Back to Long Tests report for BioC 3.20

This page was generated on 2024-06-29 23:55 -0400 (Sat, 29 Jun 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 RC (2024-04-16 r86468) -- "Puppy Cup" 4693
palomino6Windows Server 2022 Datacenterx644.4.1 (2024-06-14 ucrt) -- "Race for Your Life" 4408
lconwaymacOS 12.7.1 Montereyx86_644.4.1 RC (2024-06-06 r86719) -- "Race for Your Life" 4407
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

Package 7/32HostnameOS / ArchCHECK
biodbExpasy 1.9.0  (landing page)
Pierrick Roger
Snapshot Date: 2024-06-29 09:55 -0400 (Sat, 29 Jun 2024)
git_url: https://git.bioconductor.org/packages/biodbExpasy
git_branch: devel
git_last_commit: 25fc0fc
git_last_commit_date: 2024-04-30 11:41:12 -0400 (Tue, 30 Apr 2024)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  ERROR  
palomino6Windows Server 2022 Datacenter / x64  ERROR  
lconwaymacOS 12.7.1 Monterey / x86_64  ERROR  

CHECK results for biodbExpasy on nebbiolo2

To the developers/maintainers of the biodbExpasy package:
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: biodbExpasy
Version: 1.9.0
Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --test-dir=longtests --no-stop-on-test-error --no-codoc --no-examples --no-manual --ignore-vignettes --check-subdirs=no biodbExpasy_1.9.0.tar.gz
StartedAt: 2024-06-29 16:01:51 -0400 (Sat, 29 Jun 2024)
EndedAt: 2024-06-29 16:02:36 -0400 (Sat, 29 Jun 2024)
EllapsedTime: 45.0 seconds
RetCode: 1
Status:   ERROR  
CheckDir: biodbExpasy.Rcheck
Warnings: NA

Tests output

biodbExpasy.Rcheck/tests/testthat.Rout.fail


R version 4.4.0 RC (2024-04-16 r86468) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

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> # Script needed to run testthat automatically from ‘R CMD check’. See
> # testthat::test_dir documentation.
> library(testthat)
> library(biodbExpasy)
> Sys.setenv(TESTTHAT_REPORTER="summary")
> Sys.setenv(BIODB_LOG_DST="console")
> test_check("biodbExpasy")
biodb.INFO [2024-06-29 16:02:27.750][biodb::testContext]
biodb.INFO [2024-06-29 16:02:27.753][biodb::testContext] ********************************************************************************
biodb.INFO [2024-06-29 16:02:27.754][biodb::testContext] Test context - Generic long tests
biodb.INFO [2024-06-29 16:02:27.755][biodb::testContext] ********************************************************************************
biodb.INFO [2024-06-29 16:02:27.756][biodb::testContext]
biodb.INFO [2024-06-29 16:02:27.763][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.13.0.
biodb.DEBUG[2024-06-29 16:02:27.765][self$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.20-bioc/R/site-library/biodb/definitions.yml".
biodb.DEBUG[2024-06-29 16:02:27.772][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-06-29 16:02:27.774][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-06-29 16:02:27.775][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-06-29 16:02:27.775][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:02:27.776][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:02:27.777][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:02:27.778][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-06-29 16:02:27.798][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-06-29 16:02:27.799][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:02:27.800][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:02:27.801][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:02:27.802][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-06-29 16:02:27.803][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-06-29 16:02:27.804][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:02:27.805][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:02:27.806][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:02:27.807][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-06-29 16:02:27.808][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-06-29 16:02:27.809][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-06-29 16:02:27.810][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:02:27.811][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:02:27.812][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:02:27.813][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-06-29 16:02:27.814][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-06-29 16:02:27.815][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-06-29 16:02:27.815][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:02:27.816][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:02:27.817][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:02:27.818][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-06-29 16:02:27.819][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-06-29 16:02:27.820][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:02:27.821][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:02:27.822][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:02:27.823][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-06-29 16:02:27.824][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-06-29 16:02:27.825][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-06-29 16:02:27.826][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:02:27.827][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:02:27.828][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:02:27.829][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-06-29 16:02:27.830][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-06-29 16:02:27.831][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:02:27.832][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:02:27.832][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:02:27.833][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-06-29 16:02:27.834][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-06-29 16:02:27.836][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-06-29 16:02:27.836][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:02:27.837][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:02:27.838][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:02:27.839][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-06-29 16:02:27.840][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-06-29 16:02:27.841][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-06-29 16:02:27.842][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-06-29 16:02:27.843][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-06-29 16:02:27.844][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-06-29 16:02:27.845][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:02:27.846][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:02:27.847][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:02:27.848][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-06-29 16:02:27.849][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-06-29 16:02:27.850][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:02:27.851][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:02:27.852][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:02:27.853][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-06-29 16:02:27.854][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-06-29 16:02:27.855][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:02:27.855][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:02:27.856][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:02:27.857][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-06-29 16:02:27.858][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-06-29 16:02:27.859][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:02:27.860][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:02:27.861][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:02:27.862][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-06-29 16:02:27.863][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-06-29 16:02:27.864][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:02:27.865][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:02:27.866][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:02:27.867][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-06-29 16:02:27.868][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-06-29 16:02:27.869][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:02:27.870][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:02:27.870][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:02:27.871][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-06-29 16:02:27.872][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-06-29 16:02:27.876][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-06-29 16:02:27.877][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:02:27.878][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:02:27.879][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:02:27.880][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-06-29 16:02:27.881][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-06-29 16:02:27.882][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-06-29 16:02:27.883][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:02:27.883][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:02:27.884][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:02:27.888][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-06-29 16:02:27.925][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-06-29 16:02:27.948][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2024-06-29 16:02:27.949][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-29 16:02:27.950][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-29 16:02:27.951][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-29 16:02:27.952][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-29 16:02:27.953][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-29 16:02:27.954][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-29 16:02:27.955][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-06-29 16:02:27.955][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-29 16:02:27.956][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-06-29 16:02:27.957][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-06-29 16:02:27.958][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-29 16:02:27.959][self$setPropertyValue]
biodb.DEBUG[2024-06-29 16:02:27.960][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-29 16:02:27.961][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-06-29 16:02:27.961][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-06-29 16:02:27.961][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-06-29 16:02:27.961][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-06-29 16:02:27.961][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-06-29 16:02:27.962][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-29 16:02:27.963][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-29 16:02:27.963][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-29 16:02:27.964][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-29 16:02:27.965][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-29 16:02:27.966][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-29 16:02:27.967][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-29 16:02:27.967][self$setPropertyValue]
biodb.DEBUG[2024-06-29 16:02:27.968][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-29 16:02:27.969][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-29 16:02:27.970][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-29 16:02:27.971][self$setPropertyValue]
biodb.DEBUG[2024-06-29 16:02:27.972][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-06-29 16:02:27.974][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-06-29 16:02:27.974][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-06-29 16:02:27.975][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-29 16:02:27.976][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-29 16:02:27.977][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-29 16:02:27.978][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-29 16:02:27.979][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-29 16:02:27.980][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-29 16:02:27.981][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-06-29 16:02:27.982][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-29 16:02:27.982][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-06-29 16:02:27.983][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-06-29 16:02:27.984][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-29 16:02:27.985][self$setPropertyValue]
biodb.DEBUG[2024-06-29 16:02:27.986][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-29 16:02:27.987][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-06-29 16:02:27.987][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-06-29 16:02:27.987][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-06-29 16:02:27.987][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-06-29 16:02:27.987][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-06-29 16:02:27.988][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-29 16:02:27.989][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-29 16:02:27.989][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-29 16:02:27.990][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-29 16:02:27.991][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-29 16:02:27.992][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-29 16:02:27.993][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-29 16:02:27.994][self$setPropertyValue]
biodb.DEBUG[2024-06-29 16:02:27.995][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-29 16:02:27.995][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-29 16:02:27.996][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-29 16:02:27.997][self$setPropertyValue]
biodb.DEBUG[2024-06-29 16:02:27.998][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-06-29 16:02:28.000][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-06-29 16:02:28.001][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2024-06-29 16:02:28.001][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-29 16:02:28.002][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-29 16:02:28.003][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-29 16:02:28.004][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-29 16:02:28.005][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-29 16:02:28.006][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-29 16:02:28.007][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-06-29 16:02:28.008][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-29 16:02:28.009][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-06-29 16:02:28.009][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-06-29 16:02:28.010][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-29 16:02:28.011][self$setPropertyValue]
biodb.DEBUG[2024-06-29 16:02:28.012][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-29 16:02:28.013][self$setPropertyValue]
biodb.DEBUG[2024-06-29 16:02:28.014][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-29 16:02:28.015][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-29 16:02:28.015][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-29 16:02:28.016][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-29 16:02:28.017][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-29 16:02:28.018][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-29 16:02:28.019][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-29 16:02:28.020][self$setPropertyValue]
biodb.DEBUG[2024-06-29 16:02:28.021][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-29 16:02:28.021][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-29 16:02:28.022][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-29 16:02:28.023][self$setPropertyValue]
biodb.DEBUG[2024-06-29 16:02:28.024][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-06-29 16:02:28.026][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-06-29 16:02:28.027][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-06-29 16:02:28.027][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-29 16:02:28.028][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-29 16:02:28.029][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-29 16:02:28.030][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-29 16:02:28.031][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-29 16:02:28.032][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-29 16:02:28.033][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-06-29 16:02:28.034][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-29 16:02:28.034][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-06-29 16:02:28.035][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-06-29 16:02:28.036][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-29 16:02:28.037][self$setPropertyValue]
biodb.DEBUG[2024-06-29 16:02:28.038][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-29 16:02:28.039][self$setPropertyValue]
biodb.DEBUG[2024-06-29 16:02:28.040][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-29 16:02:28.041][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-29 16:02:28.041][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-29 16:02:28.042][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-29 16:02:28.043][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-29 16:02:28.044][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-29 16:02:28.045][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-29 16:02:28.046][self$setPropertyValue]
biodb.DEBUG[2024-06-29 16:02:28.046][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-29 16:02:28.047][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-29 16:02:28.048][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-29 16:02:28.049][self$setPropertyValue]
