Back to Long Tests report for BioC 3.20

This page was generated on 2024-05-18 23:55:03 -0400 (Sat, 18 May 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 RC (2024-04-16 r86468) -- "Puppy Cup" 4666
palomino4Windows Server 2022 Datacenterx644.4.0 RC (2024-04-16 r86468 ucrt) -- "Puppy Cup" 4401
merida1macOS 12.7.4 Montereyx86_644.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" 4428
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: 2024-05-18 09:55:01 -0400 (Sat, 18 May 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  OK  
palomino4Windows Server 2022 Datacenter / x64  OK  
merida1macOS 12.7.4 Monterey / x86_64  OK  

CHECK results for biodbExpasy on merida1


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: /Library/Frameworks/R.framework/Resources/bin/R CMD check --test-dir=longtests --no-stop-on-test-error --no-codoc --no-examples --no-manual --ignore-vignettes --check-subdirs=no biodbExpasy_1.9.0.tar.gz
StartedAt: 2024-05-18 16:02:28 -0400 (Sat, 18 May 2024)
EndedAt: 2024-05-18 16:03:37 -0400 (Sat, 18 May 2024)
EllapsedTime: 69.0 seconds
RetCode: 0
Status:   OK  
CheckDir: biodbExpasy.Rcheck
Warnings: 0

Tests output

biodbExpasy.Rcheck/tests/testthat.Rout


R version 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20

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

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

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

> # Script needed to run testthat automatically from ‘R CMD check’. See
> # testthat::test_dir documentation.
> library(testthat)
> library(biodbExpasy)
> Sys.setenv(TESTTHAT_REPORTER="summary")
> Sys.setenv(BIODB_LOG_DST="console")
> test_check("biodbExpasy")
biodb.INFO [2024-05-18 16:03:24.788][biodb::testContext]
biodb.INFO [2024-05-18 16:03:24.794][biodb::testContext] ********************************************************************************
biodb.INFO [2024-05-18 16:03:24.796][biodb::testContext] Test context - Generic long tests
biodb.INFO [2024-05-18 16:03:24.797][biodb::testContext] ********************************************************************************
biodb.INFO [2024-05-18 16:03:24.799][biodb::testContext]
biodb.INFO [2024-05-18 16:03:24.811][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.13.0.
biodb.DEBUG[2024-05-18 16:03:24.815][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2024-05-18 16:03:24.828][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-05-18 16:03:24.830][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-05-18 16:03:24.831][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-05-18 16:03:24.833][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:03:24.834][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:03:24.836][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-18 16:03:24.838][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-05-18 16:03:24.878][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-05-18 16:03:24.879][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:03:24.881][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:03:24.882][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-18 16:03:24.884][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-05-18 16:03:24.885][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-05-18 16:03:24.887][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:03:24.888][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:03:24.890][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-18 16:03:24.891][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-05-18 16:03:24.893][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-05-18 16:03:24.895][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-05-18 16:03:24.896][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:03:24.898][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:03:24.899][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-18 16:03:24.901][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-05-18 16:03:24.902][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-05-18 16:03:24.917][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-05-18 16:03:24.918][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:03:24.919][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:03:24.920][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-18 16:03:24.922][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-05-18 16:03:24.923][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-05-18 16:03:24.924][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:03:24.926][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:03:24.927][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-18 16:03:24.929][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-05-18 16:03:24.930][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-05-18 16:03:24.932][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-05-18 16:03:24.933][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:03:24.934][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:03:24.935][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-18 16:03:24.936][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-05-18 16:03:24.938][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-05-18 16:03:24.939][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:03:24.940][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:03:24.941][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-18 16:03:24.942][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-05-18 16:03:24.944][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-05-18 16:03:24.945][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-05-18 16:03:24.946][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:03:24.947][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:03:24.948][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-18 16:03:24.950][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-05-18 16:03:24.951][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-05-18 16:03:24.952][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-05-18 16:03:24.954][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-05-18 16:03:24.955][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-05-18 16:03:24.956][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-05-18 16:03:24.958][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:03:24.959][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:03:24.960][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-18 16:03:24.961][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-05-18 16:03:24.963][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-05-18 16:03:24.964][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:03:24.965][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:03:24.966][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-18 16:03:24.967][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-05-18 16:03:24.969][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-05-18 16:03:24.970][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:03:24.971][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:03:24.972][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-18 16:03:24.973][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-05-18 16:03:24.975][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-05-18 16:03:24.976][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:03:24.977][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:03:24.978][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-18 16:03:24.980][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-05-18 16:03:24.981][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-05-18 16:03:24.982][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:03:24.983][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:03:24.985][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-18 16:03:24.986][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-05-18 16:03:24.987][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-05-18 16:03:24.988][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:03:24.990][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:03:24.991][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-18 16:03:24.992][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-05-18 16:03:24.994][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-05-18 16:03:25.005][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-05-18 16:03:25.007][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:03:25.008][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:03:25.009][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-18 16:03:25.010][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-05-18 16:03:25.012][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-05-18 16:03:25.013][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-05-18 16:03:25.015][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:03:25.017][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:03:25.019][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-18 16:03:25.026][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-05-18 16:03:25.083][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-05-18 16:03:25.114][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2024-05-18 16:03:25.116][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-18 16:03:25.117][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-18 16:03:25.119][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-18 16:03:25.120][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-18 16:03:25.122][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-05-18 16:03:25.123][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-18 16:03:25.124][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-05-18 16:03:25.126][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-18 16:03:25.127][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-05-18 16:03:25.128][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-05-18 16:03:25.129][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-18 16:03:25.131][self$setPropertyValue]
biodb.DEBUG[2024-05-18 16:03:25.133][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-05-18 16:03:25.135][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-05-18 16:03:25.135][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-05-18 16:03:25.135][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-05-18 16:03:25.135][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-05-18 16:03:25.135][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-05-18 16:03:25.136][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-05-18 16:03:25.138][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-18 16:03:25.140][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-18 16:03:25.141][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-18 16:03:25.144][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-18 16:03:25.145][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-18 16:03:25.147][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-18 16:03:25.148][self$setPropertyValue]
biodb.DEBUG[2024-05-18 16:03:25.150][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-18 16:03:25.152][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-18 16:03:25.153][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-05-18 16:03:25.154][self$setPropertyValue]
biodb.DEBUG[2024-05-18 16:03:25.156][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-05-18 16:03:25.158][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-05-18 16:03:25.160][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-05-18 16:03:25.161][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-18 16:03:25.162][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-18 16:03:25.164][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-18 16:03:25.165][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-18 16:03:25.166][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-05-18 16:03:25.167][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-18 16:03:25.169][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-05-18 16:03:25.171][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-18 16:03:25.173][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-05-18 16:03:25.175][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-05-18 16:03:25.177][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-18 16:03:25.178][self$setPropertyValue]
biodb.DEBUG[2024-05-18 16:03:25.179][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-05-18 16:03:25.180][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-05-18 16:03:25.180][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-05-18 16:03:25.180][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-05-18 16:03:25.180][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-05-18 16:03:25.180][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-05-18 16:03:25.182][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-05-18 16:03:25.183][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-18 16:03:25.185][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-18 16:03:25.186][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-18 16:03:25.188][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-18 16:03:25.190][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-18 16:03:25.192][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-18 16:03:25.194][self$setPropertyValue]
biodb.DEBUG[2024-05-18 16:03:25.195][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-18 16:03:25.196][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-18 16:03:25.197][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-05-18 16:03:25.199][self$setPropertyValue]
biodb.DEBUG[2024-05-18 16:03:25.200][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-05-18 16:03:25.203][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-05-18 16:03:25.205][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2024-05-18 16:03:25.207][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-18 16:03:25.210][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-18 16:03:25.212][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-18 16:03:25.214][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-18 16:03:25.215][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-05-18 16:03:25.217][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-18 16:03:25.218][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-05-18 16:03:25.219][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-18 16:03:25.221][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-05-18 16:03:25.222][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-05-18 16:03:25.224][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-18 16:03:25.226][self$setPropertyValue]
biodb.DEBUG[2024-05-18 16:03:25.228][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-05-18 16:03:25.234][self$setPropertyValue]
biodb.DEBUG[2024-05-18 16:03:25.236][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-05-18 16:03:25.237][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-18 16:03:25.238][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-18 16:03:25.239][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-18 16:03:25.241][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-18 16:03:25.242][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-18 16:03:25.243][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-18 16:03:25.244][self$setPropertyValue]
biodb.DEBUG[2024-05-18 16:03:25.246][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-18 16:03:25.247][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-18 16:03:25.248][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-05-18 16:03:25.249][self$setPropertyValue]
biodb.DEBUG[2024-05-18 16:03:25.251][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-05-18 16:03:25.255][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-05-18 16:03:25.257][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-05-18 16:03:25.259][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-18 16:03:25.261][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-18 16:03:25.262][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-18 16:03:25.264][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-18 16:03:25.266][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-05-18 16:03:25.267][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-18 16:03:25.268][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-05-18 16:03:25.269][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-18 16:03:25.271][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-05-18 16:03:25.272][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-05-18 16:03:25.273][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-18 16:03:25.275][self$setPropertyValue]
biodb.DEBUG[2024-05-18 16:03:25.276][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-05-18 16:03:25.278][self$setPropertyValue]
biodb.DEBUG[2024-05-18 16:03:25.280][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-05-18 16:03:25.282][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-18 16:03:25.284][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-18 16:03:25.286][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-18 16:03:25.287][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-18 16:03:25.289][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-18 16:03:25.290][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-18 16:03:25.291][self$setPropertyValue]
biodb.DEBUG[2024-05-18 16:03:25.293][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-18 16:03:25.294][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-18 16:03:25.295][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-05-18 16:03:25.296][self$setPropertyValue]
