][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:13.646][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-15 08:02:13.647][biodb$getFactory()$createEntryFromCo ...] Accession numbers: MIMAT0000434.
biodb.TRACE[2023-04-15 08:02:13.665][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2023-04-15 08:02:13.666][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2023-04-15 08:02:13.667][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:13.668][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:13.669][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2023-04-15 08:02:13.669][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2023-04-15 08:02:13.670][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:13.671][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:13.672][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2023-04-15 08:02:13.672][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2023-04-15 08:02:13.673][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:13.674][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:13.675][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2023-04-15 08:02:13.676][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2023-04-15 08:02:13.676][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:13.677][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:13.678][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-15 08:02:13.679][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-15 08:02:13.680][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:13.681][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:13.685][self$getBiodb()$getEntryFields()$get] Asked field names are: mirbase.mature.id.
biodb.TRACE[2023-04-15 08:02:13.685][self$getBiodb()$getEntryFields()$get] Realnames of fields are: mirbase.mature.id.
biodb.TRACE[2023-04-15 08:02:13.686][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:13.687][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:13.691][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-15 08:02:13.692][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-15 08:02:13.693][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:13.693][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:13.694][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-15 08:02:13.695][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-15 08:02:13.696][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:13.696][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:13.697][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-15 08:02:13.698][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-15 08:02:13.699][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:13.699][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:13.701][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-15 08:02:13.702][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-15 08:02:13.702][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:13.703][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:13.704][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-15 08:02:13.705][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-15 08:02:13.705][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:13.706][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:13.707][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-15 08:02:13.708][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-15 08:02:13.708][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:13.709][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:13.710][self$getBiodb()$getEntryFields()$get] Asked field names are: mirbase.mature.id.
biodb.TRACE[2023-04-15 08:02:13.711][self$getBiodb()$getEntryFields()$get] Realnames of fields are: mirbase.mature.id.
biodb.TRACE[2023-04-15 08:02:13.712][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:13.712][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:13.713][self$getBiodb()$getEntryFields()$get] Asked field names are: mirbase.mature.id.
biodb.TRACE[2023-04-15 08:02:13.714][self$getBiodb()$getEntryFields()$get] Realnames of fields are: mirbase.mature.id.
biodb.TRACE[2023-04-15 08:02:13.715][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:13.715][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:13.716][self$getBiodb()$getEntryFields()$get] Asked field names are: mirbase.mature.id.
biodb.TRACE[2023-04-15 08:02:13.717][self$getBiodb()$getEntryFields()$get] Realnames of fields are: mirbase.mature.id.
biodb.TRACE[2023-04-15 08:02:13.718][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:13.718][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:13.731][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-15 08:02:13.732][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-15 08:02:13.733][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:13.733][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:13.734][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-15 08:02:13.735][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-15 08:02:13.735][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:13.736][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:13.737][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-15 08:02:13.737][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-15 08:02:13.738][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:13.739][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:13.740][ef$get] Asked field names are: accession.
biodb.TRACE[2023-04-15 08:02:13.740][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-15 08:02:13.741][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:13.742][ef$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:13.742][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-15 08:02:13.743][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-15 08:02:13.744][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:13.744][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:13.750][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-15 08:02:13.751][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-15 08:02:13.752][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:13.752][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:13.753][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-15 08:02:13.754][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-15 08:02:13.755][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:13.755][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:13.756][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-15 08:02:13.757][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-15 08:02:13.757][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:13.758][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:13.759][ef$get] Asked field names are: name.
biodb.TRACE[2023-04-15 08:02:13.760][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-04-15 08:02:13.760][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:13.761][ef$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:13.762][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-15 08:02:13.763][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-15 08:02:13.763][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:13.764][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:13.770][self$getBiodb()$getEntryFields()$get] Asked field names are: sequence.
biodb.TRACE[2023-04-15 08:02:13.770][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2023-04-15 08:02:13.771][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:13.772][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:13.772][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2023-04-15 08:02:13.773][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2023-04-15 08:02:13.774][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:13.775][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:13.775][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2023-04-15 08:02:13.776][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2023-04-15 08:02:13.777][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:13.778][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:13.778][ef$get] Asked field names are: sequence.
biodb.TRACE[2023-04-15 08:02:13.779][ef$get] Realnames of fields are: aa.seq.
biodb.TRACE[2023-04-15 08:02:13.780][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:13.781][ef$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:13.781][self$getBiodb()$getEntryFields()$get] Asked field names are: sequence.
biodb.TRACE[2023-04-15 08:02:13.782][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2023-04-15 08:02:13.783][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:13.784][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:13.789][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-04-15 08:02:13.790][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-04-15 08:02:13.791][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:13.792][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:13.792][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-04-15 08:02:13.793][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-04-15 08:02:13.794][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:13.795][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:13.795][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-04-15 08:02:13.796][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-04-15 08:02:13.797][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:13.798][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:13.798][ef$get] Asked field names are: description.
biodb.TRACE[2023-04-15 08:02:13.799][ef$get] Realnames of fields are: description.
biodb.TRACE[2023-04-15 08:02:13.800][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:13.801][ef$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:13.801][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-04-15 08:02:13.802][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-04-15 08:02:13.807][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:13.808][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:13.813][ef$get] Asked field names are: aa.seq.
biodb.TRACE[2023-04-15 08:02:13.814][ef$get] Realnames of fields are: aa.seq.