biodb.DEBUG[2024-06-29 16:02:28.053][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-06-29 16:02:28.054][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:02:28.054][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:02:28.055][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:02:28.056][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:02:28.057][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:02:28.058][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:02:28.058][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[2024-06-29 16:02:28.059][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:02:28.060][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:02:28.061][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:02:28.062][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:02:28.062][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[2024-06-29 16:02:28.063][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:02:28.064][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:02:28.065][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:02:28.065][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:02:28.066][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:02:28.067][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:02:28.068][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:02:28.069][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:02:28.069][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:02:28.070][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:02:28.071][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:02:28.072][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:02:28.073][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:02:28.073][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:02:28.074][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:02:28.075][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:02:28.076][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:02:28.081][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:02:28.082][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:02:28.083][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:02:28.084][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:02:28.085][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:02:28.086][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:02:28.087][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:02:28.088][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:02:28.089][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:02:28.089][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:02:28.090][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:02:28.091][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:02:28.092][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:02:28.093][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:02:28.094][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:02:28.095][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:02:28.096][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:02:28.097][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:02:28.097][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:02:28.098][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:02:28.099][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:02:28.100][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:02:28.101][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:02:28.102][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:02:28.103][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:02:28.104][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:02:28.104][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:02:28.105][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:02:28.106][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:02:28.107][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:02:28.108][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:02:28.109][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:02:28.110][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:02:28.111][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:02:28.111][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:02:28.112][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:02:28.113][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:02:28.114][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:02:28.115][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:02:28.116][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:02:28.117][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:02:28.118][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:02:28.119][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:02:28.119][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:02:28.120][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:02:28.121][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:02:28.122][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:02:28.123][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:02:28.124][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:02:28.125][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:02:28.126][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:02:28.126][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:02:28.127][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:02:28.128][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:02:28.129][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:02:28.130][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:02:28.131][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:02:28.132][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:02:28.133][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-06-29 16:02:28.138][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-06-29 16:02:28.140][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-06-29 16:02:28.141][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-06-29 16:02:28.143][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-06-29 16:02:28.144][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-06-29 16:02:28.146][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-06-29 16:02:28.147][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-06-29 16:02:28.148][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-06-29 16:02:28.150][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-06-29 16:02:28.151][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-06-29 16:02:28.152][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-06-29 16:02:28.154][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-06-29 16:02:28.155][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-06-29 16:02:28.157][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-06-29 16:02:28.158][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-06-29 16:02:28.159][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-06-29 16:02:28.161][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-06-29 16:02:28.162][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-06-29 16:02:28.164][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-06-29 16:02:28.165][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-06-29 16:02:28.166][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-06-29 16:02:28.168][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-06-29 16:02:28.169][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-06-29 16:02:28.170][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-06-29 16:02:28.172][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-06-29 16:02:28.173][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-06-29 16:02:28.175][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-06-29 16:02:28.176][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-06-29 16:02:28.177][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-06-29 16:02:28.179][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-06-29 16:02:28.180][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-06-29 16:02:28.181][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-06-29 16:02:28.183][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-06-29 16:02:28.184][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-06-29 16:02:28.185][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-06-29 16:02:28.187][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-06-29 16:02:28.188][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-06-29 16:02:28.202][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-06-29 16:02:28.203][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-06-29 16:02:28.205][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-06-29 16:02:28.206][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-06-29 16:02:28.207][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-06-29 16:02:28.209][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-06-29 16:02:28.210][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-06-29 16:02:28.212][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-06-29 16:02:28.213][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-06-29 16:02:28.214][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-06-29 16:02:28.216][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-06-29 16:02:28.217][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-06-29 16:02:28.219][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-06-29 16:02:28.220][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-06-29 16:02:28.221][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-06-29 16:02:28.223][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-06-29 16:02:28.224][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-06-29 16:02:28.225][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-06-29 16:02:28.227][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-06-29 16:02:28.228][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-06-29 16:02:28.229][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-06-29 16:02:28.231][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-06-29 16:02:28.232][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-06-29 16:02:28.233][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-06-29 16:02:28.235][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-06-29 16:02:28.236][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-06-29 16:02:28.237][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-06-29 16:02:28.239][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-06-29 16:02:28.240][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-06-29 16:02:28.242][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-06-29 16:02:28.243][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-06-29 16:02:28.244][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-06-29 16:02:28.246][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-06-29 16:02:28.247][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-06-29 16:02:28.248][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-06-29 16:02:28.250][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-06-29 16:02:28.251][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-06-29 16:02:28.252][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-06-29 16:02:28.254][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-06-29 16:02:28.255][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-06-29 16:02:28.256][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-06-29 16:02:28.258][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-06-29 16:02:28.259][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-06-29 16:02:28.260][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-06-29 16:02:28.262][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-06-29 16:02:28.268][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-06-29 16:02:28.269][initialize] This is biodb version 1.13.0.
biodb.DEBUG[2024-06-29 16:02:28.273][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-06-29 16:02:28.273][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:02:28.274][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:02:28.275][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:02:28.276][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:02:28.281][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:02:28.281][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-29 16:02:28.282][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-29 16:02:28.283][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:02:28.284][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:02:28.285][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:02:28.286][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:02:28.286][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:02:28.287][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-29 16:02:28.288][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-29 16:02:28.289][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:02:28.290][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:02:28.291][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:02:28.291][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:02:28.292][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:02:28.293][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-29 16:02:28.294][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-29 16:02:28.295][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:02:28.296][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:02:28.297][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:02:28.297][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:02:28.298][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:02:28.299][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-29 16:02:28.300][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-29 16:02:28.301][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:02:28.302][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:02:28.302][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:02:28.303][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:02:28.304][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:02:28.305][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-29 16:02:28.306][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-29 16:02:28.307][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:02:28.308][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:02:28.308][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:02:28.309][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:02:28.310][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:02:28.311][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-29 16:02:28.312][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-29 16:02:28.313][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:02:28.313][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:02:28.314][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:02:28.315][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:02:28.316][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:02:28.317][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-29 16:02:28.318][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-29 16:02:28.318][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:02:28.319][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:02:28.320][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:02:28.321][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:02:28.322][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:02:28.323][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-29 16:02:28.324][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-29 16:02:28.324][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:02:28.325][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:02:28.326][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:02:28.327][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:02:28.328][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:02:28.329][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-29 16:02:28.329][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-29 16:02:28.330][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:02:28.331][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:02:28.332][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:02:28.333][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:02:28.334][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:02:28.334][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-29 16:02:28.335][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-29 16:02:28.336][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:02:28.337][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:02:28.338][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:02:28.339][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:02:28.339][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:02:28.340][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-29 16:02:28.341][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-29 16:02:28.342][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:02:28.343][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:02:28.343][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:02:28.344][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:02:28.345][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:02:28.346][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-29 16:02:28.346][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-29 16:02:28.347][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:02:28.348][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:02:28.349][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:02:28.350][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:02:28.350][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:02:28.351][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-29 16:02:28.352][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-29 16:02:28.353][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:02:28.354][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:02:28.354][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:02:28.355][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:02:28.356][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:02:28.357][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-29 16:02:28.357][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-29 16:02:28.358][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:02:28.359][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:02:28.360][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:02:28.361][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:02:28.361][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:02:28.362][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-29 16:02:28.363][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-29 16:02:28.364][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:02:28.364][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:02:28.365][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:02:28.366][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:02:28.367][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:02:28.368][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-29 16:02:28.368][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-29 16:02:28.369][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:02:28.370][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:02:28.371][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:02:28.371][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:02:28.372][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:02:28.373][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-29 16:02:28.374][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-29 16:02:28.375][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:02:28.375][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:02:28.376][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:02:28.377][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:02:28.378][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.20-bioc-longtests/meat/biodbExpasy.Rcheck/biodbExpasy/definitions.yml".