biodb.DEBUG[2024-05-18 16:03:25.301][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-05-18 16:03:25.302][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:03:25.303][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[2024-05-18 16:03:25.304][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:03:25.305][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-18 16:03:25.306][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-18 16:03:25.308][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:03:25.309][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[2024-05-18 16:03:25.310][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:03:25.311][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-18 16:03:25.312][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-18 16:03:25.313][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:03:25.314][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[2024-05-18 16:03:25.316][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:03:25.317][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-18 16:03:25.318][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-18 16:03:25.319][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:03:25.320][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-18 16:03:25.321][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:03:25.322][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-18 16:03:25.324][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-18 16:03:25.325][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:03:25.326][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[2024-05-18 16:03:25.327][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:03:25.328][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-18 16:03:25.330][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-18 16:03:25.331][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:03:25.332][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-18 16:03:25.333][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:03:25.334][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-18 16:03:25.335][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-18 16:03:25.337][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:03:25.338][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[2024-05-18 16:03:25.339][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:03:25.341][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-18 16:03:25.342][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-18 16:03:25.344][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:03:25.345][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-18 16:03:25.346][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:03:25.347][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-18 16:03:25.348][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-18 16:03:25.350][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:03:25.351][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-18 16:03:25.352][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:03:25.353][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-18 16:03:25.354][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-18 16:03:25.355][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:03:25.357][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-18 16:03:25.358][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:03:25.359][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-18 16:03:25.360][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-18 16:03:25.361][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:03:25.363][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-18 16:03:25.364][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:03:25.365][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-18 16:03:25.366][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-18 16:03:25.368][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:03:25.369][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-18 16:03:25.370][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:03:25.371][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-18 16:03:25.372][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-18 16:03:25.374][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:03:25.375][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-18 16:03:25.376][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:03:25.377][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-18 16:03:25.378][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-18 16:03:25.380][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:03:25.381][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-18 16:03:25.382][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:03:25.383][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-18 16:03:25.384][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-18 16:03:25.385][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:03:25.387][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-18 16:03:25.388][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:03:25.389][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-18 16:03:25.391][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-18 16:03:25.393][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:03:25.394][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-18 16:03:25.395][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:03:25.396][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-18 16:03:25.398][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-18 16:03:25.400][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:03:25.402][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-18 16:03:25.404][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:03:25.406][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-18 16:03:25.408][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-18 16:03:25.409][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:03:25.410][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-18 16:03:25.412][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-05-18 16:03:25.419][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-05-18 16:03:25.422][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-05-18 16:03:25.425][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-05-18 16:03:25.428][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-05-18 16:03:25.430][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-05-18 16:03:25.432][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-05-18 16:03:25.435][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-05-18 16:03:25.437][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-05-18 16:03:25.439][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-05-18 16:03:25.442][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-05-18 16:03:25.443][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-05-18 16:03:25.445][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-05-18 16:03:25.447][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-05-18 16:03:25.449][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-05-18 16:03:25.451][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-05-18 16:03:25.453][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-05-18 16:03:25.455][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-05-18 16:03:25.457][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-05-18 16:03:25.459][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-05-18 16:03:25.461][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-05-18 16:03:25.463][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-05-18 16:03:25.467][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-05-18 16:03:25.470][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-05-18 16:03:25.473][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-05-18 16:03:25.475][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-05-18 16:03:25.476][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-05-18 16:03:25.478][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-05-18 16:03:25.480][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-05-18 16:03:25.482][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-05-18 16:03:25.484][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-05-18 16:03:25.486][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-05-18 16:03:25.490][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-05-18 16:03:25.493][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-05-18 16:03:25.496][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-05-18 16:03:25.498][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-05-18 16:03:25.501][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-05-18 16:03:25.504][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-05-18 16:03:25.507][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-05-18 16:03:25.509][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-05-18 16:03:25.511][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-05-18 16:03:25.513][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-05-18 16:03:25.514][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-05-18 16:03:25.516][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-05-18 16:03:25.518][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-05-18 16:03:25.520][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-05-18 16:03:25.522][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-05-18 16:03:25.525][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-05-18 16:03:25.528][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-05-18 16:03:25.536][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-05-18 16:03:25.538][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-05-18 16:03:25.540][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-05-18 16:03:25.542][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-05-18 16:03:25.544][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-05-18 16:03:25.546][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-05-18 16:03:25.548][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-05-18 16:03:25.550][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-05-18 16:03:25.552][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-05-18 16:03:25.553][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-05-18 16:03:25.555][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-05-18 16:03:25.557][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-05-18 16:03:25.559][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-05-18 16:03:25.562][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-05-18 16:03:25.565][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-05-18 16:03:25.567][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-05-18 16:03:25.569][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-05-18 16:03:25.571][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-05-18 16:03:25.573][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-05-18 16:03:25.575][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-05-18 16:03:25.577][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-05-18 16:03:25.579][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-05-18 16:03:25.580][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-05-18 16:03:25.582][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-05-18 16:03:25.584][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-05-18 16:03:25.587][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-05-18 16:03:25.590][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-05-18 16:03:25.593][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-05-18 16:03:25.595][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-05-18 16:03:25.597][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-05-18 16:03:25.599][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-05-18 16:03:25.601][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-05-18 16:03:25.603][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-05-18 16:03:25.605][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-05-18 16:03:25.613][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-05-18 16:03:25.616][initialize] This is biodb version 1.13.0.
biodb.DEBUG[2024-05-18 16:03:25.621][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-05-18 16:03:25.622][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-05-18 16:03:25.623][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-18 16:03:25.624][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:03:25.626][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-18 16:03:25.637][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:03:25.639][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-18 16:03:25.640][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-18 16:03:25.641][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-18 16:03:25.643][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-18 16:03:25.644][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:03:25.645][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-18 16:03:25.646][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:03:25.647][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-18 16:03:25.649][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-18 16:03:25.651][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-18 16:03:25.652][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-18 16:03:25.654][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:03:25.655][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-18 16:03:25.656][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:03:25.657][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-18 16:03:25.659][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-18 16:03:25.660][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-18 16:03:25.661][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-18 16:03:25.663][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:03:25.664][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-18 16:03:25.666][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:03:25.667][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-18 16:03:25.669][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-18 16:03:25.670][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-18 16:03:25.671][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-18 16:03:25.672][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:03:25.674][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-18 16:03:25.675][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:03:25.676][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-18 16:03:25.677][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-18 16:03:25.678][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-18 16:03:25.680][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-18 16:03:25.682][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:03:25.683][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-18 16:03:25.685][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:03:25.686][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-18 16:03:25.688][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-18 16:03:25.689][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-18 16:03:25.690][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-18 16:03:25.692][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:03:25.693][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-18 16:03:25.694][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:03:25.696][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-18 16:03:25.697][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-18 16:03:25.698][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-18 16:03:25.700][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-18 16:03:25.701][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:03:25.703][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-18 16:03:25.704][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:03:25.705][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-18 16:03:25.706][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-18 16:03:25.707][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-18 16:03:25.708][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-18 16:03:25.709][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:03:25.711][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-18 16:03:25.712][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:03:25.713][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-18 16:03:25.714][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-18 16:03:25.715][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-18 16:03:25.717][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-18 16:03:25.718][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:03:25.719][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-18 16:03:25.720][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:03:25.721][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-18 16:03:25.723][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-18 16:03:25.724][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-18 16:03:25.725][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-18 16:03:25.726][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:03:25.728][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-18 16:03:25.730][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:03:25.732][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-18 16:03:25.734][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-18 16:03:25.736][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-18 16:03:25.738][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-18 16:03:25.739][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:03:25.741][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-18 16:03:25.742][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:03:25.744][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-18 16:03:25.747][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-18 16:03:25.748][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-18 16:03:25.750][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-18 16:03:25.752][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:03:25.754][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-18 16:03:25.756][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:03:25.757][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-18 16:03:25.759][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-18 16:03:25.761][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-18 16:03:25.762][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-18 16:03:25.763][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:03:25.765][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-18 16:03:25.767][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:03:25.769][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-18 16:03:25.770][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-18 16:03:25.772][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-18 16:03:25.774][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-18 16:03:25.775][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:03:25.776][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-18 16:03:25.777][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:03:25.779][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-18 16:03:25.780][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-18 16:03:25.781][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-18 16:03:25.783][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-18 16:03:25.784][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:03:25.786][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-18 16:03:25.788][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:03:25.789][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-18 16:03:25.790][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-18 16:03:25.792][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-18 16:03:25.793][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-18 16:03:25.794][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:03:25.795][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-18 16:03:25.796][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:03:25.797][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-18 16:03:25.799][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-18 16:03:25.800][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-18 16:03:25.801][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-18 16:03:25.802][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:03:25.803][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-18 16:03:25.806][biodb$loadDefinitions] Load definitions from file "/Users/biocbuild/bbs-3.20-bioc-longtests/meat/biodbExpasy.Rcheck/biodbExpasy/definitions.yml".
