Back to Long Tests report for BioC 3.20

This page was generated on 2024-05-18 23:55:02 -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 nebbiolo2


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

raw results

Summary

Package: biodbExpasy
Version: 1.9.0
Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --test-dir=longtests --no-stop-on-test-error --no-codoc --no-examples --no-manual --ignore-vignettes --check-subdirs=no biodbExpasy_1.9.0.tar.gz
StartedAt: 2024-05-18 16:06:23 -0400 (Sat, 18 May 2024)
EndedAt: 2024-05-18 16:07:12 -0400 (Sat, 18 May 2024)
EllapsedTime: 49.4 seconds
RetCode: 0
Status:   OK  
CheckDir: biodbExpasy.Rcheck
Warnings: 0

Tests output

biodbExpasy.Rcheck/tests/testthat.Rout


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

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Type 'license()' or 'licence()' for distribution details.

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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
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> # Script needed to run testthat automatically from ‘R CMD check’. See
> # testthat::test_dir documentation.
> library(testthat)
> library(biodbExpasy)
> Sys.setenv(TESTTHAT_REPORTER="summary")
> Sys.setenv(BIODB_LOG_DST="console")
> test_check("biodbExpasy")
biodb.INFO [2024-05-18 16:06:59.859][biodb::testContext]
biodb.INFO [2024-05-18 16:06:59.861][biodb::testContext] ********************************************************************************
biodb.INFO [2024-05-18 16:06:59.862][biodb::testContext] Test context - Generic long tests
biodb.INFO [2024-05-18 16:06:59.863][biodb::testContext] ********************************************************************************
biodb.INFO [2024-05-18 16:06:59.864][biodb::testContext]
biodb.INFO [2024-05-18 16:06:59.871][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.13.0.
biodb.DEBUG[2024-05-18 16:06:59.873][self$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.20-bioc/R/site-library/biodb/definitions.yml".
biodb.DEBUG[2024-05-18 16:06:59.881][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-05-18 16:06:59.882][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-05-18 16:06:59.883][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-05-18 16:06:59.884][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:06:59.885][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:06:59.886][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-18 16:06:59.887][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-05-18 16:06:59.906][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-05-18 16:06:59.907][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:06:59.908][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:06:59.909][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-18 16:06:59.910][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-05-18 16:06:59.911][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-05-18 16:06:59.912][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:06:59.913][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:06:59.914][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-18 16:06:59.914][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-05-18 16:06:59.915][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-05-18 16:06:59.917][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-05-18 16:06:59.917][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:06:59.918][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:06:59.919][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-18 16:06:59.920][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-05-18 16:06:59.921][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-05-18 16:06:59.922][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-05-18 16:06:59.923][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:06:59.924][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:06:59.925][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-18 16:06:59.926][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-05-18 16:06:59.927][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-05-18 16:06:59.928][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:06:59.929][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:06:59.929][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-18 16:06:59.930][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-05-18 16:06:59.931][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-05-18 16:06:59.932][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-05-18 16:06:59.933][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:06:59.934][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:06:59.935][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-18 16:06:59.936][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-05-18 16:06:59.937][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-05-18 16:06:59.938][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:06:59.939][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:06:59.940][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-18 16:06:59.941][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-05-18 16:06:59.942][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-05-18 16:06:59.943][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-05-18 16:06:59.944][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:06:59.944][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:06:59.945][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-18 16:06:59.946][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-05-18 16:06:59.947][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-05-18 16:06:59.948][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-05-18 16:06:59.949][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-05-18 16:06:59.950][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-05-18 16:06:59.951][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-05-18 16:06:59.952][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:06:59.953][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:06:59.954][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:06:59.955][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-05-18 16:06:59.956][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-05-18 16:06:59.957][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:06:59.958][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:06:59.959][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-18 16:06:59.960][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-05-18 16:06:59.961][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-05-18 16:06:59.962][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:06:59.962][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:06:59.963][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:06:59.964][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-05-18 16:06:59.965][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-05-18 16:06:59.966][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:06:59.967][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:06:59.968][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-18 16:06:59.969][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-05-18 16:06:59.970][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-05-18 