biodb.DEBUG[2024-06-29 16:02:28.387][self$getDbsInfo()$define] Define connector expasy.enzyme.
biodb.DEBUG[2024-06-29 16:02:28.389][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-06-29 16:02:28.390][self$setPropertyValue] Setting property "description" to "Write here the description of this database.".
biodb.DEBUG[2024-06-29 16:02:28.391][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-29 16:02:28.391][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-29 16:02:28.392][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-29 16:02:28.393][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-29 16:02:28.394][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-06-29 16:02:28.395][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-29 16:02:28.396][self$setPropertyValue] Setting property "entry.content.type" to "txt".
biodb.DEBUG[2024-06-29 16:02:28.397][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-29 16:02:28.398][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-06-29 16:02:28.399][self$setPropertyValue] Setting property "name" to "Expasy ENZYME database.".
biodb.DEBUG[2024-06-29 16:02:28.399][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-29 16:02:28.400][self$setPropertyValue] Setting property "parsing.expr" to "^ID\s+([0-9.]+)$".
biodb.DEBUG[2024-06-29 16:02:28.400][self$setPropertyValue] Setting property "parsing.expr" to "^CA\s+(.+?)\.?$".
biodb.DEBUG[2024-06-29 16:02:28.400][self$setPropertyValue] Setting property "parsing.expr" to "^CF\s+(.+?)\.?$".
biodb.DEBUG[2024-06-29 16:02:28.400][self$setPropertyValue] Setting property "parsing.expr" to "^DE\s+(.+?)\.?$".
biodb.DEBUG[2024-06-29 16:02:28.401][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-06-29 16:02:28.402][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-06-29 16:02:28.403][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2024-06-29 16:02:28.404][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-29 16:02:28.405][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-29 16:02:28.405][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-29 16:02:28.406][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-29 16:02:28.407][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-29 16:02:28.408][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-29 16:02:28.409][self$setPropertyValue] Setting property "urls" to "https://enzyme.expasy.org/".
biodb.DEBUG[2024-06-29 16:02:28.410][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-29 16:02:28.410][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-29 16:02:28.411][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-06-29 16:02:28.412][self$setPropertyValue]
biodb.DEBUG[2024-06-29 16:02:28.418][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-06-29 16:02:28.440][super$initialize] Initialize connector expasy.enzyme.
biodb.DEBUG[2024-06-29 16:02:28.445][super$initialize] Register connector expasy.enzyme with the request scheduler
biodb.DEBUG[2024-06-29 16:02:28.449][private$bdb$getRequestScheduler()$re ...] Register connector expasy.enzyme.
biodb.DEBUG[2024-06-29 16:02:28.453][private$addConnectorRules] Create new rule for URL "enzyme.expasy.org" of connector "expasy.enzyme".
biodb.DEBUG[2024-06-29 16:02:28.457][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-06-29 16:02:28.458][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-06-29 16:02:28.459][biodb$getFactory()$createConn] Creating new connector expasy.enzyme for database class expasy.enzyme .
biodb.INFO [2024-06-29 16:02:28.468][biodb::testThat]
biodb.INFO [2024-06-29 16:02:28.469][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2024-06-29 16:02:28.470][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-29 16:02:28.471][biodb::testThat]
biodb.TRACE[2024-06-29 16:02:28.474][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/bbs-3.20-bioc-longtests/meat/biodbExpasy.Rcheck/biodbExpasy/testref/entry-expasy.enzyme-1.1.1.1-content.txt".
biodb.DEBUG[2024-06-29 16:02:28.475][biodb$getFactory()$createEntryFromCo ...] Creating Expasy ENZYME database. entries from 1 content(s).
biodb.DEBUG[2024-06-29 16:02:28.479][biodb$getFactory()$createEntryFromCo ...] Parsing 1 Expasy ENZYME database. entries.
biodb.DEBUG[2024-06-29 16:02:28.487][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-29 16:02:28.488][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-29 16:02:28.489][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-29 16:02:28.500][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:02:28.501][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:02:28.502][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:02:28.502][FUN] Functions in observer BiodbConfig: [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[2024-06-29 16:02:28.513][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-29 16:02:28.514][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-29 16:02:28.515][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:28.516][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:28.540][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-06-29 16:02:28.551][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-06-29 16:02:28.552][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:28.552][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:28.554][self$getBiodb()$getEntryFields()$get] Asked field names are: cofactor.
biodb.TRACE[2024-06-29 16:02:28.555][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-06-29 16:02:28.555][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:28.556][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:28.557][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-29 16:02:28.558][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-29 16:02:28.559][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:28.560][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:28.561][self$getBiodb()$getEntryFields()$get] Asked field names are: COFACTOR.
biodb.TRACE[2024-06-29 16:02:28.562][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-06-29 16:02:28.563][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:28.564][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:28.565][self$getBiodb()$getEntryFields()$get] Asked field names are: cofactor.
biodb.TRACE[2024-06-29 16:02:28.566][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-06-29 16:02:28.566][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:28.567][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:28.568][self$getBiodb()$getEntryFields()$get] Asked field names are: cofactor.
biodb.TRACE[2024-06-29 16:02:28.569][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-06-29 16:02:28.570][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:28.571][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:28.572][self$getBiodb()$getEntryFields()$get] Asked field names are: cofactor.
biodb.TRACE[2024-06-29 16:02:28.573][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-06-29 16:02:28.574][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:28.574][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:28.575][self$getBiodb()$getEntryFields()$get] Asked field names are: COFACTOR.
biodb.TRACE[2024-06-29 16:02:28.576][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-06-29 16:02:28.577][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:28.578][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:28.594][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-29 16:02:28.595][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-29 16:02:28.595][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:28.596][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:28.597][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-29 16:02:28.598][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-29 16:02:28.599][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:28.600][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:28.630][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-29 16:02:28.631][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-29 16:02:28.632][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:28.632][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:28.633][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-29 16:02:28.634][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-29 16:02:28.635][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:28.636][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:28.637][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-29 16:02:28.638][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-29 16:02:28.639][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:28.640][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:28.641][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-06-29 16:02:28.642][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-06-29 16:02:28.643][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:28.643][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:28.644][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-06-29 16:02:28.645][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-06-29 16:02:28.646][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:28.647][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:28.648][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-29 16:02:28.649][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-29 16:02:28.650][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:28.651][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:28.651][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-06-29 16:02:28.652][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-06-29 16:02:28.653][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:28.654][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:28.655][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-29 16:02:28.656][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-29 16:02:28.657][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:28.658][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:28.659][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-29 16:02:28.667][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-29 16:02:28.668][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:28.668][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:28.669][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-29 16:02:28.670][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-29 16:02:28.671][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:28.672][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:28.673][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-29 16:02:28.674][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-29 16:02:28.675][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:28.676][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:28.676][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-29 16:02:28.677][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-29 16:02:28.678][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:28.679][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:28.680][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-29 16:02:28.681][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-29 16:02:28.682][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:28.683][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-29 16:02:28.683][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 1.1.1.1.
biodb.TRACE[2024-06-29 16:02:28.686][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-06-29 16:02:28.687][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-06-29 16:02:28.688][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:28.688][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:28.689][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-06-29 16:02:28.690][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-06-29 16:02:28.691][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:28.692][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:28.693][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-06-29 16:02:28.694][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-06-29 16:02:28.695][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:28.695][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:28.696][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-06-29 16:02:28.697][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-06-29 16:02:28.698][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:28.699][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:28.713][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-29 16:02:28.714][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-29 16:02:28.715][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:28.716][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:28.727][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-06-29 16:02:28.728][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-06-29 16:02:28.729][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:28.730][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:28.734][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-29 16:02:28.735][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-29 16:02:28.736][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:28.737][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:28.738][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-29 16:02:28.739][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-29 16:02:28.739][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:28.740][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:28.741][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-29 16:02:28.742][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-29 16:02:28.743][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:28.744][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:28.746][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-29 16:02:28.747][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-29 16:02:28.748][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:28.749][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:28.750][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-29 16:02:28.751][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-29 16:02:28.751][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:28.752][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:28.753][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-29 16:02:28.754][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-29 16:02:28.755][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:28.756][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:28.757][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-06-29 16:02:28.758][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-06-29 16:02:28.759][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:28.759][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:28.760][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-06-29 16:02:28.761][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-06-29 16:02:28.762][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:28.763][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:28.764][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-06-29 16:02:28.765][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-06-29 16:02:28.766][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:28.766][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:28.773][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-29 16:02:28.774][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-29 16:02:28.775][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:28.776][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:28.777][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-29 16:02:28.778][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-29 16:02:28.778][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:28.779][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:28.780][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-29 16:02:28.781][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-29 16:02:28.782][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:28.783][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:28.784][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-29 16:02:28.785][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-29 16:02:28.785][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:28.786][ef$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:28.787][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-29 16:02:28.788][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-29 16:02:28.789][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:28.790][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:28.797][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-29 16:02:28.798][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-29 16:02:28.799][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:28.800][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:28.801][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-29 16:02:28.802][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-29 16:02:28.803][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:28.803][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:28.804][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-29 16:02:28.805][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-29 16:02:28.806][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:28.807][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:28.808][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-29 16:02:28.809][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-29 16:02:28.810][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:28.810][ef$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:28.811][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-29 16:02:28.812][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-29 16:02:28.813][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:28.814][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:28.821][self$getBiodb()$getEntryFields()$get] Asked field names are: cofactor.