biodb.DEBUG[2024-05-18 16:03:25.819][self$getDbsInfo()$define] Define connector expasy.enzyme.
biodb.DEBUG[2024-05-18 16:03:25.822][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-05-18 16:03:25.823][self$setPropertyValue] Setting property "description" to "Write here the description of this database.".
biodb.DEBUG[2024-05-18 16:03:25.825][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-18 16:03:25.826][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-18 16:03:25.827][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-18 16:03:25.833][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-18 16:03:25.834][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-05-18 16:03:25.836][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-18 16:03:25.837][self$setPropertyValue] Setting property "entry.content.type" to "txt".
biodb.DEBUG[2024-05-18 16:03:25.838][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-18 16:03:25.840][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-05-18 16:03:25.842][self$setPropertyValue] Setting property "name" to "Expasy ENZYME database.".
biodb.DEBUG[2024-05-18 16:03:25.843][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-18 16:03:25.844][self$setPropertyValue] Setting property "parsing.expr" to "^ID\s+([0-9.]+)$".
biodb.DEBUG[2024-05-18 16:03:25.844][self$setPropertyValue] Setting property "parsing.expr" to "^CA\s+(.+?)\.?$".
biodb.DEBUG[2024-05-18 16:03:25.844][self$setPropertyValue] Setting property "parsing.expr" to "^CF\s+(.+?)\.?$".
biodb.DEBUG[2024-05-18 16:03:25.844][self$setPropertyValue] Setting property "parsing.expr" to "^DE\s+(.+?)\.?$".
biodb.DEBUG[2024-05-18 16:03:25.845][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-05-18 16:03:25.847][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-05-18 16:03:25.848][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2024-05-18 16:03:25.849][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-18 16:03:25.850][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-18 16:03:25.852][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-18 16:03:25.853][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-18 16:03:25.854][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-18 16:03:25.855][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-18 16:03:25.856][self$setPropertyValue] Setting property "urls" to "https://enzyme.expasy.org/".
biodb.DEBUG[2024-05-18 16:03:25.858][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-18 16:03:25.859][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-18 16:03:25.860][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-05-18 16:03:25.861][self$setPropertyValue]
biodb.DEBUG[2024-05-18 16:03:25.870][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-05-18 16:03:25.896][super$initialize] Initialize connector expasy.enzyme.
biodb.DEBUG[2024-05-18 16:03:25.898][super$initialize] Register connector expasy.enzyme with the request scheduler
biodb.DEBUG[2024-05-18 16:03:25.904][private$bdb$getRequestScheduler()$re ...] Register connector expasy.enzyme.
biodb.DEBUG[2024-05-18 16:03:25.909][private$addConnectorRules] Create new rule for URL "enzyme.expasy.org" of connector "expasy.enzyme".
biodb.DEBUG[2024-05-18 16:03:25.914][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-05-18 16:03:25.916][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-05-18 16:03:25.918][biodb$getFactory()$createConn] Creating new connector expasy.enzyme for database class expasy.enzyme .
biodb.INFO [2024-05-18 16:03:25.930][biodb::testThat]
biodb.INFO [2024-05-18 16:03:25.931][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2024-05-18 16:03:25.933][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-18 16:03:25.934][biodb::testThat]
biodb.TRACE[2024-05-18 16:03:25.939][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/bbs-3.20-bioc-longtests/meat/biodbExpasy.Rcheck/biodbExpasy/testref/entry-expasy.enzyme-1.1.1.1-content.txt".
biodb.DEBUG[2024-05-18 16:03:25.941][biodb$getFactory()$createEntryFromCo ...] Creating Expasy ENZYME database. entries from 1 content(s).
biodb.DEBUG[2024-05-18 16:03:25.945][biodb$getFactory()$createEntryFromCo ...] Parsing 1 Expasy ENZYME database. entries.
biodb.DEBUG[2024-05-18 16:03:25.958][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-18 16:03:25.960][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-18 16:03:25.961][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-18 16:03:25.984][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-18 16:03:25.985][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-18 16:03:25.986][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:03:25.988][FUN] Functions in observer BiodbConfig: [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[2024-05-18 16:03:26.001][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-18 16:03:26.003][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-18 16:03:26.004][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:03:26.005][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:03:26.050][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-05-18 16:03:26.074][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-05-18 16:03:26.076][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:03:26.077][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:03:26.079][self$getBiodb()$getEntryFields()$get] Asked field names are: cofactor.
biodb.TRACE[2024-05-18 16:03:26.080][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-05-18 16:03:26.082][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:03:26.084][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:03:26.086][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-18 16:03:26.087][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-18 16:03:26.088][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:03:26.090][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:03:26.093][self$getBiodb()$getEntryFields()$get] Asked field names are: COFACTOR.
biodb.TRACE[2024-05-18 16:03:26.095][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-05-18 16:03:26.096][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:03:26.097][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:03:26.099][self$getBiodb()$getEntryFields()$get] Asked field names are: cofactor.
biodb.TRACE[2024-05-18 16:03:26.100][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-05-18 16:03:26.102][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:03:26.103][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:03:26.104][self$getBiodb()$getEntryFields()$get] Asked field names are: cofactor.
biodb.TRACE[2024-05-18 16:03:26.106][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-05-18 16:03:26.107][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:03:26.108][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:03:26.110][self$getBiodb()$getEntryFields()$get] Asked field names are: cofactor.
biodb.TRACE[2024-05-18 16:03:26.111][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-05-18 16:03:26.112][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:03:26.114][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:03:26.115][self$getBiodb()$getEntryFields()$get] Asked field names are: COFACTOR.
biodb.TRACE[2024-05-18 16:03:26.117][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-05-18 16:03:26.118][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:03:26.119][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:03:26.162][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-18 16:03:26.163][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-18 16:03:26.165][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:03:26.166][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:03:26.168][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-18 16:03:26.170][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-18 16:03:26.172][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:03:26.173][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:03:26.231][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-18 16:03:26.233][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-18 16:03:26.234][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:03:26.236][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:03:26.238][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-18 16:03:26.240][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-18 16:03:26.242][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:03:26.243][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:03:26.244][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-18 16:03:26.246][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-18 16:03:26.247][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:03:26.249][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:03:26.251][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-05-18 16:03:26.252][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-05-18 16:03:26.254][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:03:26.255][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:03:26.257][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-05-18 16:03:26.259][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-05-18 16:03:26.261][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:03:26.262][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:03:26.264][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-18 16:03:26.266][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-18 16:03:26.267][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:03:26.269][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:03:26.272][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-05-18 16:03:26.273][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-05-18 16:03:26.275][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:03:26.277][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:03:26.279][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-18 16:03:26.281][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-18 16:03:26.284][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:03:26.285][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:03:26.287][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-18 16:03:26.288][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-18 16:03:26.290][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:03:26.291][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:03:26.292][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-18 16:03:26.294][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-18 16:03:26.296][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:03:26.298][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:03:26.300][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-18 16:03:26.302][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-18 16:03:26.303][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:03:26.304][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:03:26.306][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-18 16:03:26.307][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-18 16:03:26.308][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:03:26.310][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:03:26.311][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-18 16:03:26.313][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-18 16:03:26.314][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:03:26.315][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-18 16:03:26.317][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 1.1.1.1.
biodb.TRACE[2024-05-18 16:03:26.320][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-05-18 16:03:26.322][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-05-18 16:03:26.324][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:03:26.325][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:03:26.327][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-05-18 16:03:26.328][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-05-18 16:03:26.330][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:03:26.331][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:03:26.333][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-05-18 16:03:26.334][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-05-18 16:03:26.336][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:03:26.337][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:03:26.339][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-05-18 16:03:26.340][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-05-18 16:03:26.341][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:03:26.343][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:03:26.362][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-18 16:03:26.364][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-18 16:03:26.365][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:03:26.367][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:03:26.428][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-05-18 16:03:26.430][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-05-18 16:03:26.431][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:03:26.433][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:03:26.440][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-18 16:03:26.442][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-18 16:03:26.444][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:03:26.445][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:03:26.447][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-18 16:03:26.449][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-18 16:03:26.451][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:03:26.453][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:03:26.455][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-18 16:03:26.456][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-18 16:03:26.458][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:03:26.459][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:03:26.462][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-18 16:03:26.464][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-18 16:03:26.466][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:03:26.468][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:03:26.470][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-18 16:03:26.472][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-18 16:03:26.474][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:03:26.475][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:03:26.476][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-18 16:03:26.478][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-18 16:03:26.479][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:03:26.480][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:03:26.482][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-05-18 16:03:26.483][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-05-18 16:03:26.484][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:03:26.485][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:03:26.487][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-05-18 16:03:26.488][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-05-18 16:03:26.490][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:03:26.491][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:03:26.492][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-05-18 16:03:26.494][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-05-18 16:03:26.495][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:03:26.496][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:03:26.507][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-18 16:03:26.509][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-18 16:03:26.510][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:03:26.511][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:03:26.512][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-18 16:03:26.514][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-18 16:03:26.515][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:03:26.516][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:03:26.518][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-18 16:03:26.519][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-18 16:03:26.520][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:03:26.522][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:03:26.523][ef$get] Asked field names are: accession.