biodb.TRACE[2023-04-15 08:02:13.815][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:13.815][ef$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:13.819][ef$get] Asked field names are: accession.
biodb.TRACE[2023-04-15 08:02:13.819][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-15 08:02:13.820][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:13.821][ef$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:13.824][ef$get] Asked field names are: description.
biodb.TRACE[2023-04-15 08:02:13.825][ef$get] Realnames of fields are: description.
biodb.TRACE[2023-04-15 08:02:13.826][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:13.827][ef$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:13.830][ef$get] Asked field names are: name.
biodb.TRACE[2023-04-15 08:02:13.831][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-04-15 08:02:13.832][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:13.832][ef$get] fields variable is a list.
biodb.INFO [2023-04-15 08:02:13.836][biodb::testThat]
biodb.INFO [2023-04-15 08:02:13.837][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2023-04-15 08:02:13.838][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-04-15 08:02:13.838][biodb::testThat]
biodb.DEBUG[2023-04-15 08:02:13.840][private$loadEntries] Creating entries from ids [2]: "MIMAT0000433, MIMAT0000434".
biodb.DEBUG[2023-04-15 08:02:13.845][conn$getEntryContent] Get miRBase mature database entry content(s) for 2 id(s)...
biodb.INFO [2023-04-15 08:02:13.850][self$getFolderPath] Create cache folder "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/mirbase.mature-ecbae556d51779d9d48125ba5a617e19" for "mirbase.mature-ecbae556d51779d9d48125ba5a617e19".
biodb.DEBUG[2023-04-15 08:02:13.851][self$isDownloaded] Database mirbase.mature has not yet been downloaded.
biodb.INFO [2023-04-15 08:02:13.852][self$download] Downloading whole database of mirbase.mature.
biodb.DEBUG[2023-04-15 08:02:13.853][self$getDownloadPath] Download path of mirbase.mature is "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/mirbase.mature-ecbae556d51779d9d48125ba5a617e19/download.gz".
biodb.DEBUG[2023-04-15 08:02:13.854][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 08:02:17.210][self$getDownloadPath] Download path of mirbase.mature is "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/mirbase.mature-ecbae556d51779d9d48125ba5a617e19/download.gz".
biodb.DEBUG[2023-04-15 08:02:17.211][self$download] Downloading of mirbase.mature completed.
biodb.TRACE[2023-04-15 08:02:17.212][self$addFilesToCache] Moving files to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/tmp/marker12f6748874d09marker".
biodb.TRACE[2023-04-15 08:02:17.213][private$doAddFilesToCache] Destination files are [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/mirbase.mature-ecbae556d51779d9d48125ba5a617e19/downloaded.marker".
biodb.DEBUG[2023-04-15 08:02:17.214][self$addFilesToCache] Done adding files.
biodb.DEBUG[2023-04-15 08:02:17.215][self$isDownloaded] Database mirbase.mature has already been downloaded.
biodb.INFO [2023-04-15 08:02:17.216][self$download] Extract whole database of mirbase.mature.
biodb.DEBUG[2023-04-15 08:02:17.217][self$getDownloadPath] Download path of mirbase.mature is "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/mirbase.mature-ecbae556d51779d9d48125ba5a617e19/download.gz".
biodb.DEBUG[2023-04-15 08:02:17.429][self$getDownloadPath] Download path of mirbase.mature is "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/mirbase.mature-ecbae556d51779d9d48125ba5a617e19/download.gz".
biodb.DEBUG[2023-04-15 08:02:17.429][private$doExtractDownload] Found 48885 entries in file "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/mirbase.mature-ecbae556d51779d9d48125ba5a617e19/download.gz".
biodb.TRACE[2023-04-15 08:02:17.653][private$doSaveContentToFile] Saving to cache [48885]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/mirbase.mature-ecbae556d51779d9d48125ba5a617e19/MIMAT0000001.txt, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/mirbase.mature-ecbae556d51779d9d48125ba5a617e19/MIMAT0015091.txt, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/mirbase.mature-ecbae556d51779d9d48125ba5a617e19/MIMAT0000002.txt, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/mirbase.mature-ecbae556d51779d9d48125ba5a617e19/MIMAT0015092.txt, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/mirbase.mature-ecbae556d51779d9d48125ba5a617e19/MIMAT0020301.txt, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/mirbase.mature-ecbae556d51779d9d48125ba5a617e19/MIMAT0000003.txt, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/mirbase.mature-ecbae556d51779d9d48125ba5a617e19/MIMAT0020302.txt, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/mirbase.mature-ecbae556d51779d9d48125ba5a617e19/MIMAT0000004.txt, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/mirbase.mature-ecbae556d51779d9d48125ba5a617e19/MIMAT0000005.txt, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/mirbase.mature-ecbae556d51779d9d48125ba5a617e19/MIMAT0015093.txt, ..."
biodb.TRACE[2023-04-15 08:02:25.771][self$addFilesToCache] Moving files to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/tmp/marker12f672ad2af12marker".
biodb.TRACE[2023-04-15 08:02:25.772][private$doAddFilesToCache] Destination files are [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/mirbase.mature-ecbae556d51779d9d48125ba5a617e19/extracted.marker".
biodb.DEBUG[2023-04-15 08:02:25.773][self$addFilesToCache] Done adding files.
biodb.TRACE[2023-04-15 08:02:25.774][cch$loadFileContent] Trying to load 2 files from cache: [2]: "MIMAT0000433, MIMAT0000434".