biodb.TRACE[2024-06-29 16:02:28.822][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-06-29 16:02:28.823][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:28.823][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:28.824][self$getBiodb()$getEntryFields()$get] Asked field names are: cofactor.
biodb.TRACE[2024-06-29 16:02:28.825][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-06-29 16:02:28.826][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:28.827][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:28.828][self$getBiodb()$getEntryFields()$get] Asked field names are: cofactor.
biodb.TRACE[2024-06-29 16:02:28.829][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-06-29 16:02:28.830][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:28.830][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:28.831][ef$get] Asked field names are: cofactor.
biodb.TRACE[2024-06-29 16:02:28.832][ef$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-06-29 16:02:28.833][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:28.834][ef$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:28.835][self$getBiodb()$getEntryFields()$get] Asked field names are: cofactor.
biodb.TRACE[2024-06-29 16:02:28.836][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-06-29 16:02:28.837][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:28.837][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:28.844][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-06-29 16:02:28.845][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-06-29 16:02:28.846][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:28.847][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:28.848][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-06-29 16:02:28.849][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-06-29 16:02:28.850][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:28.850][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:28.851][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-06-29 16:02:28.852][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-06-29 16:02:28.853][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:28.854][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:28.855][ef$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-06-29 16:02:28.856][ef$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-06-29 16:02:28.857][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:28.858][ef$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:28.858][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-06-29 16:02:28.859][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-06-29 16:02:28.860][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:28.861][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:28.891][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-29 16:02:28.892][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-29 16:02:28.893][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:28.894][ef$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:28.897][ef$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-06-29 16:02:28.898][ef$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-06-29 16:02:28.899][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:28.900][ef$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:28.904][ef$get] Asked field names are: cofactor.
biodb.TRACE[2024-06-29 16:02:28.905][ef$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-06-29 16:02:28.905][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:28.906][ef$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:28.910][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-29 16:02:28.911][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-29 16:02:28.912][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:28.913][ef$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:28.927][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/bbs-3.20-bioc-longtests/meat/biodbExpasy.Rcheck/biodbExpasy/testref/entry-expasy.enzyme-1.1.1.54-content.txt".
biodb.DEBUG[2024-06-29 16:02:28.959][biodb$getFactory()$createEntryFromCo ...] Creating Expasy ENZYME database. entries from 1 content(s).
biodb.DEBUG[2024-06-29 16:02:28.960][biodb$getFactory()$createEntryFromCo ...] Parsing 1 Expasy ENZYME database. entries.
biodb.DEBUG[2024-06-29 16:02:28.961][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-29 16:02:28.962][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-29 16:02:28.963][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-29 16:02:28.966][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:02:28.967][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:02:28.968][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:02:28.969][FUN] Functions in observer BiodbConfig: [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[2024-06-29 16:02:28.971][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-29 16:02:28.972][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-29 16:02:28.973][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:28.973][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:28.974][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-06-29 16:02:28.975][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-06-29 16:02:28.976][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:28.977][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:28.978][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-29 16:02:28.979][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-29 16:02:28.980][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:28.981][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:28.982][self$getBiodb()$getEntryFields()$get] Asked field names are: COFACTOR.
biodb.TRACE[2024-06-29 16:02:28.983][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-06-29 16:02:28.984][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:28.985][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:28.986][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-06-29 16:02:28.987][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-06-29 16:02:28.987][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:28.988][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:28.989][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-06-29 16:02:28.990][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-06-29 16:02:28.991][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:28.992][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:28.993][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-29 16:02:28.994][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-29 16:02:28.994][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:28.995][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:28.996][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-06-29 16:02:28.997][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-06-29 16:02:28.998][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:28.999][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:29.000][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-29 16:02:29.001][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-29 16:02:29.001][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:29.002][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:29.003][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-29 16:02:29.004][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-29 16:02:29.005][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:29.006][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:29.007][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-29 16:02:29.008][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-29 16:02:29.009][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:29.009][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:29.010][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-29 16:02:29.011][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-29 16:02:29.012][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:29.013][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:29.014][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-29 16:02:29.015][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-29 16:02:29.016][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:29.017][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:29.018][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-29 16:02:29.018][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-29 16:02:29.019][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:29.020][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-29 16:02:29.021][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 1.1.1.54.
biodb.TRACE[2024-06-29 16:02:29.039][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-06-29 16:02:29.040][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-06-29 16:02:29.041][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:29.042][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:29.043][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-06-29 16:02:29.044][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-06-29 16:02:29.045][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:29.046][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:29.046][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-06-29 16:02:29.047][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-06-29 16:02:29.048][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:29.049][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:29.050][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-06-29 16:02:29.051][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-06-29 16:02:29.052][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:29.053][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:29.054][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-29 16:02:29.055][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-29 16:02:29.056][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:29.057][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:29.061][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-06-29 16:02:29.062][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-06-29 16:02:29.063][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:29.063][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:29.067][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-29 16:02:29.068][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-29 16:02:29.073][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:29.074][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:29.075][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-29 16:02:29.076][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-29 16:02:29.077][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:29.077][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:29.078][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-29 16:02:29.079][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-29 16:02:29.080][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:29.081][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:29.083][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-29 16:02:29.084][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-29 16:02:29.085][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:29.086][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:29.087][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-29 16:02:29.088][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-29 16:02:29.088][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:29.089][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:29.090][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-29 16:02:29.091][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-29 16:02:29.092][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:29.093][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:29.094][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-06-29 16:02:29.095][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-06-29 16:02:29.096][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:29.097][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:29.097][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-06-29 16:02:29.098][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-06-29 16:02:29.099][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:29.100][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:29.101][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-06-29 16:02:29.102][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-06-29 16:02:29.103][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:29.104][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:29.118][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-29 16:02:29.119][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-29 16:02:29.120][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:29.121][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:29.122][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-29 16:02:29.123][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-29 16:02:29.124][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:29.125][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:29.126][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-29 16:02:29.126][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-29 16:02:29.127][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:29.128][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:29.129][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-29 16:02:29.130][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-29 16:02:29.131][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:29.132][ef$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:29.133][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-29 16:02:29.134][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-29 16:02:29.134][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:29.135][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:29.142][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-29 16:02:29.143][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-29 16:02:29.144][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:29.145][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:29.146][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-29 16:02:29.147][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-29 16:02:29.148][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:29.149][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:29.149][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-29 16:02:29.150][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-29 16:02:29.151][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:29.152][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:29.153][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-29 16:02:29.154][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-29 16:02:29.155][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:29.156][ef$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:29.157][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-29 16:02:29.158][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-29 16:02:29.158][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:29.159][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:29.166][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-06-29 16:02:29.167][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-06-29 16:02:29.168][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:29.169][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:29.170][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-06-29 16:02:29.171][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-06-29 16:02:29.172][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:29.173][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:29.173][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-06-29 16:02:29.174][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-06-29 16:02:29.175][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:29.176][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:29.177][ef$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-06-29 16:02:29.178][ef$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-06-29 16:02:29.179][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:29.180][ef$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:29.180][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-06-29 16:02:29.181][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-06-29 16:02:29.182][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:29.183][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:29.190][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-29 16:02:29.191][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-29 16:02:29.192][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:29.193][ef$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:29.196][ef$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-06-29 16:02:29.197][ef$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-06-29 16:02:29.198][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:29.199][ef$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:29.203][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-29 16:02:29.204][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-29 16:02:29.205][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:29.205][ef$get] fields variable is a list.
biodb.INFO [2024-06-29 16:02:29.212][biodb::testThat]
biodb.INFO [2024-06-29 16:02:29.213][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2024-06-29 16:02:29.213][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-29 16:02:29.214][biodb::testThat]
biodb.DEBUG[2024-06-29 16:02:29.216][private$loadEntries] Creating entries from ids [2]: "1.1.1.1, 1.1.1.54".
biodb.DEBUG[2024-06-29 16:02:29.223][conn$getEntryContent] Get Expasy ENZYME database. entry content(s) for 2 id(s)...
biodb.TRACE[2024-06-29 16:02:29.227][cch$loadFileContent] Trying to load 2 files from cache: [2]: "1.1.1.1, 1.1.1.54".
biodb.INFO [2024-06-29 16:02:29.228][self$getFolderPath] Create cache folder "/home/biocbuild/.cache/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280" for "expasy.enzyme-b59b84d962b6741050ba8f70ff4db280".