16:06:59.971][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:06:59.972][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:06:59.973][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:06:59.974][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-05-18 16:06:59.975][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-05-18 16:06:59.975][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:06:59.976][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:06:59.977][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-18 16:06:59.978][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-05-18 16:06:59.979][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-05-18 16:06:59.983][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-05-18 16:06:59.984][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:06:59.984][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:06:59.985][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 16:06:59.986][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-05-18 16:06:59.987][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-05-18 16:06:59.988][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-05-18 16:06:59.989][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:06:59.990][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:06:59.991][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-18 16:06:59.995][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-05-18 16:07:00.031][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-05-18 16:07:00.053][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2024-05-18 16:07:00.054][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-18 16:07:00.055][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-18 16:07:00.056][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-18 16:07:00.056][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-18 16:07:00.057][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-05-18 16:07:00.058][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-18 16:07:00.059][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-05-18 16:07:00.060][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-18 16:07:00.061][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-05-18 16:07:00.062][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-05-18 16:07:00.063][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-18 16:07:00.063][self$setPropertyValue]
biodb.DEBUG[2024-05-18 16:07:00.064][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-05-18 16:07:00.065][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-05-18 16:07:00.065][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-05-18 16:07:00.065][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-05-18 16:07:00.065][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-05-18 16:07:00.065][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-05-18 16:07:00.066][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-05-18 16:07:00.067][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-18 16:07:00.068][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-18 16:07:00.069][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-18 16:07:00.069][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-18 16:07:00.070][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-18 16:07:00.071][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-18 16:07:00.072][self$setPropertyValue]
biodb.DEBUG[2024-05-18 16:07:00.073][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-18 16:07:00.073][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-18 16:07:00.074][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-05-18 16:07:00.075][self$setPropertyValue]
biodb.DEBUG[2024-05-18 16:07:00.076][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-05-18 16:07:00.078][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-05-18 16:07:00.079][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-05-18 16:07:00.080][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-18 16:07:00.080][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-18 16:07:00.081][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-18 16:07:00.082][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-18 16:07:00.083][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-05-18 16:07:00.084][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-18 16:07:00.085][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-05-18 16:07:00.086][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-18 16:07:00.087][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-05-18 16:07:00.087][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-05-18 16:07:00.088][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-18 16:07:00.089][self$setPropertyValue]
biodb.DEBUG[2024-05-18 16:07:00.090][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-05-18 16:07:00.091][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-05-18 16:07:00.091][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-05-18 16:07:00.091][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-05-18 16:07:00.091][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-05-18 16:07:00.091][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-05-18 16:07:00.092][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-05-18 16:07:00.093][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-18 16:07:00.094][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-18 16:07:00.094][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-18 16:07:00.095][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-18 16:07:00.096][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-18 16:07:00.097][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-18 16:07:00.098][self$setPropertyValue]
biodb.DEBUG[2024-05-18 16:07:00.099][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-18 16:07:00.099][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-18 16:07:00.100][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-05-18 16:07:00.101][self$setPropertyValue]
biodb.DEBUG[2024-05-18 16:07:00.102][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-05-18 16:07:00.104][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-05-18 16:07:00.104][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2024-05-18 16:07:00.105][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-18 16:07:00.106][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-18 16:07:00.107][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-18 16:07:00.108][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-18 16:07:00.109][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-05-18 16:07:00.110][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-18 16:07:00.111][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-05-18 16:07:00.111][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-18 16:07:00.112][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-05-18 16:07:00.113][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-05-18 16:07:00.114][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-18 16:07:00.115][self$setPropertyValue]
biodb.DEBUG[2024-05-18 16:07:00.116][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-05-18 16:07:00.117][self$setPropertyValue]