biodb.TRACE[2023-04-15 08:02:25.774][cch$loadFileContent] file.exist = [2]: "TRUE, TRUE".
biodb.TRACE[2023-04-15 08:02:25.797][loadFileContents] Loaded 2 files from cache: [2]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/mirbase.mature-ecbae556d51779d9d48125ba5a617e19/MIMAT0000433.txt, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/mirbase.mature-ecbae556d51779d9d48125ba5a617e19/MIMAT0000434.txt".
biodb.DEBUG[2023-04-15 08:02:25.798][conn$getEntryContent] 2 miRBase mature database entry content(s) loaded from cache.
biodb.DEBUG[2023-04-15 08:02:25.799][self$createEntryFromContent] Creating miRBase mature database entries from 2 content(s).
biodb.DEBUG[2023-04-15 08:02:25.800][self$createEntryFromContent] Parsing 2 miRBase mature database entries.
biodb.DEBUG[2023-04-15 08:02:25.801][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-15 08:02:25.802][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-15 08:02:25.802][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-15 08:02:25.806][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:02:25.807][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-15 08:02:25.807][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:02:25.808][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-15 08:02:25.810][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-15 08:02:25.810][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-15 08:02:25.811][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:25.812][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:25.813][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-04-15 08:02:25.813][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-04-15 08:02:25.814][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:25.815][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:25.816][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-15 08:02:25.816][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-15 08:02:25.817][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:25.818][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:25.819][self$getBiodb()$getEntryFields()$get] Asked field names are: sequence.
biodb.TRACE[2023-04-15 08:02:25.819][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2023-04-15 08:02:25.820][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:25.821][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:25.822][self$getBiodb()$getEntryFields()$get] Asked field names are: mirbase.mature.id.
biodb.TRACE[2023-04-15 08:02:25.822][self$getBiodb()$getEntryFields()$get] Realnames of fields are: mirbase.mature.id.
biodb.TRACE[2023-04-15 08:02:25.823][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:25.824][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:25.824][self$getBiodb()$getEntryFields()$get] Asked field names are: mirbase.mature.id.
biodb.TRACE[2023-04-15 08:02:25.825][self$getBiodb()$getEntryFields()$get] Realnames of fields are: mirbase.mature.id.
biodb.TRACE[2023-04-15 08:02:25.826][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:25.826][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:25.827][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-15 08:02:25.828][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-15 08:02:25.829][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:25.829][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:25.830][self$getBiodb()$getEntryFields()$get] Asked field names are: mirbase.mature.id.
biodb.TRACE[2023-04-15 08:02:25.831][self$getBiodb()$getEntryFields()$get] Realnames of fields are: mirbase.mature.id.
biodb.TRACE[2023-04-15 08:02:25.831][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:25.832][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:25.833][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-15 08:02:25.834][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-15 08:02:25.834][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:25.835][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:25.836][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-15 08:02:25.836][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-15 08:02:25.837][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:25.838][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:25.838][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-15 08:02:25.839][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-15 08:02:25.840][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:25.841][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-15 08:02:25.841][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-15 08:02:25.842][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-15 08:02:25.843][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-15 08:02:25.846][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:02:25.847][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-15 08:02:25.848][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:02:25.848][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-15 08:02:25.850][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-15 08:02:25.851][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-15 08:02:25.851][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:25.852][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:25.853][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-04-15 08:02:25.854][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-04-15 08:02:25.854][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:25.855][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:25.856][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-15 08:02:25.857][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-15 08:02:25.857][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:25.858][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:25.859][self$getBiodb()$getEntryFields()$get] Asked field names are: sequence.
biodb.TRACE[2023-04-15 08:02:25.860][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2023-04-15 08:02:25.860][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:25.861][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:25.862][self$getBiodb()$getEntryFields()$get] Asked field names are: mirbase.mature.id.
biodb.TRACE[2023-04-15 08:02:25.863][self$getBiodb()$getEntryFields()$get] Realnames of fields are: mirbase.mature.id.
biodb.TRACE[2023-04-15 08:02:25.863][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:25.864][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:25.865][self$getBiodb()$getEntryFields()$get] Asked field names are: mirbase.mature.id.
biodb.TRACE[2023-04-15 08:02:25.865][self$getBiodb()$getEntryFields()$get] Realnames of fields are: mirbase.mature.id.
biodb.TRACE[2023-04-15 08:02:25.866][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:25.867][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:25.868][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-15 08:02:25.868][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-15 08:02:25.869][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:25.870][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:25.870][self$getBiodb()$getEntryFields()$get] Asked field names are: mirbase.mature.id.
biodb.TRACE[2023-04-15 08:02:25.871][self$getBiodb()$getEntryFields()$get] Realnames of fields are: mirbase.mature.id.
biodb.TRACE[2023-04-15 08:02:25.872][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:25.873][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:25.874][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-15 08:02:25.874][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-15 08:02:25.875][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:25.876][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:25.876][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-15 08:02:25.877][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-15 08:02:25.878][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:25.879][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:25.879][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-15 08:02:25.880][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-15 08:02:25.881][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:25.881][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:25.882][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-15 08:02:25.883][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-15 08:02:25.884][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:25.903][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:25.903][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-15 08:02:25.904][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-15 08:02:25.905][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:25.905][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:25.906][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-15 08:02:25.907][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-15 08:02:25.908][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:25.908][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:25.909][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-15 08:02:25.910][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-15 08:02:25.910][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:25.911][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:25.912][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-15 08:02:25.913][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-15 08:02:25.913][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:25.914][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:25.915][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-15 08:02:25.915][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-15 08:02:25.916][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:25.917][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-15 08:02:25.917][self$createEntryFromContent] Accession numbers: MIMAT0000433, MIMAT0000434.