biodb.TRACE[2024-06-29 16:02:29.229][cch$loadFileContent] file.exist = [2]: "FALSE, FALSE".
biodb.TRACE[2024-06-29 16:02:29.230][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-06-29 16:02:29.231][conn$getEntryContent] 0 Expasy ENZYME database. entry content(s) loaded from cache.
biodb.DEBUG[2024-06-29 16:02:29.232][conn$getEntryContent] 2 entry content(s) need to be fetched from Expasy ENZYME database. database "https://enzyme.expasy.org/".
biodb.DEBUG[2024-06-29 16:02:29.233][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-06-29 16:02:29.234][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-06-29 16:02:29.239][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-29 16:02:29.240][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-29 16:02:29.240][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-29 16:02:29.244][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:02:29.245][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:02:29.246][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:02:29.247][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:02:29.248][scheduler$sendRequest] Getting content of get URL request "https://enzyme.expasy.org/EC/1.1.1.1.txt".
biodb.DEBUG[2024-06-29 16:02:29.266][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-29 16:02:29.267][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-29 16:02:29.272][private$doSendRequestOnce] Sent URL is "https://enzyme.expasy.org/EC/1.1.1.1.txt".
biodb.TRACE[2024-06-29 16:02:30.092][getRCurlRequestResult] Using RCurl package for sending request (https://enzyme.expasy.org/EC/1.1.1.1.txt).
biodb.DEBUG[2024-06-29 16:02:30.561][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-06-29 16:02:30.564][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280/a52675cfd2f0c2b41556caa64d9341e3.content"
biodb.TRACE[2024-06-29 16:02:30.577][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280/a52675cfd2f0c2b41556caa64d9341e3.request"
biodb.DEBUG[2024-06-29 16:02:30.578][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-29 16:02:30.579][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-29 16:02:30.580][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-29 16:02:30.584][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:02:30.585][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:02:30.586][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:02:30.586][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:02:30.605][scheduler$sendRequest] Getting content of get URL request "https://enzyme.expasy.org/EC/1.1.1.54.txt".
biodb.DEBUG[2024-06-29 16:02:30.619][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-29 16:02:30.620][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-29 16:02:30.634][private$doSendRequestOnce] Sent URL is "https://enzyme.expasy.org/EC/1.1.1.54.txt".
biodb.TRACE[2024-06-29 16:02:31.065][getRCurlRequestResult] Using RCurl package for sending request (https://enzyme.expasy.org/EC/1.1.1.54.txt).
biodb.DEBUG[2024-06-29 16:02:31.485][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-06-29 16:02:31.487][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280/a9b93566a091cbe35a06e4b3871f95c9.content"
biodb.TRACE[2024-06-29 16:02:31.490][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280/a9b93566a091cbe35a06e4b3871f95c9.request"
biodb.TRACE[2024-06-29 16:02:31.492][private$doSaveContentToFile] Saving to cache [2]: "/home/biocbuild/.cache/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280/1.1.1.1.txt, /home/biocbuild/.cache/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280/1.1.1.54.txt"
biodb.DEBUG[2024-06-29 16:02:31.493][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-06-29 16:02:31.494][self$createEntryFromContent] Creating Expasy ENZYME database. entries from 2 content(s).
biodb.DEBUG[2024-06-29 16:02:31.496][self$createEntryFromContent] Parsing 2 Expasy ENZYME database. entries.
biodb.DEBUG[2024-06-29 16:02:31.497][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-29 16:02:31.498][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-29 16:02:31.499][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-29 16:02:31.503][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:02:31.503][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:02:31.504][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:02:31.505][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-29 16:02:31.507][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-29 16:02:31.508][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-29 16:02:31.509][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:31.510][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:31.511][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-06-29 16:02:31.512][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-06-29 16:02:31.513][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:31.514][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:31.515][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-29 16:02:31.516][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-29 16:02:31.517][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:31.518][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:31.519][self$getBiodb()$getEntryFields()$get] Asked field names are: COFACTOR.
biodb.TRACE[2024-06-29 16:02:31.520][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-06-29 16:02:31.520][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:31.521][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:31.522][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-29 16:02:31.523][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-29 16:02:31.524][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:31.525][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:31.526][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-29 16:02:31.527][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-29 16:02:31.528][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:31.528][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:31.529][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-29 16:02:31.530][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-29 16:02:31.531][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:31.532][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:31.533][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-29 16:02:31.534][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-29 16:02:31.535][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:31.535][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:31.536][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-29 16:02:31.537][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-29 16:02:31.538][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:31.539][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:31.540][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-06-29 16:02:31.541][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-06-29 16:02:31.542][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:31.543][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:31.543][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-06-29 16:02:31.544][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-06-29 16:02:31.545][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:31.546][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:31.547][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-29 16:02:31.548][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-29 16:02:31.549][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:31.549][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:31.550][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-06-29 16:02:31.551][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-06-29 16:02:31.552][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:31.553][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:31.554][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-29 16:02:31.555][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-29 16:02:31.556][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:31.557][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:31.557][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-29 16:02:31.558][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-29 16:02:31.559][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:31.560][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:31.561][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-29 16:02:31.562][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-29 16:02:31.563][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:31.564][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-29 16:02:31.565][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-29 16:02:31.565][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-29 16:02:31.566][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-29 16:02:31.570][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:02:31.571][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:02:31.572][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:02:31.573][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-29 16:02:31.574][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-29 16:02:31.575][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-29 16:02:31.576][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:31.577][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:31.578][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-06-29 16:02:31.579][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-06-29 16:02:31.580][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:31.581][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:31.582][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-29 16:02:31.583][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-29 16:02:31.584][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:31.584][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:31.585][self$getBiodb()$getEntryFields()$get] Asked field names are: COFACTOR.
biodb.TRACE[2024-06-29 16:02:31.586][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-06-29 16:02:31.587][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:31.588][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:31.589][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-06-29 16:02:31.590][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-06-29 16:02:31.591][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:31.592][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:31.593][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-06-29 16:02:31.594][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-06-29 16:02:31.594][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:31.595][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:31.596][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-29 16:02:31.597][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-29 16:02:31.598][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:31.599][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:31.600][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-06-29 16:02:31.601][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-06-29 16:02:31.601][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:31.602][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:31.603][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-29 16:02:31.604][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-29 16:02:31.605][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:31.606][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:31.607][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-29 16:02:31.608][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-29 16:02:31.608][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:31.609][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:31.610][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-29 16:02:31.611][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-29 16:02:31.612][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:31.613][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:31.614][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-29 16:02:31.615][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-29 16:02:31.616][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:31.616][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:31.617][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-29 16:02:31.618][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-29 16:02:31.619][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:31.620][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:31.621][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-29 16:02:31.622][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-29 16:02:31.623][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:31.623][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:31.624][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-29 16:02:31.625][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-29 16:02:31.626][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:31.627][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:31.628][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-29 16:02:31.629][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-29 16:02:31.630][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:31.630][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:31.631][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-29 16:02:31.632][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-29 16:02:31.633][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:31.634][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-29 16:02:31.635][self$createEntryFromContent] Accession numbers: 1.1.1.1, 1.1.1.54.
biodb.TRACE[2024-06-29 16:02:31.636][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2024-06-29 16:02:31.637][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2024-06-29 16:02:31.638][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:31.638][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:31.639][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2024-06-29 16:02:31.640][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2024-06-29 16:02:31.641][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:31.642][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:31.643][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2024-06-29 16:02:31.644][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2024-06-29 16:02:31.645][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:31.646][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:31.650][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2024-06-29 16:02:31.651][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2024-06-29 16:02:31.655][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:31.658][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:31.658][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2024-06-29 16:02:31.659][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2024-06-29 16:02:31.660][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:31.661][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:31.662][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2024-06-29 16:02:31.663][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2024-06-29 16:02:31.664][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:31.665][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-06-29 16:02:31.671][biodb::testThat]
biodb.INFO [2024-06-29 16:02:31.672][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2024-06-29 16:02:31.673][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-29 16:02:31.674][biodb::testThat]
biodb.TRACE[2024-06-29 16:02:31.676][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-29 16:02:31.677][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-29 16:02:31.678][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:31.679][ef$get] fields variable is a list.
biodb.DEBUG[2024-06-29 16:02:31.680][function(conn, opt)] Testing searchForEntries() with entry "1.1.1.1" and field "name".
biodb.TRACE[2024-06-29 16:02:31.701][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-29 16:02:31.702][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-29 16:02:31.703][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:31.704][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:31.705][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-29 16:02:31.706][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-29 16:02:31.707][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:31.708][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:31.709][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-29 16:02:31.710][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-29 16:02:31.710][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:31.711][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-29 16:02:31.714][function(conn, opt)] With value "alcohol dehydrogenase".
biodb.DEBUG[2024-06-29 16:02:31.716][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://enzyme.expasy.org/enzyme-byname.html?alcohol dehydrogenase".