biodb.TRACE[2024-05-18 16:03:26.524][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-18 16:03:26.526][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:03:26.527][ef$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:03:26.528][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-18 16:03:26.530][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-18 16:03:26.531][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:03:26.532][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:03:26.544][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-18 16:03:26.546][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-18 16:03:26.547][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:03:26.548][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:03:26.550][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-18 16:03:26.551][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-18 16:03:26.552][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:03:26.554][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:03:26.556][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-18 16:03:26.557][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-18 16:03:26.559][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:03:26.560][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:03:26.561][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-18 16:03:26.563][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-18 16:03:26.565][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:03:26.566][ef$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:03:26.567][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-18 16:03:26.570][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-18 16:03:26.572][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:03:26.573][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:03:26.585][self$getBiodb()$getEntryFields()$get] Asked field names are: cofactor.
biodb.TRACE[2024-05-18 16:03:26.586][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-05-18 16:03:26.588][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:03:26.589][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:03:26.590][self$getBiodb()$getEntryFields()$get] Asked field names are: cofactor.
biodb.TRACE[2024-05-18 16:03:26.592][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-05-18 16:03:26.593][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:03:26.594][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:03:26.596][self$getBiodb()$getEntryFields()$get] Asked field names are: cofactor.
biodb.TRACE[2024-05-18 16:03:26.597][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-05-18 16:03:26.598][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:03:26.600][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:03:26.601][ef$get] Asked field names are: cofactor.
biodb.TRACE[2024-05-18 16:03:26.602][ef$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-05-18 16:03:26.604][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:03:26.606][ef$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:03:26.608][self$getBiodb()$getEntryFields()$get] Asked field names are: cofactor.
biodb.TRACE[2024-05-18 16:03:26.609][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-05-18 16:03:26.610][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:03:26.612][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:03:26.624][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-05-18 16:03:26.626][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-05-18 16:03:26.627][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:03:26.628][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:03:26.629][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-05-18 16:03:26.631][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-05-18 16:03:26.632][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:03:26.633][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:03:26.635][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-05-18 16:03:26.636][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-05-18 16:03:26.637][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:03:26.639][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:03:26.640][ef$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-05-18 16:03:26.642][ef$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-05-18 16:03:26.643][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:03:26.645][ef$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:03:26.646][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-05-18 16:03:26.647][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-05-18 16:03:26.650][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:03:26.652][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:03:26.666][ef$get] Asked field names are: accession.
biodb.TRACE[2024-05-18 16:03:26.673][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-18 16:03:26.675][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:03:26.677][ef$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:03:26.684][ef$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-05-18 16:03:26.686][ef$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-05-18 16:03:26.687][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:03:26.689][ef$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:03:26.698][ef$get] Asked field names are: cofactor.
biodb.TRACE[2024-05-18 16:03:26.700][ef$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-05-18 16:03:26.702][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:03:26.704][ef$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:03:26.711][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-18 16:03:26.714][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-18 16:03:26.715][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:03:26.716][ef$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:03:26.749][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/bbs-3.20-bioc-longtests/meat/biodbExpasy.Rcheck/biodbExpasy/testref/entry-expasy.enzyme-1.1.1.54-content.txt".
biodb.DEBUG[2024-05-18 16:03:26.816][biodb$getFactory()$createEntryFromCo ...] Creating Expasy ENZYME database. entries from 1 content(s).
biodb.DEBUG[2024-05-18 16:03:26.818][biodb$getFactory()$createEntryFromCo ...] Parsing 1 Expasy ENZYME database. entries.
biodb.DEBUG[2024-05-18 16:03:26.822][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-18 16:03:26.823][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-18 16:03:26.825][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-18 16:03:26.832][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-18 16:03:26.834][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-18 16:03:26.835][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:03:26.836][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-18 16:03:26.839][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-18 16:03:26.841][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-18 16:03:26.844][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:03:26.846][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:03:26.847][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-05-18 16:03:26.849][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-05-18 16:03:26.850][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:03:26.851][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:03:26.853][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-18 16:03:26.854][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-18 16:03:26.856][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:03:26.857][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:03:26.858][self$getBiodb()$getEntryFields()$get] Asked field names are: COFACTOR.
biodb.TRACE[2024-05-18 16:03:26.860][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-05-18 16:03:26.861][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:03:26.862][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:03:26.864][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-05-18 16:03:26.865][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-05-18 16:03:26.866][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:03:26.868][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:03:26.869][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-05-18 16:03:26.870][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-05-18 16:03:26.872][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:03:26.873][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:03:26.874][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-18 16:03:26.876][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-18 16:03:26.877][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:03:26.878][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:03:26.880][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-05-18 16:03:26.881][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-05-18 16:03:26.882][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:03:26.883][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:03:26.885][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-18 16:03:26.886][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-18 16:03:26.888][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:03:26.889][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:03:26.890][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-18 16:03:26.892][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-18 16:03:26.893][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:03:26.894][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:03:26.895][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-18 16:03:26.897][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-18 16:03:26.898][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:03:26.899][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:03:26.901][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-18 16:03:26.902][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-18 16:03:26.904][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:03:26.905][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:03:26.906][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-18 16:03:26.907][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-18 16:03:26.909][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:03:26.910][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:03:26.911][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-18 16:03:26.913][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-18 16:03:26.914][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:03:26.915][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-18 16:03:26.917][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 1.1.1.54.
biodb.TRACE[2024-05-18 16:03:26.954][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-05-18 16:03:26.956][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-05-18 16:03:26.957][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:03:26.958][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:03:26.959][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-05-18 16:03:26.961][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-05-18 16:03:26.962][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:03:26.963][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:03:26.965][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-05-18 16:03:26.966][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-05-18 16:03:26.967][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:03:26.969][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:03:26.970][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-05-18 16:03:26.971][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-05-18 16:03:26.973][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:03:26.974][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:03:26.976][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-18 16:03:26.978][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-18 16:03:26.980][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:03:26.981][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:03:26.989][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-05-18 16:03:26.991][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-05-18 16:03:26.993][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:03:26.994][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:03:27.003][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-18 16:03:27.004][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-18 16:03:27.006][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:03:27.007][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:03:27.008][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-18 16:03:27.010][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-18 16:03:27.011][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:03:27.013][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:03:27.015][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-18 16:03:27.017][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-18 16:03:27.019][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:03:27.020][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:03:27.024][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-18 16:03:27.025][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-18 16:03:27.027][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:03:27.028][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:03:27.029][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-18 16:03:27.031][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-18 16:03:27.033][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:03:27.035][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:03:27.037][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-18 16:03:27.039][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-18 16:03:27.041][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:03:27.043][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:03:27.044][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-05-18 16:03:27.046][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-05-18 16:03:27.048][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:03:27.050][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:03:27.051][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-05-18 16:03:27.052][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-05-18 16:03:27.054][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:03:27.055][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:03:27.056][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-05-18 16:03:27.058][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-05-18 16:03:27.059][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:03:27.061][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:03:27.093][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-18 16:03:27.096][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-18 16:03:27.097][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:03:27.099][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:03:27.100][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-18 16:03:27.102][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-18 16:03:27.103][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:03:27.105][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:03:27.107][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-18 16:03:27.109][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-18 16:03:27.111][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:03:27.112][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:03:27.113][ef$get] Asked field names are: accession.
biodb.TRACE[2024-05-18 16:03:27.115][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-18 16:03:27.116][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:03:27.118][ef$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:03:27.119][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-18 16:03:27.121][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-18 16:03:27.122][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:03:27.123][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:03:27.138][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-18 16:03:27.139][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-18 16:03:27.140][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:03:27.142][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:03:27.144][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-18 16:03:27.145][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-18 16:03:27.146][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:03:27.148][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:03:27.151][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-18 16:03:27.154][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-18 16:03:27.155][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:03:27.157][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:03:27.158][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-18 16:03:27.160][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-18 16:03:27.161][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:03:27.162][ef$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:03:27.164][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-18 16:03:27.165][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-18 16:03:27.166][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:03:27.167][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:03:27.184][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-05-18 16:03:27.185][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-05-18 16:03:27.187][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:03:27.188][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:03:27.189][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-05-18 16:03:27.190][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-05-18 16:03:27.192][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:03:27.193][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:03:27.195][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-05-18 16:03:27.196][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-05-18 16:03:27.197][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:03:27.198][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:03:27.200][ef$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-05-18 16:03:27.201][ef$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-05-18 16:03:27.202][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:03:27.203][ef$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:03:27.205][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-05-18 16:03:27.206][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-05-18 16:03:27.207][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:03:27.209][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:03:27.220][ef$get] Asked field names are: accession.
biodb.TRACE[2024-05-18 16:03:27.221][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-18 16:03:27.223][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:03:27.224][ef$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:03:27.230][ef$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-05-18 16:03:27.232][ef$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-05-18 16:03:27.233][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:03:27.234][ef$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:03:27.241][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-18 16:03:27.242][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-18 16:03:27.243][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:03:27.245][ef$get] fields variable is a list.