biodb.TRACE[2023-04-15 08:02:25.918][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2023-04-15 08:02:25.919][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2023-04-15 08:02:25.920][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:25.920][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:25.921][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2023-04-15 08:02:25.922][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2023-04-15 08:02:25.923][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:25.923][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:25.924][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2023-04-15 08:02:25.925][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2023-04-15 08:02:25.926][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:25.926][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:25.930][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2023-04-15 08:02:25.931][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2023-04-15 08:02:25.932][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:25.933][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:25.933][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2023-04-15 08:02:25.934][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2023-04-15 08:02:25.935][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:25.936][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:25.936][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2023-04-15 08:02:25.937][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2023-04-15 08:02:25.938][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:25.939][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2023-04-15 08:02:25.943][biodb::testThat]
biodb.INFO [2023-04-15 08:02:25.944][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2023-04-15 08:02:25.945][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-04-15 08:02:25.945][biodb::testThat]
biodb.INFO [2023-04-15 08:02:25.948][biodb::testThat]
biodb.INFO [2023-04-15 08:02:25.949][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2023-04-15 08:02:25.949][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-04-15 08:02:25.950][biodb::testThat]
biodb.WARN [2023-04-15 08:02:25.968][self$searchForEntries] This database is not searchable by field "name".
biodb.WARN [2023-04-15 08:02:25.982][self$searchForEntries] This database is not searchable by field "name".
biodb.INFO [2023-04-15 08:02:26.006][biodb::testThat]
biodb.INFO [2023-04-15 08:02:26.007][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2023-04-15 08:02:26.008][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-04-15 08:02:26.008][biodb::testThat]
biodb.TRACE[2023-04-15 08:02:26.023][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2023-04-15 08:02:26.024][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2023-04-15 08:02:26.025][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:26.026][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:26.026][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2023-04-15 08:02:26.027][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2023-04-15 08:02:26.028][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:26.028][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:26.029][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2023-04-15 08:02:26.030][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2023-04-15 08:02:26.031][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:26.031][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:26.032][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2023-04-15 08:02:26.033][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2023-04-15 08:02:26.033][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:26.034][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:26.055][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2023-04-15 08:02:26.056][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2023-04-15 08:02:26.057][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:26.058][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:26.058][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2023-04-15 08:02:26.059][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2023-04-15 08:02:26.060][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:26.061][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:26.061][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2023-04-15 08:02:26.062][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2023-04-15 08:02:26.063][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:26.063][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:26.064][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2023-04-15 08:02:26.065][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2023-04-15 08:02:26.065][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:26.066][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2023-04-15 08:02:26.069][biodb::testThat]
biodb.INFO [2023-04-15 08:02:26.070][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2023-04-15 08:02:26.070][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-04-15 08:02:26.071][biodb::testThat]
biodb.INFO [2023-04-15 08:02:26.075][biodb::testThat]
biodb.INFO [2023-04-15 08:02:26.076][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2023-04-15 08:02:26.076][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-04-15 08:02:26.077][biodb::testThat]
biodb.INFO [2023-04-15 08:02:26.099][biodb::testThat]
biodb.INFO [2023-04-15 08:02:26.100][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2023-04-15 08:02:26.101][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-04-15 08:02:26.101][biodb::testThat]
biodb.DEBUG[2023-04-15 08:02:26.104][function(conn, opt)] Trying to download "http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000433".
biodb.DEBUG[2023-04-15 08:02:28.342][getUrlContent] Use RCurl for downloading content of URL http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000433.
biodb.INFO [2023-04-15 08:02:28.553][biodb::testThat]
biodb.INFO [2023-04-15 08:02:28.554][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2023-04-15 08:02:28.555][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-04-15 08:02:28.555][biodb::testThat]
biodb.INFO [2023-04-15 08:02:28.558][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2023-04-15 08:02:28.559][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector mirbase.mature from the request scheduler
biodb.INFO [2023-04-15 08:02:28.560][self$deleteConn] Connector "mirbase.mature" deleted.
biodb.DEBUG[2023-04-15 08:02:28.560][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2023-04-15 08:02:28.561][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-15 08:02:28.561][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-15 08:02:28.562][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:02:28.563][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-15 08:02:28.563][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:02:28.564][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2023-04-15 08:02:28.571][biodb::testContext]
biodb.INFO [2023-04-15 08:02:28.572][biodb::testContext] ********************************************************************************
biodb.INFO [2023-04-15 08:02:28.573][biodb::testContext] Test context - Example long tests
biodb.INFO [2023-04-15 08:02:28.573][biodb::testContext] ********************************************************************************
biodb.INFO [2023-04-15 08:02:28.574][biodb::testContext]
biodb.INFO [2023-04-15 08:02:28.576][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.6.1.