biodb.DEBUG[2024-05-18 16:07:00.118][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-05-18 16:07:00.118][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-18 16:07:00.119][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-18 16:07:00.120][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-18 16:07:00.121][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-18 16:07:00.122][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-18 16:07:00.123][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-18 16:07:00.123][self$setPropertyValue]
biodb.DEBUG[2024-05-18 16:07:00.124][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-18 16:07:00.125][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-18 16:07:00.126][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-05-18 16:07:00.127][self$setPropertyValue]
biodb.DEBUG[2024-05-18 16:07:00.128][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-05-18 16:07:00.129][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-05-18 16:07:00.130][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-05-18 16:07:00.131][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-18 16:07:00.132][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-18 16:07:00.133][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-18 16:07:00.134][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-18 16:07:00.135][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-05-18 16:07:00.135][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-18 16:07:00.136][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-05-18 16:07:00.137][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-18 16:07:00.138][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-05-18 16:07:00.139][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-05-18 16:07:00.140][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-18 16:07:00.141][self$setPropertyValue]
biodb.DEBUG[2024-05-18 16:07:00.142][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-05-18 16:07:00.143][self$setPropertyValue]
biodb.DEBUG[2024-05-18 16:07:00.143][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-05-18 16:07:00.144][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-18 16:07:00.145][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-18 16:07:00.146][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-18 16:07:00.147][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-18 16:07:00.147][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-18 16:07:00.148][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-18 16:07:00.149][self$setPropertyValue]
biodb.DEBUG[2024-05-18 16:07:00.150][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-18 16:07:00.151][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-18 16:07:00.152][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-05-18 16:07:00.153][self$setPropertyValue]
biodb.DEBUG[2024-05-18 16:07:00.156][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-05-18 16:07:00.157][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:07:00.158][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-18 16:07:00.159][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:07:00.159][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-18 16:07:00.160][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 16:07:00.161][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:07:00.162][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:07:00.163][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:07:00.163][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-18 16:07:00.164][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 16:07:00.165][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:07:00.166][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:07:00.166][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:07:00.167][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-18 16:07:00.168][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 16:07:00.169][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:07:00.170][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:07:00.170][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:07:00.171][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-18 16:07:00.172][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 16:07:00.173][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:07:00.173][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:07:00.174][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:07:00.175][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-18 16:07:00.176][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 16:07:00.177][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:07:00.177][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:07:00.178][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:07:00.179][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-18 16:07:00.180][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 16:07:00.180][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:07:00.181][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:07:00.182][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:07:00.183][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-18 16:07:00.184][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 16:07:00.184][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:07:00.189][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:07:00.190][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:07:00.191][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-18 16:07:00.192][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 16:07:00.193][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:07:00.194][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:07:00.195][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:07:00.195][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-18 16:07:00.196][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 16:07:00.197][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:07:00.198][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:07:00.199][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:07:00.200][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-18 16:07:00.201][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 16:07:00.202][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:07:00.202][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:07:00.203][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:07:00.204][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-18 16:07:00.205][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-18 16:07:00.206][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:07:00.207][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-18 16:07:00.208][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:07:00.208][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-18 16:07:00.209][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 16:07:00.210][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:07:00.211][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:07:00.212][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:07:00.213][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-18 16:07:00.214][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 16:07:00.215][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:07:00.215][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:07:00.216][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:07:00.217][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-18 16:07:00.218][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 