biodb.INFO [2024-05-18 16:03:27.255][biodb::testThat]
biodb.INFO [2024-05-18 16:03:27.257][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2024-05-18 16:03:27.258][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-18 16:03:27.259][biodb::testThat]
biodb.DEBUG[2024-05-18 16:03:27.262][private$loadEntries] Creating entries from ids [2]: "1.1.1.1, 1.1.1.54".
biodb.DEBUG[2024-05-18 16:03:27.270][conn$getEntryContent] Get Expasy ENZYME database. entry content(s) for 2 id(s)...
biodb.TRACE[2024-05-18 16:03:27.277][cch$loadFileContent] Trying to load 2 files from cache: [2]: "1.1.1.1, 1.1.1.54".
biodb.INFO [2024-05-18 16:03:27.279][self$getFolderPath] Create cache folder "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280" for "expasy.enzyme-b59b84d962b6741050ba8f70ff4db280".
biodb.TRACE[2024-05-18 16:03:27.281][cch$loadFileContent] file.exist = [2]: "FALSE, FALSE".
biodb.TRACE[2024-05-18 16:03:27.282][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-05-18 16:03:27.284][conn$getEntryContent] 0 Expasy ENZYME database. entry content(s) loaded from cache.
biodb.DEBUG[2024-05-18 16:03:27.286][conn$getEntryContent] 2 entry content(s) need to be fetched from Expasy ENZYME database. database "https://enzyme.expasy.org/".
biodb.DEBUG[2024-05-18 16:03:27.289][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-05-18 16:03:27.290][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-05-18 16:03:27.297][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-18 16:03:27.299][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-18 16:03:27.300][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-18 16:03:27.306][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-18 16:03:27.308][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-18 16:03:27.309][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:03:27.310][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-18 16:03:27.312][scheduler$sendRequest] Getting content of get URL request "https://enzyme.expasy.org/EC/1.1.1.1.txt".
biodb.DEBUG[2024-05-18 16:03:27.343][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-18 16:03:27.344][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-18 16:03:27.346][private$doSendRequestOnce] Sent URL is "https://enzyme.expasy.org/EC/1.1.1.1.txt".
biodb.TRACE[2024-05-18 16:03:28.251][getRCurlRequestResult] Using RCurl package for sending request (https://enzyme.expasy.org/EC/1.1.1.1.txt).
biodb.DEBUG[2024-05-18 16:03:28.895][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-05-18 16:03:28.898][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280/a52675cfd2f0c2b41556caa64d9341e3.content"
biodb.TRACE[2024-05-18 16:03:28.919][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280/a52675cfd2f0c2b41556caa64d9341e3.request"
biodb.DEBUG[2024-05-18 16:03:28.921][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-18 16:03:28.922][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-18 16:03:28.923][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-18 16:03:28.930][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-18 16:03:28.931][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-18 16:03:28.932][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:03:28.933][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-18 16:03:28.964][scheduler$sendRequest] Getting content of get URL request "https://enzyme.expasy.org/EC/1.1.1.54.txt".
biodb.DEBUG[2024-05-18 16:03:28.995][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-18 16:03:28.996][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-18 16:03:29.019][private$doSendRequestOnce] Sent URL is "https://enzyme.expasy.org/EC/1.1.1.54.txt".
biodb.TRACE[2024-05-18 16:03:29.674][getRCurlRequestResult] Using RCurl package for sending request (https://enzyme.expasy.org/EC/1.1.1.54.txt).
biodb.DEBUG[2024-05-18 16:03:30.297][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-05-18 16:03:30.300][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280/a9b93566a091cbe35a06e4b3871f95c9.content"
biodb.TRACE[2024-05-18 16:03:30.524][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280/a9b93566a091cbe35a06e4b3871f95c9.request"
biodb.TRACE[2024-05-18 16:03:30.606][private$doSaveContentToFile] Saving to cache [2]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280/1.1.1.1.txt, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280/1.1.1.54.txt"
biodb.DEBUG[2024-05-18 16:03:30.731][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-05-18 16:03:30.733][self$createEntryFromContent] Creating Expasy ENZYME database. entries from 2 content(s).
biodb.DEBUG[2024-05-18 16:03:30.734][self$createEntryFromContent] Parsing 2 Expasy ENZYME database. entries.
biodb.DEBUG[2024-05-18 16:03:30.736][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-18 16:03:30.737][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-18 16:03:30.738][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-18 16:03:30.745][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-18 16:03:30.746][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-18 16:03:30.747][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:03:30.748][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-18 16:03:30.751][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-18 16:03:30.752][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-18 16:03:30.754][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:03:30.755][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:03:30.756][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-05-18 16:03:30.758][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-05-18 16:03:30.759][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:03:30.760][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:03:30.761][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-18 16:03:30.763][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-18 16:03:30.764][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:03:30.765][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:03:30.766][self$getBiodb()$getEntryFields()$get] Asked field names are: COFACTOR.
biodb.TRACE[2024-05-18 16:03:30.768][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-05-18 16:03:30.769][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:03:30.770][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:03:30.771][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-18 16:03:30.773][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-18 16:03:30.774][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:03:30.775][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:03:30.776][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-18 16:03:30.778][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-18 16:03:30.779][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:03:30.780][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:03:30.781][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-18 16:03:30.783][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-18 16:03:30.784][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:03:30.785][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:03:30.786][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-18 16:03:30.787][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-18 16:03:30.789][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:03:30.790][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:03:30.791][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-18 16:03:30.792][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-18 16:03:30.793][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:03:30.795][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:03:30.796][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-05-18 16:03:30.797][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-05-18 16:03:30.798][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:03:30.800][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:03:30.801][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-05-18 16:03:30.802][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-05-18 16:03:30.803][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:03:30.804][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:03:30.806][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-18 16:03:30.807][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-18 16:03:30.808][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:03:30.809][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:03:30.811][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-05-18 16:03:30.812][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-05-18 16:03:30.813][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:03:30.814][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:03:30.816][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-18 16:03:30.817][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-18 16:03:30.818][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:03:30.819][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:03:30.821][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-18 16:03:30.822][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-18 16:03:30.823][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:03:30.824][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:03:30.825][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-18 16:03:30.827][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-18 16:03:30.828][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:03:30.829][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-18 16:03:30.837][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-18 16:03:30.838][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-18 16:03:30.839][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-18 16:03:30.845][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-18 16:03:30.847][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-18 16:03:30.848][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:03:30.849][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-18 16:03:30.851][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-18 16:03:30.853][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-18 16:03:30.854][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:03:30.855][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:03:30.856][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-05-18 16:03:30.858][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-05-18 16:03:30.859][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:03:30.860][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:03:30.862][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-18 16:03:30.863][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-18 16:03:30.864][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:03:30.865][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:03:30.867][self$getBiodb()$getEntryFields()$get] Asked field names are: COFACTOR.
biodb.TRACE[2024-05-18 16:03:30.868][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-05-18 16:03:30.869][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:03:30.870][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:03:30.872][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-05-18 16:03:30.873][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-05-18 16:03:30.874][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:03:30.875][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:03:30.877][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-05-18 16:03:30.878][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-05-18 16:03:30.879][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:03:30.880][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:03:30.881][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-18 16:03:30.883][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-18 16:03:30.884][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:03:30.885][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:03:30.886][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-05-18 16:03:30.888][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-05-18 16:03:30.889][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:03:30.890][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:03:30.891][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-18 16:03:30.893][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-18 16:03:30.894][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:03:30.895][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:03:30.896][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-18 16:03:30.897][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-18 16:03:30.899][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:03:30.900][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:03:30.901][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-18 16:03:30.902][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-18 16:03:30.903][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:03:30.905][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:03:30.906][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-18 16:03:30.907][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-18 16:03:30.909][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:03:30.910][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:03:30.911][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-18 16:03:30.912][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-18 16:03:30.913][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:03:30.915][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:03:30.916][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-18 16:03:30.917][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-18 16:03:30.918][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:03:30.919][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:03:30.921][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-18 16:03:30.922][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-18 16:03:30.923][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:03:30.924][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:03:30.925][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-18 16:03:30.927][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-18 16:03:30.928][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:03:30.929][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:03:30.930][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-18 16:03:30.932][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-18 16:03:30.933][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:03:30.934][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-18 16:03:30.935][self$createEntryFromContent] Accession numbers: 1.1.1.1, 1.1.1.54.
biodb.TRACE[2024-05-18 16:03:30.937][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2024-05-18 16:03:30.938][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2024-05-18 16:03:30.939][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:03:30.940][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:03:30.941][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2024-05-18 16:03:30.943][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2024-05-18 16:03:30.944][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:03:30.945][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:03:30.946][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2024-05-18 16:03:30.948][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2024-05-18 16:03:30.949][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:03:30.950][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:03:30.957][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2024-05-18 16:03:30.958][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2024-05-18 16:03:30.959][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:03:30.961][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:03:30.962][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2024-05-18 16:03:30.963][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2024-05-18 16:03:30.964][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:03:30.965][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:03:30.967][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2024-05-18 16:03:30.968][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2024-05-18 16:03:30.969][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:03:30.970][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-05-18 16:03:30.981][biodb::testThat]
biodb.INFO [2024-05-18 16:03:30.982][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2024-05-18 16:03:30.983][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-18 16:03:30.984][biodb::testThat]
biodb.TRACE[2024-05-18 16:03:30.988][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-18 16:03:30.990][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-18 16:03:30.991][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:03:30.992][ef$get] fields variable is a list.