biodb.DEBUG[2023-04-15 08:02:28.577][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.2/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2023-04-15 08:02:28.580][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-04-15 08:02:28.581][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2023-04-15 08:02:28.581][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2023-04-15 08:02:28.582][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:02:28.583][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:02:28.583][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:02:28.584][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2023-04-15 08:02:28.585][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2023-04-15 08:02:28.585][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:02:28.586][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:02:28.587][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:02:28.587][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2023-04-15 08:02:28.588][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2023-04-15 08:02:28.589][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:02:28.589][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:02:28.590][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:02:28.591][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2023-04-15 08:02:28.592][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2023-04-15 08:02:28.592][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2023-04-15 08:02:28.593][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:02:28.594][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:02:28.594][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:02:28.595][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2023-04-15 08:02:28.596][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2023-04-15 08:02:28.597][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2023-04-15 08:02:28.597][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:02:28.598][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:02:28.598][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:02:28.599][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2023-04-15 08:02:28.600][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2023-04-15 08:02:28.600][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:02:28.601][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:02:28.602][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:02:28.602][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2023-04-15 08:02:28.603][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2023-04-15 08:02:28.604][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2023-04-15 08:02:28.604][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:02:28.605][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:02:28.606][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:02:28.607][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2023-04-15 08:02:28.607][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2023-04-15 08:02:28.608][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:02:28.609][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:02:28.609][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:02:28.610][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2023-04-15 08:02:28.611][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2023-04-15 08:02:28.611][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2023-04-15 08:02:28.612][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:02:28.613][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:02:28.613][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:02:28.694][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2023-04-15 08:02:28.695][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2023-04-15 08:02:28.696][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2023-04-15 08:02:28.698][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2023-04-15 08:02:28.699][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2023-04-15 08:02:28.700][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2023-04-15 08:02:28.701][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:02:28.702][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:02:28.703][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:02:28.704][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2023-04-15 08:02:28.705][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2023-04-15 08:02:28.706][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:02:28.707][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:02:28.707][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:02:28.708][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2023-04-15 08:02:28.709][self$set] Set key entries.sep to "|".
biodb.DEBUG[2023-04-15 08:02:28.709][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:02:28.710][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:02:28.711][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:02:28.711][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2023-04-15 08:02:28.712][self$set] Set key offline to FALSE.
biodb.DEBUG[2023-04-15 08:02:28.713][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:02:28.713][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:02:28.714][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:02:28.715][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2023-04-15 08:02:28.715][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2023-04-15 08:02:28.716][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:02:28.717][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:02:28.717][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:02:28.718][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2023-04-15 08:02:28.719][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2023-04-15 08:02:28.719][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:02:28.720][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:02:28.721][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:02:28.722][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2023-04-15 08:02:28.722][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2023-04-15 08:02:28.738][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2023-04-15 08:02:28.738][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:02:28.739][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:02:28.740][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:02:28.740][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2023-04-15 08:02:28.741][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2023-04-15 08:02:28.742][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2023-04-15 08:02:28.743][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:02:28.743][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:02:28.744][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:02:28.745][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2023-04-15 08:02:28.746][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-04-15 08:02:28.747][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2023-04-15 08:02:28.748][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-04-15 08:02:28.749][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-04-15 08:02:28.750][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-04-15 08:02:28.750][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-04-15 08:02:28.751][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-04-15 08:02:28.752][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-04-15 08:02:28.753][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2023-04-15 08:02:28.753][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-04-15 08:02:28.754][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-04-15 08:02:28.755][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2023-04-15 08:02:28.756][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-04-15 08:02:28.756][self$setPropertyValue]
biodb.DEBUG[2023-04-15 08:02:28.757][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-04-15 08:02:28.758][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2023-04-15 08:02:28.758][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2023-04-15 08:02:28.758][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2023-04-15 08:02:28.758][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2023-04-15 08:02:28.758][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2023-04-15 08:02:28.759][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-04-15 08:02:28.760][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-15 08:02:28.760][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-15 08:02:28.761][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-04-15 08:02:28.762][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-15 08:02:28.763][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-15 08:02:28.763][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-04-15 08:02:28.764][self$setPropertyValue]
biodb.DEBUG[2023-04-15 08:02:28.765][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-04-15 08:02:28.766][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-04-15 08:02:28.766][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-04-15 08:02:28.767][self$setPropertyValue]
biodb.DEBUG[2023-04-15 08:02:28.768][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2023-04-15 08:02:28.769][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-04-15 08:02:28.770][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2023-04-15 08:02:28.771][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-04-15 08:02:28.772][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-04-15 08:02:28.772][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-04-15 08:02:28.773][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-04-15 08:02:28.774][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-04-15 08:02:28.775][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-04-15 08:02:28.775][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2023-04-15 08:02:28.776][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-04-15 08:02:28.777][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-04-15 08:02:28.778][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2023-04-15 08:02:28.779][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-04-15 08:02:28.779][self$setPropertyValue]
biodb.DEBUG[2023-04-15 08:02:28.780][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-04-15 08:02:28.781][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2023-04-15 08:02:28.781][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2023-04-15 08:02:28.781][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2023-04-15 08:02:28.781][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2023-04-15 08:02:28.781][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2023-04-15 08:02:28.782][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-04-15 08:02:28.782][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-15 08:02:28.783][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-15 08:02:28.784][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-04-15 08:02:28.784][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-15 08:02:28.785][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-15 08:02:28.786][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-04-15 08:02:28.787][self$setPropertyValue]
biodb.DEBUG[2023-04-15 08:02:28.787][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-04-15 08:02:28.788][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-04-15 08:02:28.789][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-04-15 08:02:28.789][self$setPropertyValue]
biodb.DEBUG[2023-04-15 08:02:28.790][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2023-04-15 08:02:28.792][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2023-04-15 08:02:28.792][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2023-04-15 08:02:28.793][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-04-15 08:02:28.794][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-04-15 08:02:28.795][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-04-15 08:02:28.795][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-04-15 08:02:28.796][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-04-15 08:02:28.797][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-04-15 08:02:28.798][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2023-04-15 08:02:28.798][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-04-15 08:02:28.799][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2023-04-15 08:02:28.800][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2023-04-15 08:02:28.800][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-04-15 08:02:28.801][self$setPropertyValue]