biodb.DEBUG[2024-06-29 16:02:31.719][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-29 16:02:31.720][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-29 16:02:31.721][private$doSendRequestOnce] Sent URL is "https://enzyme.expasy.org/enzyme-byname.html?alcohol%20dehydrogenase".
biodb.TRACE[2024-06-29 16:02:32.170][getRCurlRequestResult] Using RCurl package for sending request (https://enzyme.expasy.org/enzyme-byname.html?alcohol%20dehydrogenase).
biodb.DEBUG[2024-06-29 16:02:32.621][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-06-29 16:02:32.624][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280/f603fa2a57aec59588edc37541c6f6d5.content"
biodb.TRACE[2024-06-29 16:02:32.628][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280/f603fa2a57aec59588edc37541c6f6d5.request"
biodb.DEBUG[2024-06-29 16:02:32.636][function(conn, opt)] With found IDs [1]: "1.1.1.1".
biodb.INFO [2024-06-29 16:02:32.650][biodb::testThat]
biodb.INFO [2024-06-29 16:02:32.651][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2024-06-29 16:02:32.652][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-29 16:02:32.653][biodb::testThat]
biodb.TRACE[2024-06-29 16:02:32.677][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-29 16:02:32.678][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-29 16:02:32.679][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:32.680][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:32.681][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-29 16:02:32.682][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-29 16:02:32.683][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:32.684][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:32.685][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-29 16:02:32.686][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-29 16:02:32.687][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:32.688][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-29 16:02:32.716][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://enzyme.expasy.org/enzyme-byname.html?alcohol dehydrogenase".
biodb.DEBUG[2024-06-29 16:02:32.718][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-06-29 16:02:32.749][cch$loadFileContent] Trying to load 1 files from cache: [1]: "f603fa2a57aec59588edc37541c6f6d5".
biodb.TRACE[2024-06-29 16:02:32.750][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-06-29 16:02:32.752][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280/f603fa2a57aec59588edc37541c6f6d5.content".
biodb.INFO [2024-06-29 16:02:32.767][biodb::testThat]
biodb.INFO [2024-06-29 16:02:32.768][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2024-06-29 16:02:32.769][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-29 16:02:32.770][biodb::testThat]
biodb.TRACE[2024-06-29 16:02:32.779][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-06-29 16:02:32.780][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-06-29 16:02:32.781][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:32.782][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:32.783][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-06-29 16:02:32.784][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-06-29 16:02:32.785][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:32.786][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:32.787][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-06-29 16:02:32.788][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-06-29 16:02:32.789][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:32.790][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:32.791][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-06-29 16:02:32.792][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-06-29 16:02:32.793][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:32.794][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:32.825][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-06-29 16:02:32.826][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-06-29 16:02:32.827][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:32.828][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:32.829][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-06-29 16:02:32.830][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-06-29 16:02:32.831][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:32.831][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:32.832][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-06-29 16:02:32.833][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-06-29 16:02:32.834][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:32.835][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:32.836][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-06-29 16:02:32.837][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-06-29 16:02:32.838][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:32.838][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-06-29 16:02:32.843][biodb::testThat]
biodb.INFO [2024-06-29 16:02:32.844][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2024-06-29 16:02:32.845][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-29 16:02:32.846][biodb::testThat]
biodb.INFO [2024-06-29 16:02:32.853][biodb::testThat]
biodb.INFO [2024-06-29 16:02:32.854][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2024-06-29 16:02:32.855][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-29 16:02:32.856][biodb::testThat]
biodb.INFO [2024-06-29 16:02:32.862][biodb::testThat]
biodb.INFO [2024-06-29 16:02:32.863][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2024-06-29 16:02:32.864][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-29 16:02:32.865][biodb::testThat]
biodb.DEBUG[2024-06-29 16:02:32.877][function(conn, opt)] Trying to download "https://enzyme.expasy.org/cgi-bin/enzyme/enzyme-search-ec?field1=1&field2=1&field3=1&field4=1".
biodb.DEBUG[2024-06-29 16:02:33.318][getUrlContent] Use RCurl for downloading content of URL https://enzyme.expasy.org/cgi-bin/enzyme/enzyme-search-ec?field1=1&field2=1&field3=1&field4=1.
biodb.INFO [2024-06-29 16:02:33.765][biodb::testThat]
biodb.INFO [2024-06-29 16:02:33.766][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2024-06-29 16:02:33.767][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-29 16:02:33.768][biodb::testThat]
biodb.DEBUG[2024-06-29 16:02:34.203][getUrlContent] Use base::url() for downloading content of URL https://enzyme.expasy.org/images/1.1.1.1/image.png.
biodb.TRACE[2024-06-29 16:02:35.040][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-29 16:02:35.042][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-29 16:02:35.044][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:35.045][ef$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:35.047][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-29 16:02:35.049][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-29 16:02:35.050][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:35.052][ef$get] fields variable is a list.
biodb.INFO [2024-06-29 16:02:35.053][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-06-29 16:02:35.055][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector expasy.enzyme from the request scheduler
biodb.INFO [2024-06-29 16:02:35.056][self$deleteConn] Connector "expasy.enzyme" deleted.
biodb.DEBUG[2024-06-29 16:02:35.058][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-06-29 16:02:35.059][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-29 16:02:35.060][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-29 16:02:35.061][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:02:35.062][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:02:35.063][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:02:35.064][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2024-06-29 16:02:35.075][biodb::testContext]
biodb.INFO [2024-06-29 16:02:35.076][biodb::testContext] ********************************************************************************
biodb.INFO [2024-06-29 16:02:35.076][biodb::testContext] Test context - Example long tests
biodb.INFO [2024-06-29 16:02:35.077][biodb::testContext] ********************************************************************************
biodb.INFO [2024-06-29 16:02:35.078][biodb::testContext]
biodb.INFO [2024-06-29 16:02:35.080][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.13.0.
biodb.DEBUG[2024-06-29 16:02:35.082][self$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.20-bioc/R/site-library/biodb/definitions.yml".
biodb.DEBUG[2024-06-29 16:02:35.086][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-06-29 16:02:35.087][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-06-29 16:02:35.088][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-06-29 16:02:35.088][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:02:35.089][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:02:35.090][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[2024-06-29 16:02:35.091][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-06-29 16:02:35.092][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-06-29 16:02:35.093][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:02:35.093][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:02:35.094][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:02:35.095][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-06-29 16:02:35.096][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-06-29 16:02:35.097][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:02:35.098][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:02:35.098][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[2024-06-29 16:02:35.099][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-06-29 16:02:35.100][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-06-29 16:02:35.101][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-06-29 16:02:35.102][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:02:35.103][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:02:35.104][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:02:35.104][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-06-29 16:02:35.105][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-06-29 16:02:35.106][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-06-29 16:02:35.107][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:02:35.108][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:02:35.109][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:02:35.109][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-06-29 16:02:35.110][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-06-29 16:02:35.111][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:02:35.112][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:02:35.113][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:02:35.114][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-06-29 16:02:35.115][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-06-29 16:02:35.116][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-06-29 16:02:35.116][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:02:35.117][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:02:35.118][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:02:35.119][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-06-29 16:02:35.120][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-06-29 16:02:35.120][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:02:35.121][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:02:35.122][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:02:35.123][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-06-29 16:02:35.124][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-06-29 16:02:35.125][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-06-29 16:02:35.126][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:02:35.126][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:02:35.127][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:02:35.128][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-06-29 16:02:35.129][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-06-29 16:02:35.130][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-06-29 16:02:35.131][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-06-29 16:02:35.132][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-06-29 16:02:35.133][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-06-29 16:02:35.133][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:02:35.134][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:02:35.135][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:02:35.136][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-06-29 16:02:35.137][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-06-29 16:02:35.138][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:02:35.138][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:02:35.139][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:02:35.140][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-06-29 16:02:35.141][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-06-29 16:02:35.142][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:02:35.143][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:02:35.143][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:02:35.144][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-06-29 16:02:35.145][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-06-29 16:02:35.146][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:02:35.147][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:02:35.147][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:02:35.148][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-06-29 16:02:35.149][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-06-29 16:02:35.150][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:02:35.151][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:02:35.152][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:02:35.153][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-06-29 16:02:35.153][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-06-29 16:02:35.154][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:02:35.155][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:02:35.156][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:02:35.157][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-06-29 16:02:35.158][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-06-29 16:02:35.161][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-06-29 16:02:35.162][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:02:35.163][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:02:35.164][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:02:35.165][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-06-29 16:02:35.166][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-06-29 16:02:35.167][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-06-29 16:02:35.167][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:02:35.168][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:02:35.169][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:02:35.170][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-06-29 16:02:35.172][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-06-29 16:02:35.173][self$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[2024-06-29 16:02:35.173][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-29 16:02:35.174][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-29 16:02:35.175][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-29 16:02:35.176][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-29 16:02:35.177][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-29 16:02:35.178][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-29 16:02:35.179][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-06-29 16:02:35.180][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-29 16:02:35.181][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-06-29 16:02:35.182][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-06-29 16:02:35.182][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-29 16:02:35.183][self$setPropertyValue]
biodb.DEBUG[2024-06-29 16:02:35.184][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-29 16:02:35.185][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-06-29 16:02:35.185][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-06-29 16:02:35.185][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-06-29 16:02:35.185][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-06-29 16:02:35.185][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-06-29 16:02:35.186][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-29 16:02:35.187][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-29 16:02:35.188][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-29 16:02:35.189][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-29 16:02:35.190][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-29 16:02:35.190][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-29 16:02:35.191][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-29 16:02:35.192][self$setPropertyValue]
biodb.DEBUG[2024-06-29 16:02:35.193][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-29 16:02:35.194][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-29 16:02:35.195][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-29 16:02:35.195][self$setPropertyValue]