biodb.DEBUG[2024-05-18 16:03:30.993][function(conn, opt)] Testing searchForEntries() with entry "1.1.1.1" and field "name".
biodb.TRACE[2024-05-18 16:03:31.032][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-18 16:03:31.034][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-18 16:03:31.035][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:03:31.036][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:03:31.038][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-18 16:03:31.039][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-18 16:03:31.040][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:03:31.041][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:03:31.043][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-18 16:03:31.044][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-18 16:03:31.045][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:03:31.046][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-18 16:03:31.051][function(conn, opt)] With value "alcohol dehydrogenase".
biodb.DEBUG[2024-05-18 16:03:31.053][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://enzyme.expasy.org/enzyme-byname.html?alcohol dehydrogenase".
biodb.DEBUG[2024-05-18 16:03:31.057][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-18 16:03:31.058][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-18 16:03:31.059][private$doSendRequestOnce] Sent URL is "https://enzyme.expasy.org/enzyme-byname.html?alcohol%20dehydrogenase".
biodb.TRACE[2024-05-18 16:03:31.763][getRCurlRequestResult] Using RCurl package for sending request (https://enzyme.expasy.org/enzyme-byname.html?alcohol%20dehydrogenase).
biodb.DEBUG[2024-05-18 16:03:32.460][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-05-18 16:03:32.462][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280/f603fa2a57aec59588edc37541c6f6d5.content"
biodb.TRACE[2024-05-18 16:03:32.467][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280/f603fa2a57aec59588edc37541c6f6d5.request"
biodb.DEBUG[2024-05-18 16:03:32.512][function(conn, opt)] With found IDs [1]: "1.1.1.1".
biodb.INFO [2024-05-18 16:03:32.532][biodb::testThat]
biodb.INFO [2024-05-18 16:03:32.533][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2024-05-18 16:03:32.534][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-18 16:03:32.535][biodb::testThat]
biodb.TRACE[2024-05-18 16:03:32.568][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-18 16:03:32.570][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-18 16:03:32.571][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:03:32.572][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:03:32.574][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-18 16:03:32.575][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-18 16:03:32.576][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:03:32.578][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:03:32.579][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-18 16:03:32.580][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-18 16:03:32.581][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:03:32.583][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-18 16:03:32.628][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://enzyme.expasy.org/enzyme-byname.html?alcohol dehydrogenase".
biodb.DEBUG[2024-05-18 16:03:32.632][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-05-18 16:03:32.654][cch$loadFileContent] Trying to load 1 files from cache: [1]: "f603fa2a57aec59588edc37541c6f6d5".
biodb.TRACE[2024-05-18 16:03:32.656][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-05-18 16:03:32.658][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280/f603fa2a57aec59588edc37541c6f6d5.content".
biodb.INFO [2024-05-18 16:03:32.682][biodb::testThat]
biodb.INFO [2024-05-18 16:03:32.683][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2024-05-18 16:03:32.685][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-18 16:03:32.686][biodb::testThat]
biodb.TRACE[2024-05-18 16:03:32.699][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-05-18 16:03:32.701][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-05-18 16:03:32.702][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:03:32.703][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:03:32.704][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-05-18 16:03:32.706][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-05-18 16:03:32.707][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:03:32.709][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:03:32.710][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-05-18 16:03:32.712][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-05-18 16:03:32.713][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:03:32.714][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:03:32.715][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-05-18 16:03:32.717][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-05-18 16:03:32.718][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:03:32.719][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:03:32.774][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-05-18 16:03:32.775][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-05-18 16:03:32.776][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:03:32.778][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:03:32.779][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-05-18 16:03:32.780][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-05-18 16:03:32.781][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:03:32.783][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:03:32.784][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-05-18 16:03:32.785][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-05-18 16:03:32.786][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:03:32.788][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:03:32.789][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-05-18 16:03:32.790][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-05-18 16:03:32.791][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:03:32.793][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-05-18 16:03:33.012][biodb::testThat]
biodb.INFO [2024-05-18 16:03:33.013][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2024-05-18 16:03:33.014][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-18 16:03:33.016][biodb::testThat]
biodb.INFO [2024-05-18 16:03:33.027][biodb::testThat]
biodb.INFO [2024-05-18 16:03:33.029][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2024-05-18 16:03:33.030][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-18 16:03:33.031][biodb::testThat]
biodb.INFO [2024-05-18 16:03:33.041][biodb::testThat]
biodb.INFO [2024-05-18 16:03:33.043][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2024-05-18 16:03:33.044][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-18 16:03:33.045][biodb::testThat]
biodb.DEBUG[2024-05-18 16:03:33.064][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[2024-05-18 16:03:33.724][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 [2024-05-18 16:03:34.440][biodb::testThat]
biodb.INFO [2024-05-18 16:03:34.441][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2024-05-18 16:03:34.442][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-18 16:03:34.443][biodb::testThat]
biodb.DEBUG[2024-05-18 16:03:35.573][getUrlContent] Use RCurl for downloading content of URL https://enzyme.expasy.org/images/1.1.1.1/image.png.
biodb.TRACE[2024-05-18 16:03:35.925][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-18 16:03:35.928][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-18 16:03:35.929][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:03:35.930][ef$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:03:35.932][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-18 16:03:35.933][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-18 16:03:35.934][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:03:35.935][ef$get] fields variable is a list.
biodb.INFO [2024-05-18 16:03:35.937][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-05-18 16:03:35.938][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector expasy.enzyme from the request scheduler
biodb.INFO [2024-05-18 16:03:35.940][self$deleteConn] Connector "expasy.enzyme" deleted.
biodb.DEBUG[2024-05-18 16:03:35.941][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-05-18 16:03:35.942][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-18 16:03:35.943][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-18 16:03:35.944][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-18 16:03:35.945][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-18 16:03:35.946][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:03:35.948][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2024-05-18 16:03:35.960][biodb::testContext]
biodb.INFO [2024-05-18 16:03:35.964][biodb::testContext] ********************************************************************************
biodb.INFO [2024-05-18 16:03:35.965][biodb::testContext] Test context - Example long tests
biodb.INFO [2024-05-18 16:03:35.966][biodb::testContext] ********************************************************************************
biodb.INFO [2024-05-18 16:03:35.967][biodb::testContext]
biodb.INFO [2024-05-18 16:03:35.980][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.13.0.