biodb.DEBUG[2023-04-15 08:02:28.802][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-04-15 08:02:28.803][self$setPropertyValue]
biodb.DEBUG[2023-04-15 08:02:28.803][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-04-15 08:02:28.804][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-15 08:02:28.805][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-15 08:02:28.805][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-04-15 08:02:28.806][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-15 08:02:28.807][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-15 08:02:28.808][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-04-15 08:02:28.808][self$setPropertyValue]
biodb.DEBUG[2023-04-15 08:02:28.809][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-04-15 08:02:28.810][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-04-15 08:02:28.811][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-04-15 08:02:28.811][self$setPropertyValue]
biodb.DEBUG[2023-04-15 08:02:28.812][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2023-04-15 08:02:28.814][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2023-04-15 08:02:28.814][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2023-04-15 08:02:28.815][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-04-15 08:02:28.816][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-04-15 08:02:28.817][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-04-15 08:02:28.818][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-04-15 08:02:28.830][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-04-15 08:02:28.831][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-04-15 08:02:28.832][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2023-04-15 08:02:28.834][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-04-15 08:02:28.835][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2023-04-15 08:02:28.835][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2023-04-15 08:02:28.836][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-04-15 08:02:28.837][self$setPropertyValue]
biodb.DEBUG[2023-04-15 08:02:28.838][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-04-15 08:02:28.839][self$setPropertyValue]
biodb.DEBUG[2023-04-15 08:02:28.841][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-04-15 08:02:28.842][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-15 08:02:28.843][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-15 08:02:28.843][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-04-15 08:02:28.844][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-15 08:02:28.845][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-15 08:02:28.846][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-04-15 08:02:28.846][self$setPropertyValue]
biodb.DEBUG[2023-04-15 08:02:28.847][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-04-15 08:02:28.848][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-04-15 08:02:28.849][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-04-15 08:02:28.849][self$setPropertyValue]
biodb.DEBUG[2023-04-15 08:02:28.850][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-04-15 08:02:28.851][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:02:28.860][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:02:28.861][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:02:28.862][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:02:28.871][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-15 08:02:28.872][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:02:28.873][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:02:28.874][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:02:28.875][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:02:28.876][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-15 08:02:28.877][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:02:28.878][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 08:02:28.879][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:02:28.880][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:02:28.881][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-15 08:02:28.882][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:02:28.882][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 08:02:28.883][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:02:28.884][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:02:28.884][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-15 08:02:28.885][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:02:28.886][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 08:02:28.886][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:02:28.887][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:02:28.888][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-15 08:02:28.889][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:02:28.889][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 08:02:28.890][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:02:28.891][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:02:28.891][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-15 08:02:28.892][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:02:28.893][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 08:02:28.893][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:02:28.894][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:02:28.895][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-15 08:02:28.895][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:02:28.896][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:02:28.897][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:02:28.898][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:02:28.898][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-15 08:02:28.899][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:02:28.900][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 08:02:28.900][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:02:28.901][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:02:28.902][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-15 08:02:28.902][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:02:28.903][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:02:28.904][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:02:28.904][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:02:28.905][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-15 08:02:28.906][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:02:28.906][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:02:28.907][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:02:28.908][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:02:28.908][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-15 08:02:28.909][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:02:28.910][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 08:02:28.910][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:02:28.911][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:02:28.912][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-15 08:02:28.912][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:02:28.913][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 08:02:28.914][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:02:28.914][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:02:28.915][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-15 08:02:28.916][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:02:28.916][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 08:02:28.917][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:02:28.918][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:02:28.918][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-15 08:02:28.919][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:02:28.920][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 08:02:28.920][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:02:28.921][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:02:28.922][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-15 08:02:28.922][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:02:28.923][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 08:02:28.924][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:02:28.924][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:02:28.925][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-15 08:02:28.926][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:02:28.926][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:02:28.927][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:02:28.928][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:02:28.928][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-15 08:02:28.929][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:02:28.929][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:02:28.930][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2023-04-15 08:02:28.932][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2023-04-15 08:02:28.933][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2023-04-15 08:02:28.934][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2023-04-15 08:02:28.935][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2023-04-15 08:02:28.936][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2023-04-15 08:02:28.937][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2023-04-15 08:02:28.938][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2023-04-15 08:02:28.939][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2023-04-15 08:02:28.940][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2023-04-15 08:02:28.941][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2023-04-15 08:02:28.942][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2023-04-15 08:02:28.943][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2023-04-15 08:02:28.944][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2023-04-15 08:02:28.945][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2023-04-15 08:02:28.946][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2023-04-15 08:02:28.947][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2023-04-15 08:02:28.948][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2023-04-15 08:02:28.949][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2023-04-15 08:02:28.950][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2023-04-15 08:02:28.951][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2023-04-15 08:02:28.952][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2023-04-15 08:02:28.953][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2023-04-15 08:02:28.955][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2023-04-15 08:02:28.956][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2023-04-15 08:02:28.957][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2023-04-15 08:02:28.958][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2023-04-15 08:02:28.959][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2023-04-15 08:02:28.960][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2023-04-15 08:02:28.961][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2023-04-15 08:02:28.962][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2023-04-15 08:02:28.963][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2023-04-15 08:02:28.964][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2023-04-15 08:02:28.965][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2023-04-15 08:02:28.966][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2023-04-15 08:02:28.967][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2023-04-15 