16:07:00.219][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:07:00.220][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:07:00.221][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:07:00.221][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-18 16:07:00.222][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-18 16:07:00.223][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:07:00.224][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-18 16:07:00.225][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:07:00.226][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-18 16:07:00.227][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-18 16:07:00.227][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:07:00.228][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:07:00.229][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:07:00.230][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-18 16:07:00.231][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 16:07:00.232][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:07:00.233][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:07:00.234][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-05-18 16:07:00.239][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-05-18 16:07:00.241][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-05-18 16:07:00.242][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-05-18 16:07:00.243][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-05-18 16:07:00.245][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-05-18 16:07:00.246][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-05-18 16:07:00.247][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-05-18 16:07:00.249][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-05-18 16:07:00.250][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-05-18 16:07:00.252][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-05-18 16:07:00.253][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-05-18 16:07:00.254][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-05-18 16:07:00.256][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-05-18 16:07:00.257][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-05-18 16:07:00.258][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-05-18 16:07:00.259][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-05-18 16:07:00.261][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-05-18 16:07:00.262][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-05-18 16:07:00.263][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-05-18 16:07:00.265][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-05-18 16:07:00.266][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-05-18 16:07:00.267][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-05-18 16:07:00.269][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-05-18 16:07:00.270][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-05-18 16:07:00.272][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-05-18 16:07:00.273][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-05-18 16:07:00.274][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-05-18 16:07:00.276][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-05-18 16:07:00.277][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-05-18 16:07:00.278][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-05-18 16:07:00.280][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-05-18 16:07:00.281][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-05-18 16:07:00.282][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-05-18 16:07:00.284][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-05-18 16:07:00.285][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-05-18 16:07:00.286][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-05-18 16:07:00.300][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-05-18 16:07:00.301][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-05-18 16:07:00.303][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-05-18 16:07:00.304][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-05-18 16:07:00.305][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-05-18 16:07:00.307][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-05-18 16:07:00.308][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-05-18 16:07:00.309][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-05-18 16:07:00.311][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-05-18 16:07:00.312][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-05-18 16:07:00.314][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-05-18 16:07:00.315][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-05-18 16:07:00.316][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-05-18 16:07:00.318][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-05-18 16:07:00.319][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-05-18 16:07:00.320][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-05-18 16:07:00.322][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-05-18 16:07:00.323][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-05-18 16:07:00.325][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-05-18 16:07:00.326][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-05-18 16:07:00.327][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-05-18 16:07:00.329][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-05-18 16:07:00.330][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-05-18 16:07:00.331][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-05-18 16:07:00.333][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-05-18 16:07:00.334][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-05-18 16:07:00.335][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-05-18 16:07:00.337][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-05-18 16:07:00.338][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-05-18 16:07:00.339][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-05-18 16:07:00.341][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-05-18 16:07:00.342][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-05-18 16:07:00.343][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-05-18 16:07:00.345][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-05-18 16:07:00.346][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-05-18 16:07:00.347][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-05-18 16:07:00.349][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-05-18 16:07:00.350][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-05-18 16:07:00.351][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-05-18 16:07:00.353][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-05-18 16:07:00.354][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-05-18 16:07:00.355][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-05-18 16:07:00.357][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-05-18 16:07:00.358][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-05-18 16:07:00.359][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-05-18 16:07:00.361][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-05-18 16:07:00.367][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-05-18 16:07:00.368][initialize] This is biodb version 1.13.0.