biodb.DEBUG[2024-05-18 16:03:35.982][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2024-05-18 16:03:35.986][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-05-18 16:03:35.987][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-05-18 16:03:35.988][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-05-18 16:03:35.989][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:03:35.991][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:03:35.992][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-18 16:03:35.997][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-05-18 16:03:35.999][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-05-18 16:03:36.000][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:03:36.001][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:03:36.002][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-18 16:03:36.003][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-05-18 16:03:36.014][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-05-18 16:03:36.016][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:03:36.017][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:03:36.018][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-18 16:03:36.019][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-05-18 16:03:36.025][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-05-18 16:03:36.027][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-05-18 16:03:36.028][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:03:36.029][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:03:36.030][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-18 16:03:36.039][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-05-18 16:03:36.041][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-05-18 16:03:36.042][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-05-18 16:03:36.043][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:03:36.044][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:03:36.046][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-18 16:03:36.047][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-05-18 16:03:36.048][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-05-18 16:03:36.049][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:03:36.050][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:03:36.052][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-18 16:03:36.053][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-05-18 16:03:36.054][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-05-18 16:03:36.055][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-05-18 16:03:36.056][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:03:36.058][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:03:36.059][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-18 16:03:36.060][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-05-18 16:03:36.061][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-05-18 16:03:36.062][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:03:36.063][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:03:36.065][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-18 16:03:36.066][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-05-18 16:03:36.067][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-05-18 16:03:36.068][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-05-18 16:03:36.069][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:03:36.071][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:03:36.072][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-18 16:03:36.073][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-05-18 16:03:36.074][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-05-18 16:03:36.075][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-05-18 16:03:36.077][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-05-18 16:03:36.078][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-05-18 16:03:36.079][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-05-18 16:03:36.080][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:03:36.082][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:03:36.083][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-18 16:03:36.084][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-05-18 16:03:36.085][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-05-18 16:03:36.086][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:03:36.087][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:03:36.089][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-18 16:03:36.090][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-05-18 16:03:36.091][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-05-18 16:03:36.092][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:03:36.093][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:03:36.094][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-18 16:03:36.096][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-05-18 16:03:36.097][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-05-18 16:03:36.098][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:03:36.099][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:03:36.100][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-18 16:03:36.101][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-05-18 16:03:36.103][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-05-18 16:03:36.104][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:03:36.105][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:03:36.106][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-18 16:03:36.107][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-05-18 16:03:36.109][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-05-18 16:03:36.110][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:03:36.111][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:03:36.112][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-18 16:03:36.113][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-05-18 16:03:36.114][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-05-18 16:03:36.125][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-05-18 16:03:36.126][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:03:36.127][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:03:36.128][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-18 16:03:36.129][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-05-18 16:03:36.131][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-05-18 16:03:36.132][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-05-18 16:03:36.133][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:03:36.134][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:03:36.136][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-18 16:03:36.137][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-05-18 16:03:36.139][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-05-18 16:03:36.140][self$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[2024-05-18 16:03:36.142][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-18 16:03:36.143][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-18 16:03:36.144][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-18 16:03:36.145][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-18 16:03:36.147][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-05-18 16:03:36.148][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-18 16:03:36.149][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-05-18 16:03:36.150][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-18 16:03:36.152][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-05-18 16:03:36.153][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-05-18 16:03:36.154][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-18 16:03:36.155][self$setPropertyValue]
biodb.DEBUG[2024-05-18 16:03:36.156][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-05-18 16:03:36.158][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-05-18 16:03:36.158][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-05-18 16:03:36.158][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-05-18 16:03:36.158][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-05-18 16:03:36.158][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-05-18 16:03:36.159][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-05-18 16:03:36.160][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-18 16:03:36.161][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-18 16:03:36.163][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-18 16:03:36.164][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-18 16:03:36.165][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-18 16:03:36.170][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-18 16:03:36.171][self$setPropertyValue]
biodb.DEBUG[2024-05-18 16:03:36.172][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-18 16:03:36.173][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-18 16:03:36.174][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-05-18 16:03:36.176][self$setPropertyValue]
biodb.DEBUG[2024-05-18 16:03:36.177][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-05-18 16:03:36.179][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-05-18 16:03:36.181][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-05-18 16:03:36.182][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-18 16:03:36.183][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-18 16:03:36.184][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-18 16:03:36.185][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-18 16:03:36.187][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-05-18 16:03:36.188][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-18 16:03:36.189][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-05-18 16:03:36.190][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-18 16:03:36.192][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-05-18 16:03:36.193][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-05-18 16:03:36.194][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-18 16:03:36.195][self$setPropertyValue]
biodb.DEBUG[2024-05-18 16:03:36.196][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-05-18 16:03:36.198][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-05-18 16:03:36.198][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-05-18 16:03:36.198][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-05-18 16:03:36.198][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-05-18 16:03:36.198][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-05-18 16:03:36.199][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-05-18 16:03:36.200][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-18 16:03:36.201][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-18 16:03:36.202][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-18 16:03:36.204][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-18 16:03:36.205][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-18 16:03:36.206][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-18 16:03:36.207][self$setPropertyValue]
biodb.DEBUG[2024-05-18 16:03:36.208][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-18 16:03:36.209][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-18 16:03:36.211][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-05-18 16:03:36.212][self$setPropertyValue]
biodb.DEBUG[2024-05-18 16:03:36.213][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-05-18 16:03:36.216][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-05-18 16:03:36.217][self$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[2024-05-18 16:03:36.218][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-18 16:03:36.219][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-18 16:03:36.221][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-18 16:03:36.222][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-18 16:03:36.223][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-05-18 16:03:36.224][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-18 16:03:36.225][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-05-18 16:03:36.227][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-18 16:03:36.228][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-05-18 16:03:36.229][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-05-18 16:03:36.230][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-18 16:03:36.232][self$setPropertyValue]
biodb.DEBUG[2024-05-18 16:03:36.233][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-05-18 16:03:36.234][self$setPropertyValue]
biodb.DEBUG[2024-05-18 16:03:36.235][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-05-18 16:03:36.237][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-18 16:03:36.238][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-18 16:03:36.239][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-18 16:03:36.240][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-18 16:03:36.241][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-18 16:03:36.243][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-18 16:03:36.244][self$setPropertyValue]
biodb.DEBUG[2024-05-18 16:03:36.245][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-18 16:03:36.246][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-18 16:03:36.247][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-05-18 16:03:36.249][self$setPropertyValue]
biodb.DEBUG[2024-05-18 16:03:36.250][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-05-18 16:03:36.252][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-05-18 16:03:36.253][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-05-18 16:03:36.255][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-18 16:03:36.256][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-18 16:03:36.257][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-18 16:03:36.259][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-18 16:03:36.260][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-05-18 16:03:36.261][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-18 16:03:36.262][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-05-18 16:03:36.264][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-18 16:03:36.265][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-05-18 16:03:36.266][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-05-18 16:03:36.267][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-18 16:03:36.269][self$setPropertyValue]
biodb.DEBUG[2024-05-18 16:03:36.270][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-05-18 16:03:36.271][self$setPropertyValue]
biodb.DEBUG[2024-05-18 16:03:36.272][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-05-18 16:03:36.274][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-18 16:03:36.275][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-18 16:03:36.276][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-18 16:03:36.277][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-18 16:03:36.278][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-18 16:03:36.279][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-18 16:03:36.281][self$setPropertyValue]
biodb.DEBUG[2024-05-18 16:03:36.282][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-18 16:03:36.283][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-18 16:03:36.284][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-05-18 16:03:36.286][self$setPropertyValue]
biodb.DEBUG[2024-05-18 16:03:36.287][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-05-18 16:03:36.288][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:03:36.289][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-18 16:03:36.291][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:03:36.292][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-18 16:03:36.293][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-18 16:03:36.294][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:03:36.295][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[2024-05-18 16:03:36.296][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:03:36.297][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-18 16:03:36.298][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-18 16:03:36.300][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:03:36.301][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-18 16:03:36.302][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:03:36.303][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-18 16:03:36.304][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-18 16:03:36.305][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:03:36.306][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[2024-05-18 16:03:36.308][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:03:36.309][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-18 16:03:36.310][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-18 16:03:36.311][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:03:36.312][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-18 16:03:36.313][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:03:36.314][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-18 16:03:36.315][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-18 16:03:36.317][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:03:36.322][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[2024-05-18 16:03:36.323][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:03:36.324][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-18 16:03:36.325][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-18 16:03:36.326][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:03:36.328][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-18 16:03:36.329][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:03:36.330][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-18 16:03:36.331][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-18 16:03:36.332][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:03:36.333][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[2024-05-18 16:03:36.334][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:03:36.335][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-18 16:03:36.336][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-18 16:03:36.338][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:03:36.339][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[2024-05-18 16:03:36.340][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:03:36.341][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-18 16:03:36.342][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-18 16:03:36.343][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:03:36.344][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[2024-05-18 16:03:36.345][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:03:36.346][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-18 16:03:36.347][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-18 16:03:36.348][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:03:36.350][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[2024-05-18 16:03:36.351][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:03:36.352][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-18 16:03:36.353][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-18 16:03:36.354][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:03:36.355][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[2024-05-18 16:03:36.356][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:03:36.357][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-18 16:03:36.358][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-18 16:03:36.360][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:03:36.361][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[2024-05-18 16:03:36.362][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:03:36.363][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-18 16:03:36.364][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-18 16:03:36.365][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:03:36.366][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[2024-05-18 16:03:36.367][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:03:36.368][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-18 16:03:36.370][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-18 16:03:36.371][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:03:36.372][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-18 16:03:36.373][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:03:36.374][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-18 16:03:36.375][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-18 16:03:36.376][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:03:36.377][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[2024-05-18 16:03:36.378][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:03:36.379][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-18 16:03:36.381][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-18 16:03:36.382][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:03:36.383][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-18 16:03:36.384][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:03:36.385][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-18 16:03:36.386][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-18 16:03:36.387][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:03:36.388][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-18 16:03:36.389][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-05-18 16:03:36.391][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-05-18 16:03:36.393][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-05-18 16:03:36.395][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-05-18 16:03:36.396][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-05-18 16:03:36.398][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-05-18 16:03:36.400][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-05-18 16:03:36.401][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-05-18 16:03:36.403][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-05-18 16:03:36.405][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-05-18 16:03:36.406][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-05-18 16:03:36.408][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-05-18 16:03:36.410][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-05-18 16:03:36.412][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-05-18 16:03:36.413][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-05-18 16:03:36.415][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-05-18 16:03:36.417][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-05-18 16:03:36.418][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-05-18 16:03:36.420][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-05-18 16:03:36.422][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-05-18 16:03:36.424][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-05-18 16:03:36.425][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-05-18 16:03:36.427][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-05-18 16:03:36.429][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-05-18 16:03:36.431][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-05-18 16:03:36.432][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-05-18 16:03:36.434][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-05-18 16:03:36.436][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-05-18 16:03:36.437][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-05-18 16:03:36.439][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-05-18 16:03:36.441][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-05-18 16:03:36.443][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-05-18 16:03:36.444][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-05-18 16:03:36.446][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-05-18 16:03:36.448][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-05-18 16:03:36.449][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-05-18 16:03:36.451][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-05-18 16:03:36.453][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-05-18 16:03:36.455][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-05-18 16:03:36.456][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-05-18 16:03:36.458][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-05-18 16:03:36.460][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-05-18 16:03:36.461][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-05-18 16:03:36.463][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-05-18 16:03:36.465][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-05-18 16:03:36.471][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-05-18 16:03:36.473][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-05-18 16:03:36.474][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-05-18 16:03:36.476][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-05-18 16:03:36.478][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-05-18 16:03:36.480][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-05-18 16:03:36.481][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-05-18 16:03:36.483][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-05-18 16:03:36.485][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-05-18 16:03:36.486][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-05-18 16:03:36.488][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-05-18 16:03:36.490][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-05-18 16:03:36.492][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-05-18 16:03:36.493][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-05-18 16:03:36.495][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-05-18 16:03:36.497][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-05-18 16:03:36.498][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-05-18 16:03:36.500][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-05-18 16:03:36.502][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-05-18 16:03:36.503][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-05-18 16:03:36.505][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-05-18 16:03:36.507][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-05-18 16:03:36.509][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-05-18 16:03:36.511][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-05-18 16:03:36.513][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-05-18 16:03:36.514][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-05-18 16:03:36.516][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-05-18 16:03:36.518][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-05-18 16:03:36.520][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-05-18 16:03:36.521][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-05-18 16:03:36.523][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-05-18 16:03:36.525][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-05-18 16:03:36.526][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-05-18 16:03:36.528][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-05-18 16:03:36.530][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-05-18 16:03:36.532][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-05-18 16:03:36.533][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-05-18 16:03:36.535][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-05-18 16:03:36.537][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-05-18 16:03:36.539][initialize] This is biodb version 1.13.0.