08:02:28.968][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2023-04-15 08:02:28.969][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2023-04-15 08:02:28.970][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2023-04-15 08:02:28.971][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2023-04-15 08:02:28.972][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2023-04-15 08:02:28.973][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2023-04-15 08:02:28.974][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2023-04-15 08:02:28.975][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2023-04-15 08:02:28.976][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2023-04-15 08:02:28.977][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2023-04-15 08:02:28.978][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2023-04-15 08:02:28.979][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2023-04-15 08:02:28.980][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2023-04-15 08:02:28.981][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2023-04-15 08:02:28.982][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2023-04-15 08:02:28.986][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2023-04-15 08:02:28.987][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2023-04-15 08:02:28.988][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2023-04-15 08:02:29.012][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2023-04-15 08:02:29.017][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2023-04-15 08:02:29.025][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2023-04-15 08:02:29.031][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2023-04-15 08:02:29.032][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2023-04-15 08:02:29.043][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2023-04-15 08:02:29.044][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2023-04-15 08:02:29.046][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2023-04-15 08:02:29.047][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2023-04-15 08:02:29.049][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2023-04-15 08:02:29.050][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2023-04-15 08:02:29.052][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2023-04-15 08:02:29.053][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2023-04-15 08:02:29.055][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2023-04-15 08:02:29.056][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2023-04-15 08:02:29.057][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2023-04-15 08:02:29.058][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2023-04-15 08:02:29.059][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2023-04-15 08:02:29.060][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2023-04-15 08:02:29.061][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2023-04-15 08:02:29.062][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2023-04-15 08:02:29.063][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2023-04-15 08:02:29.064][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2023-04-15 08:02:29.065][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2023-04-15 08:02:29.066][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2023-04-15 08:02:29.067][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2023-04-15 08:02:29.068][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2023-04-15 08:02:29.069][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2023-04-15 08:02:29.070][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2023-04-15 08:02:29.071][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2023-04-15 08:02:29.073][initialize] This is biodb version 1.6.1.
biodb.DEBUG[2023-04-15 08:02:29.073][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-04-15 08:02:29.074][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:02:29.075][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-15 08:02:29.075][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:02:29.076][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:02:29.077][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:02:29.077][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-15 08:02:29.078][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-15 08:02:29.079][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:02:29.079][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 08:02:29.080][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:02:29.081][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:02:29.081][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:02:29.082][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-15 08:02:29.083][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-15 08:02:29.083][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:02:29.084][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-15 08:02:29.085][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:02:29.085][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:02:29.086][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:02:29.087][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-15 08:02:29.087][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-15 08:02:29.088][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:02:29.088][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 08:02:29.089][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:02:29.090][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:02:29.090][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:02:29.091][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-15 08:02:29.092][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-15 08:02:29.092][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:02:29.093][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-15 08:02:29.094][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:02:29.094][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:02:29.095][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:02:29.095][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-15 08:02:29.096][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-15 08:02:29.097][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:02:29.097][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-15 08:02:29.098][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:02:29.099][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 08:02:29.099][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:02:29.100][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-15 08:02:29.101][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-15 08:02:29.101][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:02:29.102][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-15 08:02:29.103][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:02:29.103][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:02:29.104][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:02:29.105][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-15 08:02:29.105][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-15 08:02:29.106][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:02:29.106][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-15 08:02:29.107][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:02:29.108][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:02:29.108][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:02:29.109][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-15 08:02:29.110][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-15 08:02:29.110][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:02:29.111][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-15 08:02:29.112][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:02:29.112][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.DEBUG[2023-04-15 08:02:29.113][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:02:29.114][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-15 08:02:29.114][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-15 08:02:29.115][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:02:29.116][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-15 08:02:29.116][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:02:29.117][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:02:29.118][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:02:29.118][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-15 08:02:29.119][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-15 08:02:29.120][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:02:29.120][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-15 08:02:29.121][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:02:29.122][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:02:29.122][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:02:29.123][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-15 08:02:29.123][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-15 08:02:29.124][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:02:29.125][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-15 08:02:29.125][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:02:29.126][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:02:29.127][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:02:29.127][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-15 08:02:29.128][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-15 08:02:29.129][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:02:29.129][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-15 08:02:29.130][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:02:29.131][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:02:29.132][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:02:29.132][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-15 08:02:29.133][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-15 08:02:29.133][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:02:29.134][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 08:02:29.135][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:02:29.136][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:02:29.136][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:02:29.137][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-15 08:02:29.137][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-15 08:02:29.138][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:02:29.139][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-15 08:02:29.139][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:02:29.140][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:02:29.141][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:02:29.141][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-15 08:02:29.142][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-15 08:02:29.143][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:02:29.143][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-15 08:02:29.144][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:02:29.145][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:02:29.145][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:02:29.146][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-15 08:02:29.147][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-15 08:02:29.147][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:02:29.148][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-15 08:02:29.148][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:02:29.149][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:02:29.150][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:02:29.150][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-15 08:02:29.151][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-15 08:02:29.152][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:02:29.152][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-15 08:02:29.153][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:02:29.154][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:02:29.155][biodb$loadDefinitions] Load definitions from file "/Users/biocbuild/bbs-3.16-bioc-longtests/meat/biodbMirbase.Rcheck/biodbMirbase/definitions.yml".