biodb.DEBUG[2024-05-18 16:07:00.372][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-05-18 16:07:00.372][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-05-18 16:07:00.373][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 16:07:00.374][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:07:00.375][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 16:07:00.379][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:07:00.380][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-18 16:07:00.381][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-18 16:07:00.382][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-18 16:07:00.383][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 16:07:00.384][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:07:00.384][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:07:00.385][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:07:00.386][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-18 16:07:00.387][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-18 16:07:00.388][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-18 16:07:00.389][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 16:07:00.390][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:07:00.390][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:07:00.391][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:07:00.392][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-18 16:07:00.393][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-18 16:07:00.394][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-18 16:07:00.395][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 16:07:00.395][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:07:00.396][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:07:00.397][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:07:00.398][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-18 16:07:00.399][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-18 16:07:00.400][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-18 16:07:00.400][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 16:07:00.401][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:07:00.402][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 16:07:00.403][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:07:00.404][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-18 16:07:00.405][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-18 16:07:00.405][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-18 16:07:00.406][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 16:07:00.407][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:07:00.408][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:07:00.409][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:07:00.410][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-18 16:07:00.410][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-18 16:07:00.411][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-18 16:07:00.412][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 16:07:00.413][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:07:00.414][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:07:00.415][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:07:00.416][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-18 16:07:00.416][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-18 16:07:00.417][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-18 16:07:00.418][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 16:07:00.419][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:07:00.420][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:07:00.421][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:07:00.421][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-18 16:07:00.422][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-18 16:07:00.423][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-18 16:07:00.424][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 16:07:00.425][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:07:00.426][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:07:00.426][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:07:00.427][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-18 16:07:00.428][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-18 16:07:00.429][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-18 16:07:00.430][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 16:07:00.431][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:07:00.431][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:07:00.432][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:07:00.433][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-18 16:07:00.434][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-18 16:07:00.435][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-18 16:07:00.436][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 16:07:00.436][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:07:00.437][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:07:00.438][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:07:00.439][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-18 16:07:00.440][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-18 16:07:00.441][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-18 16:07:00.441][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 16:07:00.442][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:07:00.443][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:07:00.444][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:07:00.445][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-18 16:07:00.445][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-18 16:07:00.446][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-18 16:07:00.447][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 16:07:00.448][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:07:00.449][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:07:00.449][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:07:00.450][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-18 16:07:00.451][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-18 16:07:00.452][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-18 16:07:00.452][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 16:07:00.453][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:07:00.454][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:07:00.455][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:07:00.456][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-18 16:07:00.456][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-18 16:07:00.457][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-18 16:07:00.458][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 16:07:00.459][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:07:00.460][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:07:00.460][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:07:00.461][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-18 16:07:00.462][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-18 16:07:00.463][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-18 16:07:00.463][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-18 16:07:00.464][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:07:00.465][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-18 16:07:00.466][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:07:00.467][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-18 16:07:00.467][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-18 16:07:00.468][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-18 16:07:00.469][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 16:07:00.470][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:07:00.470][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:07:00.471][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:07:00.472][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-18 16:07:00.473][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-18 16:07:00.474][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-18 16:07:00.474][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 16:07:00.475][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:07:00.476][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:07:00.477][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.20-bioc-longtests/meat/biodbExpasy.Rcheck/biodbExpasy/definitions.yml".
biodb.DEBUG[2024-05-18 16:07:00.486][self$getDbsInfo()$define] Define connector expasy.enzyme.
biodb.DEBUG[2024-05-18 16:07:00.488][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-05-18 16:07:00.489][self$setPropertyValue] Setting property "description" to "Write here the description of this database.".
biodb.DEBUG[2024-05-18 16:07:00.489][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-18 16:07:00.490][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-18 16:07:00.491][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-18 16:07:00.492][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-18 16:07:00.493][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-05-18 16:07:00.494][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-18 16:07:00.495][self$setPropertyValue] Setting property "entry.content.type" to "txt".
biodb.DEBUG[2024-05-18 16:07:00.496][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-18 16:07:00.497][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-05-18 16:07:00.497][self$setPropertyValue] Setting property "name" to "Expasy ENZYME database.".
biodb.DEBUG[2024-05-18 16:07:00.498][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-18 16:07:00.499][self$setPropertyValue] Setting property "parsing.expr" to "^ID\s+([0-9.]+)$".
biodb.DEBUG[2024-05-18 16:07:00.499][self$setPropertyValue] Setting property "parsing.expr" to "^CA\s+(.+?)\.?$".
biodb.DEBUG[2024-05-18 16:07:00.499][self$setPropertyValue] Setting property "parsing.expr" to "^CF\s+(.+?)\.?$".
biodb.DEBUG[2024-05-18 16:07:00.499][self$setPropertyValue] Setting property "parsing.expr" to "^DE\s+(.+?)\.?$".