biodb.DEBUG[2024-05-18 16:03:36.540][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-05-18 16:03:36.541][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-05-18 16:03:36.542][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-18 16:03:36.543][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:03:36.544][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-18 16:03:36.545][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:03:36.546][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-18 16:03:36.547][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-18 16:03:36.549][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-18 16:03:36.550][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-18 16:03:36.551][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:03:36.552][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-18 16:03:36.553][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:03:36.554][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-18 16:03:36.555][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-18 16:03:36.556][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-18 16:03:36.557][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-18 16:03:36.558][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:03:36.559][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-18 16:03:36.560][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:03:36.562][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-18 16:03:36.563][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-18 16:03:36.564][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-18 16:03:36.565][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-18 16:03:36.566][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:03:36.567][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-18 16:03:36.568][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:03:36.569][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-18 16:03:36.570][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-18 16:03:36.571][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-18 16:03:36.572][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-18 16:03:36.573][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:03:36.575][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[2024-05-18 16:03:36.576][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:03:36.577][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-18 16:03:36.578][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-18 16:03:36.579][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-18 16:03:36.580][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-18 16:03:36.581][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:03:36.582][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-18 16:03:36.583][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:03:36.584][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-18 16:03:36.585][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-18 16:03:36.586][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-18 16:03:36.588][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-18 16:03:36.589][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:03:36.590][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-18 16:03:36.591][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:03:36.592][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-18 16:03:36.593][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-18 16:03:36.594][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-18 16:03:36.595][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-18 16:03:36.596][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:03:36.597][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-18 16:03:36.599][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:03:36.600][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-18 16:03:36.601][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-18 16:03:36.602][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-18 16:03:36.603][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-18 16:03:36.604][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:03:36.605][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-18 16:03:36.606][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:03:36.607][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-18 16:03:36.608][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-18 16:03:36.609][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-18 16:03:36.610][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-18 16:03:36.612][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:03:36.617][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-18 16:03:36.619][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:03:36.620][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-18 16:03:36.621][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-18 16:03:36.622][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-18 16:03:36.623][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-18 16:03:36.624][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:03:36.625][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-18 16:03:36.626][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:03:36.627][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-18 16:03:36.629][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-18 16:03:36.630][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-18 16:03:36.631][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-18 16:03:36.632][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:03:36.633][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-18 16:03:36.634][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:03:36.635][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-18 16:03:36.637][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-18 16:03:36.638][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-18 16:03:36.639][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-18 16:03:36.640][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:03:36.641][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-18 16:03:36.642][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:03:36.643][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-18 16:03:36.644][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-18 16:03:36.645][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-18 16:03:36.646][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-18 16:03:36.648][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:03:36.649][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-18 16:03:36.650][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:03:36.651][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-18 16:03:36.652][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-18 16:03:36.653][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-18 16:03:36.654][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-18 16:03:36.655][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:03:36.656][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-18 16:03:36.658][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:03:36.659][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-18 16:03:36.660][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-18 16:03:36.661][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-18 16:03:36.662][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-18 16:03:36.663][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:03:36.664][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-18 16:03:36.665][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:03:36.666][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-18 16:03:36.667][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-18 16:03:36.668][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-18 16:03:36.670][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-18 16:03:36.671][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:03:36.672][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-18 16:03:36.673][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:03:36.674][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-18 16:03:36.675][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-18 16:03:36.676][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-18 16:03:36.677][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-18 16:03:36.678][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:03:36.679][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-18 16:03:36.682][biodb$loadDefinitions] Load definitions from file "/Users/biocbuild/bbs-3.20-bioc-longtests/meat/biodbExpasy.Rcheck/biodbExpasy/definitions.yml".
biodb.DEBUG[2024-05-18 16:03:36.684][self$getDbsInfo()$define] Define connector expasy.enzyme.
biodb.DEBUG[2024-05-18 16:03:36.686][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-05-18 16:03:36.687][self$setPropertyValue] Setting property "description" to "Write here the description of this database.".
biodb.DEBUG[2024-05-18 16:03:36.688][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-18 16:03:36.690][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-18 16:03:36.691][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-18 16:03:36.692][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-18 16:03:36.693][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-05-18 16:03:36.695][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-18 16:03:36.696][self$setPropertyValue] Setting property "entry.content.type" to "txt".
biodb.DEBUG[2024-05-18 16:03:36.697][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-18 16:03:36.698][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-05-18 16:03:36.700][self$setPropertyValue] Setting property "name" to "Expasy ENZYME database.".
biodb.DEBUG[2024-05-18 16:03:36.701][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-18 16:03:36.702][self$setPropertyValue] Setting property "parsing.expr" to "^ID\s+([0-9.]+)$".
biodb.DEBUG[2024-05-18 16:03:36.702][self$setPropertyValue] Setting property "parsing.expr" to "^CA\s+(.+?)\.?$".
biodb.DEBUG[2024-05-18 16:03:36.702][self$setPropertyValue] Setting property "parsing.expr" to "^CF\s+(.+?)\.?$".
biodb.DEBUG[2024-05-18 16:03:36.702][self$setPropertyValue] Setting property "parsing.expr" to "^DE\s+(.+?)\.?$".
biodb.DEBUG[2024-05-18 16:03:36.703][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-05-18 16:03:36.705][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-05-18 16:03:36.706][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2024-05-18 16:03:36.707][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-18 16:03:36.708][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-18 16:03:36.709][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-18 16:03:36.711][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-18 16:03:36.712][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-18 16:03:36.713][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-18 16:03:36.714][self$setPropertyValue] Setting property "urls" to "https://enzyme.expasy.org/".
biodb.DEBUG[2024-05-18 16:03:36.716][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-18 16:03:36.717][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-18 16:03:36.718][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-05-18 16:03:36.719][self$setPropertyValue]
biodb.DEBUG[2024-05-18 16:03:36.721][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-05-18 16:03:36.725][super$initialize] Initialize connector expasy.enzyme.
biodb.DEBUG[2024-05-18 16:03:36.726][super$initialize] Register connector expasy.enzyme with the request scheduler
biodb.DEBUG[2024-05-18 16:03:36.727][private$bdb$getRequestScheduler()$re ...] Register connector expasy.enzyme.
biodb.DEBUG[2024-05-18 16:03:36.729][private$addConnectorRules] Create new rule for URL "enzyme.expasy.org" of connector "expasy.enzyme".
biodb.DEBUG[2024-05-18 16:03:36.731][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-05-18 16:03:36.732][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-05-18 16:03:36.733][biodb$getFactory()$createConn] Creating new connector expasy.enzyme for database class expasy.enzyme .
biodb.INFO [2024-05-18 16:03:36.734][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-05-18 16:03:36.736][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector expasy.enzyme from the request scheduler
biodb.INFO [2024-05-18 16:03:36.737][self$deleteConn] Connector "expasy.enzyme" deleted.
biodb.DEBUG[2024-05-18 16:03:36.738][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-05-18 16:03:36.739][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-18 16:03:36.740][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-18 16:03:36.742][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-18 16:03:36.743][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-18 16:03:36.744][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:03:36.745][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 86 ]
> 
> proc.time()
   user  system elapsed 
  6.832   0.427  14.684

'R CMD check' output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --test-dir=longtests --no-stop-on-test-error --no-codoc --no-examples --no-manual --ignore-vignettes --check-subdirs=no biodbExpasy_1.9.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.20-bioc-longtests/meat/biodbExpasy.Rcheck’
* using R version 4.4.0 Patched (2024-04-24 r86482)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.4
* 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 dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... SKIPPED
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... SKIPPED
* checking examples ... SKIPPED
* checking for unstated dependencies in ‘longtests’ ... OK
* checking tests in ‘longtests’ ...
  Running ‘testthat.R’
 OK
* DONE

Status: 1 NOTE
See
  ‘/Users/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)