biodb.DEBUG[2023-04-15 08:02:29.156][self$getDbsInfo()$define] Define connector mirbase.mature.
biodb.DEBUG[2023-04-15 08:02:29.157][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-04-15 08:02:29.158][self$setPropertyValue] Setting property "description" to "Write here the description of this database.".
biodb.DEBUG[2023-04-15 08:02:29.159][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-04-15 08:02:29.160][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-04-15 08:02:29.160][self$setPropertyValue] Setting property "downloadable" to "TRUE".
biodb.DEBUG[2023-04-15 08:02:29.161][self$setPropertyValue] Setting property "dwnld.ext" to "gz".
biodb.DEBUG[2023-04-15 08:02:29.162][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2023-04-15 08:02:29.163][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-04-15 08:02:29.163][self$setPropertyValue] Setting property "entry.content.type" to "txt".
biodb.DEBUG[2023-04-15 08:02:29.164][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-04-15 08:02:29.174][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-04-15 08:02:29.175][self$setPropertyValue] Setting property "name" to "miRBase mature database".
biodb.DEBUG[2023-04-15 08:02:29.176][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-04-15 08:02:29.178][self$setPropertyValue] Setting property "parsing.expr" to "^>[^ ]+ *(MIMAT[0-9]+) .*$".
biodb.DEBUG[2023-04-15 08:02:29.178][self$setPropertyValue] Setting property "parsing.expr" to "^>[^ ]+ *MIMAT[0-9]+ (.*)$".
biodb.DEBUG[2023-04-15 08:02:29.178][self$setPropertyValue] Setting property "parsing.expr" to "^>([^ ]+) *MIMAT[0-9]+ .*$".
biodb.DEBUG[2023-04-15 08:02:29.178][self$setPropertyValue] Setting property "parsing.expr" to "^([ACGU]+)$".
biodb.DEBUG[2023-04-15 08:02:29.179][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2023-04-15 08:02:29.180][self$setPropertyValue]
biodb.DEBUG[2023-04-15 08:02:29.181][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2023-04-15 08:02:29.182][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-15 08:02:29.183][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-15 08:02:29.184][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-04-15 08:02:29.185][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-15 08:02:29.186][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-15 08:02:29.187][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-04-15 08:02:29.188][self$setPropertyValue] Setting property "urls" to "http://www.mirbase.org/".
biodb.DEBUG[2023-04-15 08:02:29.188][self$setPropertyValue] Setting property "urls" to "https://www.mirbase.org/ftp/CURRENT/mature.fa.gz".
biodb.DEBUG[2023-04-15 08:02:29.188][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-04-15 08:02:29.189][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-04-15 08:02:29.190][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2023-04-15 08:02:29.190][self$setPropertyValue]
biodb.DEBUG[2023-04-15 08:02:29.191][self$getEntryFields()$define] Define field mirbase.mature.id.
biodb.DEBUG[2023-04-15 08:02:29.194][initialize] Initialize connector mirbase.mature.
biodb.DEBUG[2023-04-15 08:02:29.194][initialize] Register connector mirbase.mature with the request scheduler
biodb.DEBUG[2023-04-15 08:02:29.195][private$bdb$getRequestScheduler()$re ...] Register connector mirbase.mature.
biodb.DEBUG[2023-04-15 08:02:29.196][private$addConnectorRules] Create new rule for URL "www.mirbase.org" of connector "mirbase.mature".
biodb.DEBUG[2023-04-15 08:02:29.197][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2023-04-15 08:02:29.198][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2023-04-15 08:02:29.199][rule$addConnector] Connector "mirbase.mature" is already listed in rule "www.mirbase.org".
biodb.DEBUG[2023-04-15 08:02:29.200][biodb$getFactory()$createConn] Creating new connector mirbase.mature for database class mirbase.mature .
biodb.INFO [2023-04-15 08:02:29.200][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2023-04-15 08:02:29.201][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector mirbase.mature from the request scheduler
biodb.INFO [2023-04-15 08:02:29.202][self$deleteConn] Connector "mirbase.mature" deleted.
biodb.DEBUG[2023-04-15 08:02:29.203][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2023-04-15 08:02:29.203][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-15 08:02:29.204][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-15 08:02:29.205][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:02:29.205][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-15 08:02:29.206][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:02:29.207][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 75 ]
> 
> proc.time()
   user  system elapsed 
  5.774   6.420  18.218

'R CMD check' output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --test-dir=longtests --no-stop-on-test-error --no-codoc --no-examples --no-manual --ignore-vignettes --check-subdirs=no biodbMirbase_1.2.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.16-bioc-longtests/meat/biodbMirbase.Rcheck’
* using R version 4.2.3 (2023-03-15)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using options ‘--no-codoc --no-examples --no-manual --ignore-vignettes --no-stop-on-test-error’
* checking for file ‘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 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)