biodb.DEBUG[2024-05-18 16:07:00.500][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-05-18 16:07:00.501][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-05-18 16:07:00.502][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2024-05-18 16:07:00.503][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-18 16:07:00.503][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-18 16:07:00.504][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-18 16:07:00.505][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-18 16:07:00.506][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-18 16:07:00.507][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-18 16:07:00.508][self$setPropertyValue] Setting property "urls" to "https://enzyme.expasy.org/".
biodb.DEBUG[2024-05-18 16:07:00.509][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-18 16:07:00.509][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-18 16:07:00.510][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-05-18 16:07:00.511][self$setPropertyValue]
biodb.DEBUG[2024-05-18 16:07:00.516][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-05-18 16:07:00.543][super$initialize] Initialize connector expasy.enzyme.
biodb.DEBUG[2024-05-18 16:07:00.544][super$initialize] Register connector expasy.enzyme with the request scheduler
biodb.DEBUG[2024-05-18 16:07:00.548][private$bdb$getRequestScheduler()$re ...] Register connector expasy.enzyme.
biodb.DEBUG[2024-05-18 16:07:00.552][private$addConnectorRules] Create new rule for URL "enzyme.expasy.org" of connector "expasy.enzyme".
biodb.DEBUG[2024-05-18 16:07:00.556][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-05-18 16:07:00.556][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-05-18 16:07:00.557][biodb$getFactory()$createConn] Creating new connector expasy.enzyme for database class expasy.enzyme .
biodb.INFO [2024-05-18 16:07:00.566][biodb::testThat]
biodb.INFO [2024-05-18 16:07:00.567][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2024-05-18 16:07:00.568][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-18 16:07:00.569][biodb::testThat]
biodb.TRACE[2024-05-18 16:07:00.572][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/bbs-3.20-bioc-longtests/meat/biodbExpasy.Rcheck/biodbExpasy/testref/entry-expasy.enzyme-1.1.1.1-content.txt".
biodb.DEBUG[2024-05-18 16:07:00.574][biodb$getFactory()$createEntryFromCo ...] Creating Expasy ENZYME database. entries from 1 content(s).
biodb.DEBUG[2024-05-18 16:07:00.577][biodb$getFactory()$createEntryFromCo ...] Parsing 1 Expasy ENZYME database. entries.
biodb.DEBUG[2024-05-18 16:07:00.585][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-18 16:07:00.586][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-18 16:07:00.587][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-18 16:07:00.598][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-18 16:07:00.599][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-18 16:07:00.600][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:07:00.601][FUN] Functions in observer BiodbConfig: [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 16:07:00.611][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-18 16:07:00.612][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-18 16:07:00.613][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:07:00.614][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:07:00.637][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-05-18 16:07:00.648][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-05-18 16:07:00.649][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:07:00.650][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:07:00.651][self$getBiodb()$getEntryFields()$get] Asked field names are: cofactor.
biodb.TRACE[2024-05-18 16:07:00.652][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-05-18 16:07:00.653][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:07:00.654][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:07:00.655][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-18 16:07:00.656][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-18 16:07:00.657][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:07:00.658][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:07:00.659][self$getBiodb()$getEntryFields()$get] Asked field names are: COFACTOR.
biodb.TRACE[2024-05-18 16:07:00.660][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-05-18 16:07:00.660][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:07:00.661][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:07:00.662][self$getBiodb()$getEntryFields()$get] Asked field names are: cofactor.
biodb.TRACE[2024-05-18 16:07:00.663][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-05-18 16:07:00.664][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:07:00.665][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:07:00.666][self$getBiodb()$getEntryFields()$get] Asked field names are: cofactor.
biodb.TRACE[2024-05-18 16:07:00.667][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-05-18 16:07:00.668][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:07:00.668][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:07:00.669][self$getBiodb()$getEntryFields()$get] Asked field names are: cofactor.
biodb.TRACE[2024-05-18 16:07:00.670][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-05-18 16:07:00.671][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:07:00.672][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:07:00.673][self$getBiodb()$getEntryFields()$get] Asked field names are: COFACTOR.