biodb.DEBUG[2024-06-29 16:02:35.197][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-06-29 16:02:35.198][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-06-29 16:02:35.199][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-06-29 16:02:35.200][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-29 16:02:35.201][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-29 16:02:35.202][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-29 16:02:35.203][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-29 16:02:35.204][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-29 16:02:35.205][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-29 16:02:35.205][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-06-29 16:02:35.206][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-29 16:02:35.207][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-06-29 16:02:35.208][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-06-29 16:02:35.209][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-29 16:02:35.210][self$setPropertyValue]
biodb.DEBUG[2024-06-29 16:02:35.211][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-29 16:02:35.212][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-06-29 16:02:35.212][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-06-29 16:02:35.212][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-06-29 16:02:35.212][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-06-29 16:02:35.212][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-06-29 16:02:35.218][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-29 16:02:35.219][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-29 16:02:35.219][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-29 16:02:35.220][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-29 16:02:35.221][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-29 16:02:35.222][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-29 16:02:35.223][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-29 16:02:35.224][self$setPropertyValue]
biodb.DEBUG[2024-06-29 16:02:35.225][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-29 16:02:35.225][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-29 16:02:35.226][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-29 16:02:35.227][self$setPropertyValue]
biodb.DEBUG[2024-06-29 16:02:35.228][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-06-29 16:02:35.230][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-06-29 16:02:35.231][self$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[2024-06-29 16:02:35.232][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-29 16:02:35.233][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-29 16:02:35.234][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-29 16:02:35.234][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-29 16:02:35.235][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-29 16:02:35.236][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-29 16:02:35.237][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-06-29 16:02:35.238][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-29 16:02:35.239][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-06-29 16:02:35.240][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-06-29 16:02:35.241][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-29 16:02:35.242][self$setPropertyValue]
biodb.DEBUG[2024-06-29 16:02:35.243][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-29 16:02:35.243][self$setPropertyValue]
biodb.DEBUG[2024-06-29 16:02:35.244][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-29 16:02:35.245][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-29 16:02:35.246][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-29 16:02:35.247][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-29 16:02:35.248][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-29 16:02:35.249][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-29 16:02:35.249][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-29 16:02:35.250][self$setPropertyValue]
biodb.DEBUG[2024-06-29 16:02:35.251][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-29 16:02:35.252][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-29 16:02:35.253][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-29 16:02:35.254][self$setPropertyValue]
biodb.DEBUG[2024-06-29 16:02:35.255][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-06-29 16:02:35.256][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-06-29 16:02:35.257][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-06-29 16:02:35.258][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-29 16:02:35.259][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-29 16:02:35.260][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-29 16:02:35.261][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-29 16:02:35.262][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-29 16:02:35.263][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-29 16:02:35.264][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-06-29 16:02:35.264][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-29 16:02:35.265][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-06-29 16:02:35.266][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-06-29 16:02:35.267][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-29 16:02:35.268][self$setPropertyValue]
biodb.DEBUG[2024-06-29 16:02:35.269][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-29 16:02:35.270][self$setPropertyValue]
biodb.DEBUG[2024-06-29 16:02:35.271][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-29 16:02:35.272][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-29 16:02:35.272][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-29 16:02:35.273][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-29 16:02:35.274][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-29 16:02:35.275][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-29 16:02:35.276][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-29 16:02:35.277][self$setPropertyValue]
biodb.DEBUG[2024-06-29 16:02:35.277][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-29 16:02:35.278][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-29 16:02:35.279][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-29 16:02:35.280][self$setPropertyValue]
biodb.DEBUG[2024-06-29 16:02:35.281][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-06-29 16:02:35.282][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:02:35.283][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:02:35.283][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:02:35.284][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:02:35.285][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:02:35.286][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:02:35.287][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:02:35.287][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:02:35.288][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:02:35.289][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:02:35.290][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:02:35.291][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:02:35.291][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:02:35.292][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:02:35.293][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:02:35.294][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:02:35.295][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:02:35.295][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:02:35.296][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:02:35.297][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:02:35.298][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:02:35.298][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:02:35.299][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:02:35.300][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:02:35.301][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:02:35.302][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:02:35.302][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:02:35.303][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:02:35.304][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:02:35.305][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:02:35.306][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:02:35.306][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:02:35.307][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:02:35.308][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:02:35.309][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:02:35.309][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:02:35.310][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:02:35.311][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:02:35.312][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:02:35.313][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:02:35.313][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:02:35.314][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:02:35.315][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:02:35.316][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:02:35.317][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:02:35.317][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:02:35.318][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:02:35.319][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:02:35.320][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:02:35.321][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:02:35.321][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:02:35.322][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:02:35.323][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:02:35.324][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:02:35.325][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:02:35.325][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:02:35.326][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:02:35.327][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:02:35.328][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:02:35.328][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:02:35.329][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:02:35.330][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:02:35.331][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:02:35.332][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:02:35.332][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:02:35.333][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:02:35.334][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:02:35.335][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:02:35.336][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:02:35.336][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:02:35.337][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:02:35.338][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:02:35.339][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:02:35.339][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:02:35.340][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:02:35.341][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:02:35.342][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:02:35.343][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:02:35.343][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:02:35.344][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:02:35.345][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:02:35.346][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:02:35.347][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:02:35.347][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:02:35.348][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:02:35.349][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:02:35.350][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:02:35.351][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-06-29 16:02:35.352][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-06-29 16:02:35.353][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-06-29 16:02:35.355][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-06-29 16:02:35.356][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-06-29 16:02:35.357][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-06-29 16:02:35.358][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-06-29 16:02:35.359][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-06-29 16:02:35.361][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-06-29 16:02:35.362][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-06-29 16:02:35.363][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-06-29 16:02:35.364][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-06-29 16:02:35.366][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-06-29 16:02:35.367][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-06-29 16:02:35.368][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-06-29 16:02:35.369][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-06-29 16:02:35.371][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-06-29 16:02:35.372][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-06-29 16:02:35.373][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-06-29 16:02:35.378][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-06-29 16:02:35.380][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-06-29 16:02:35.381][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-06-29 16:02:35.382][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-06-29 16:02:35.383][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-06-29 16:02:35.385][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-06-29 16:02:35.386][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-06-29 16:02:35.387][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-06-29 16:02:35.388][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-06-29 16:02:35.390][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-06-29 16:02:35.391][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-06-29 16:02:35.392][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-06-29 16:02:35.393][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-06-29 16:02:35.395][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-06-29 16:02:35.396][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-06-29 16:02:35.397][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-06-29 16:02:35.398][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-06-29 16:02:35.400][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-06-29 16:02:35.401][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-06-29 16:02:35.402][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-06-29 16:02:35.403][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-06-29 16:02:35.404][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-06-29 16:02:35.406][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-06-29 16:02:35.407][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-06-29 16:02:35.408][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-06-29 16:02:35.409][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-06-29 16:02:35.411][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-06-29 16:02:35.412][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-06-29 16:02:35.413][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-06-29 16:02:35.414][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-06-29 16:02:35.416][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-06-29 16:02:35.417][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-06-29 16:02:35.418][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-06-29 16:02:35.419][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-06-29 16:02:35.421][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-06-29 16:02:35.422][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-06-29 16:02:35.423][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-06-29 16:02:35.424][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-06-29 16:02:35.426][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-06-29 16:02:35.427][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-06-29 16:02:35.428][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-06-29 16:02:35.429][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-06-29 16:02:35.430][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-06-29 16:02:35.432][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-06-29 16:02:35.433][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-06-29 16:02:35.434][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-06-29 16:02:35.435][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-06-29 16:02:35.437][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-06-29 16:02:35.438][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-06-29 16:02:35.439][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-06-29 16:02:35.440][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-06-29 16:02:35.442][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-06-29 16:02:35.443][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-06-29 16:02:35.444][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-06-29 16:02:35.445][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-06-29 16:02:35.446][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-06-29 16:02:35.448][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-06-29 16:02:35.449][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-06-29 16:02:35.450][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-06-29 16:02:35.452][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-06-29 16:02:35.453][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-06-29 16:02:35.454][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-06-29 16:02:35.455][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-06-29 16:02:35.456][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-06-29 16:02:35.458][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-06-29 16:02:35.459][initialize] This is biodb version 1.13.0.
biodb.DEBUG[2024-06-29 16:02:35.460][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-06-29 16:02:35.461][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:02:35.462][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:02:35.462][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:02:35.463][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:02:35.464][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:02:35.465][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-29 16:02:35.466][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-29 16:02:35.466][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:02:35.467][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:02:35.471][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:02:35.473][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:02:35.474][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:02:35.474][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-29 16:02:35.475][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-29 16:02:35.476][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:02:35.477][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:02:35.478][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:02:35.479][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:02:35.480][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:02:35.481][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-29 16:02:35.482][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-29 16:02:35.482][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:02:35.483][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:02:35.484][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:02:35.485][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:02:35.486][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:02:35.487][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-29 16:02:35.488][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-29 16:02:35.488][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:02:35.489][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:02:35.490][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:02:35.491][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:02:35.492][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:02:35.493][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-29 16:02:35.494][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-29 16:02:35.495][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:02:35.496][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:02:35.496][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:02:35.497][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:02:35.498][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:02:35.499][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-29 16:02:35.500][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-29 16:02:35.501][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:02:35.502][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:02:35.503][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:02:35.503][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:02:35.504][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:02:35.505][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-29 16:02:35.506][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-29 16:02:35.507][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:02:35.508][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:02:35.509][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:02:35.510][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:02:35.511][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:02:35.511][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-29 16:02:35.512][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-29 16:02:35.513][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:02:35.514][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:02:35.515][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:02:35.516][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:02:35.517][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:02:35.518][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-29 16:02:35.518][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-29 16:02:35.519][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:02:35.520][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:02:35.521][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:02:35.522][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:02:35.523][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:02:35.524][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-29 16:02:35.525][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-29 16:02:35.525][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:02:35.526][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:02:35.527][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:02:35.528][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:02:35.529][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:02:35.530][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-29 16:02:35.531][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-29 16:02:35.532][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:02:35.532][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:02:35.533][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:02:35.534][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:02:35.535][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:02:35.536][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-29 16:02:35.537][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-29 16:02:35.538][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:02:35.539][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:02:35.539][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:02:35.540][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:02:35.541][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:02:35.542][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-29 16:02:35.543][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-29 16:02:35.544][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:02:35.561][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:02:35.562][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:02:35.563][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:02:35.564][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:02:35.564][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-29 16:02:35.565][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-29 16:02:35.566][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:02:35.567][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:02:35.568][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:02:35.569][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:02:35.570][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:02:35.571][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-29 16:02:35.571][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-29 16:02:35.572][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:02:35.573][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:02:35.574][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:02:35.575][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:02:35.576][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:02:35.577][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-29 16:02:35.578][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-29 16:02:35.579][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:02:35.579][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:02:35.580][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:02:35.581][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:02:35.582][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:02:35.583][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-29 16:02:35.584][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-29 16:02:35.585][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:02:35.586][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:02:35.586][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:02:35.587][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[2024-06-29 16:02:35.589][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.20-bioc-longtests/meat/biodbExpasy.Rcheck/biodbExpasy/definitions.yml".
biodb.DEBUG[2024-06-29 16:02:35.590][self$getDbsInfo()$define] Define connector expasy.enzyme.
biodb.DEBUG[2024-06-29 16:02:35.592][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-06-29 16:02:35.593][self$setPropertyValue] Setting property "description" to "Write here the description of this database.".
biodb.DEBUG[2024-06-29 16:02:35.594][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-29 16:02:35.595][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-29 16:02:35.596][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-29 16:02:35.597][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-29 16:02:35.598][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-06-29 16:02:35.599][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-29 16:02:35.600][self$setPropertyValue] Setting property "entry.content.type" to "txt".
biodb.DEBUG[2024-06-29 16:02:35.601][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-29 16:02:35.602][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-06-29 16:02:35.603][self$setPropertyValue] Setting property "name" to "Expasy ENZYME database.".
biodb.DEBUG[2024-06-29 16:02:35.604][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-29 16:02:35.605][self$setPropertyValue] Setting property "parsing.expr" to "^ID\s+([0-9.]+)$".
biodb.DEBUG[2024-06-29 16:02:35.605][self$setPropertyValue] Setting property "parsing.expr" to "^CA\s+(.+?)\.?$".
biodb.DEBUG[2024-06-29 16:02:35.605][self$setPropertyValue] Setting property "parsing.expr" to "^CF\s+(.+?)\.?$".
biodb.DEBUG[2024-06-29 16:02:35.605][self$setPropertyValue] Setting property "parsing.expr" to "^DE\s+(.+?)\.?$".
biodb.DEBUG[2024-06-29 16:02:35.606][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-06-29 16:02:35.607][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-06-29 16:02:35.607][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2024-06-29 16:02:35.608][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-29 16:02:35.609][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-29 16:02:35.610][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-29 16:02:35.611][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-29 16:02:35.612][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-29 16:02:35.613][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-29 16:02:35.614][self$setPropertyValue] Setting property "urls" to "https://enzyme.expasy.org/".
biodb.DEBUG[2024-06-29 16:02:35.615][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-29 16:02:35.616][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-29 16:02:35.616][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-06-29 16:02:35.617][self$setPropertyValue]
biodb.DEBUG[2024-06-29 16:02:35.619][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-06-29 16:02:35.622][super$initialize] Initialize connector expasy.enzyme.
biodb.DEBUG[2024-06-29 16:02:35.623][super$initialize] Register connector expasy.enzyme with the request scheduler
biodb.DEBUG[2024-06-29 16:02:35.624][private$bdb$getRequestScheduler()$re ...] Register connector expasy.enzyme.
biodb.DEBUG[2024-06-29 16:02:35.626][private$addConnectorRules] Create new rule for URL "enzyme.expasy.org" of connector "expasy.enzyme".
biodb.DEBUG[2024-06-29 16:02:35.627][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-06-29 16:02:35.628][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-06-29 16:02:35.629][biodb$getFactory()$createConn] Creating new connector expasy.enzyme for database class expasy.enzyme .
biodb.INFO [2024-06-29 16:02:35.630][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-06-29 16:02:35.631][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector expasy.enzyme from the request scheduler
biodb.INFO [2024-06-29 16:02:35.632][self$deleteConn] Connector "expasy.enzyme" deleted.
biodb.DEBUG[2024-06-29 16:02:35.633][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-06-29 16:02:35.633][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-29 16:02:35.634][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-29 16:02:35.635][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:02:35.636][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:02:35.637][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:02:35.638][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
[ FAIL 1 | WARN 0 | SKIP 0 | PASS 85 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test_long_100_generic.R:37:1'): The entry image URL can be downloaded. ──
Error in `charToRaw(content)`: argument must be a character vector of length 1
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb (local) `<fn>`(conn = `<ExpsyEnC>`, opt = `<named list>`)
 3.   └─biodb:::getUrlContent(url, binary = TRUE)
 4.     └─biodb:::getBaseUrlContent(u, binary = binary)
 5.       └─base::charToRaw(content)

[ FAIL 1 | WARN 0 | SKIP 0 | PASS 85 ]
Error: Test failures
Execution halted

'R CMD check' output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --test-dir=longtests --no-stop-on-test-error --no-codoc --no-examples --no-manual --ignore-vignettes --check-subdirs=no biodbExpasy_1.9.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.20-bioc-longtests/meat/biodbExpasy.Rcheck’
* using R version 4.4.0 RC (2024-04-16 r86468)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
    GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* using options ‘--no-codoc --no-examples --no-manual --ignore-vignettes --no-stop-on-test-error’
* checking for file ‘biodbExpasy/DESCRIPTION’ ... OK
* this is package ‘biodbExpasy’ version ‘1.9.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘biodbExpasy’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Title field: should not end in a period.
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... SKIPPED
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... SKIPPED
* checking examples ... SKIPPED
* checking for unstated dependencies in ‘longtests’ ... OK
* checking tests in ‘longtests’ ...
  Running ‘testthat.R’
 ERROR
Running the tests in ‘longtests/testthat.R’ failed.
Last 13 lines of output:
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test_long_100_generic.R:37:1'): The entry image URL can be downloaded. ──
  Error in `charToRaw(content)`: argument must be a character vector of length 1
  Backtrace:
      ▆
   1. ├─base::do.call(fct, params)
   2. └─biodb (local) `<fn>`(conn = `<ExpsyEnC>`, opt = `<named list>`)
   3.   └─biodb:::getUrlContent(url, binary = TRUE)
   4.     └─biodb:::getBaseUrlContent(u, binary = binary)
   5.       └─base::charToRaw(content)
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 85 ]
  Error: Test failures
  Execution halted
* DONE

Status: 1 ERROR, 1 NOTE
See
  ‘/home/biocbuild/bbs-3.20-bioc-longtests/meat/biodbExpasy.Rcheck/00check.log’
for details.

Installation output

biodbExpasy.Rcheck/00install.out

* installing *source* package ‘biodbExpasy’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (biodbExpasy)