biodb.TRACE[2024-05-18 16:07:00.674][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-05-18 16:07:00.675][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:07:00.675][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:07:00.691][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-18 16:07:00.692][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-18 16:07:00.693][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:07:00.694][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:07:00.695][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-18 16:07:00.696][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-18 16:07:00.697][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:07:00.697][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:07:00.727][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-18 16:07:00.728][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-18 16:07:00.729][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:07:00.730][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:07:00.731][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-18 16:07:00.732][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-18 16:07:00.733][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:07:00.734][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:07:00.735][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-18 16:07:00.735][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-18 16:07:00.736][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:07:00.737][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:07:00.738][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-05-18 16:07:00.739][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-05-18 16:07:00.740][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:07:00.741][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:07:00.742][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-05-18 16:07:00.743][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-05-18 16:07:00.744][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:07:00.744][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:07:00.745][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-18 16:07:00.746][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-18 16:07:00.747][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:07:00.748][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:07:00.749][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-05-18 16:07:00.750][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-05-18 16:07:00.751][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:07:00.752][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:07:00.752][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-18 16:07:00.753][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-18 16:07:00.754][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:07:00.755][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:07:00.763][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-18 16:07:00.764][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-18 16:07:00.765][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:07:00.766][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:07:00.767][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-18 16:07:00.768][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-18 16:07:00.768][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:07:00.769][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:07:00.770][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-18 16:07:00.771][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-18 16:07:00.772][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:07:00.773][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:07:00.774][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-18 16:07:00.775][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-18 16:07:00.775][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:07:00.776][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:07:00.777][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-18 16:07:00.778][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-18 16:07:00.779][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:07:00.780][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-18 16:07:00.781][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 1.1.1.1.
biodb.TRACE[2024-05-18 16:07:00.783][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-05-18 16:07:00.784][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-05-18 16:07:00.785][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:07:00.786][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:07:00.786][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-05-18 16:07:00.787][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-05-18 16:07:00.788][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:07:00.789][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:07:00.790][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-05-18 16:07:00.791][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-05-18 16:07:00.792][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:07:00.793][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:07:00.794][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-05-18 16:07:00.794][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-05-18 16:07:00.795][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:07:00.796][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:07:00.810][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-18 16:07:00.811][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-18 16:07:00.812][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:07:00.813][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:07:00.824][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-05-18 16:07:00.825][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-05-18 16:07:00.826][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:07:00.827][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:07:00.831][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-18 16:07:00.832][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-18 16:07:00.833][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:07:00.834][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:07:00.834][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-18 16:07:00.835][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-18 16:07:00.836][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:07:00.837][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:07:00.838][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-18 16:07:00.839][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-18 16:07:00.840][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:07:00.841][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:07:00.843][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-18 16:07:00.844][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-18 16:07:00.845][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:07:00.846][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:07:00.846][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-18 16:07:00.847][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-18 16:07:00.848][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:07:00.849][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:07:00.850][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-18 16:07:00.851][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-18 16:07:00.852][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:07:00.853][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:07:00.854][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-05-18 16:07:00.855][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-05-18 16:07:00.855][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:07:00.856][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:07:00.857][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-05-18 16:07:00.858][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-05-18 16:07:00.859][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:07:00.860][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:07:00.861][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-05-18 16:07:00.862][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-05-18 16:07:00.862][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:07:00.863][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:07:00.870][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-18 16:07:00.871][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-18 16:07:00.872][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:07:00.872][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:07:00.873][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-18 16:07:00.874][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-18 16:07:00.875][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:07:00.876][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:07:00.877][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-18 16:07:00.878][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-18 16:07:00.879][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:07:00.879][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:07:00.880][ef$get] Asked field names are: accession.
biodb.TRACE[2024-05-18 16:07:00.881][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-18 16:07:00.882][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:07:00.883][ef$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:07:00.884][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-18 16:07:00.885][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-18 16:07:00.886][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:07:00.886][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:07:00.894][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-18 16:07:00.895][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-18 16:07:00.896][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:07:00.897][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:07:00.897][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-18 16:07:00.898][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-18 16:07:00.899][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:07:00.900][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:07:00.901][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-18 16:07:00.902][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-18 16:07:00.903][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:07:00.903][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:07:00.904][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-18 16:07:00.905][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-18 16:07:00.906][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:07:00.907][ef$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:07:00.908][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-18 16:07:00.909][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-18 16:07:00.910][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:07:00.910][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:07:00.917][self$getBiodb()$getEntryFields()$get] Asked field names are: cofactor.
biodb.TRACE[2024-05-18 16:07:00.918][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-05-18 16:07:00.919][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:07:00.920][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:07:00.921][self$getBiodb()$getEntryFields()$get] Asked field names are: cofactor.
biodb.TRACE[2024-05-18 16:07:00.922][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-05-18 16:07:00.923][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:07:00.923][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:07:00.924][self$getBiodb()$getEntryFields()$get] Asked field names are: cofactor.
biodb.TRACE[2024-05-18 16:07:00.925][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-05-18 16:07:00.926][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:07:00.927][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:07:00.928][ef$get] Asked field names are: cofactor.
biodb.TRACE[2024-05-18 16:07:00.929][ef$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-05-18 16:07:00.930][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:07:00.930][ef$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:07:00.931][self$getBiodb()$getEntryFields()$get] Asked field names are: cofactor.
biodb.TRACE[2024-05-18 16:07:00.932][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-05-18 16:07:00.933][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:07:00.934][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:07:00.941][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-05-18 16:07:00.942][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-05-18 16:07:00.943][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:07:00.943][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:07:00.944][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-05-18 16:07:00.945][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-05-18 16:07:00.946][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:07:00.947][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:07:00.948][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-05-18 16:07:00.949][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-05-18 16:07:00.950][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:07:00.950][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:07:00.951][ef$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-05-18 16:07:00.952][ef$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-05-18 16:07:00.953][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:07:00.954][ef$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:07:00.955][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-05-18 16:07:00.956][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-05-18 16:07:00.957][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:07:00.957][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:07:00.986][ef$get] Asked field names are: accession.
biodb.TRACE[2024-05-18 16:07:00.987][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-18 16:07:00.988][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:07:00.989][ef$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:07:00.992][ef$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-05-18 16:07:00.993][ef$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-05-18 16:07:00.994][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:07:00.995][ef$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:07:00.999][ef$get] Asked field names are: cofactor.
biodb.TRACE[2024-05-18 16:07:01.000][ef$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-05-18 16:07:01.000][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:07:01.001][ef$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:07:01.005][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-18 16:07:01.006][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-18 16:07:01.007][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:07:01.007][ef$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:07:01.022][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/bbs-3.20-bioc-longtests/meat/biodbExpasy.Rcheck/biodbExpasy/testref/entry-expasy.enzyme-1.1.1.54-content.txt".
biodb.DEBUG[2024-05-18 16:07:01.053][biodb$getFactory()$createEntryFromCo ...] Creating Expasy ENZYME database. entries from 1 content(s).
biodb.DEBUG[2024-05-18 16:07:01.054][biodb$getFactory()$createEntryFromCo ...] Parsing 1 Expasy ENZYME database. entries.
biodb.DEBUG[2024-05-18 16:07:01.056][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-18 16:07:01.056][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-18 16:07:01.057][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-18 16:07:01.061][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-18 16:07:01.062][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-18 16:07:01.063][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:07:01.063][FUN] Functions in observer BiodbConfig: [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 16:07:01.065][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-18 16:07:01.066][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-18 16:07:01.067][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:07:01.068][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:07:01.069][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-05-18 16:07:01.070][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-05-18 16:07:01.071][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:07:01.071][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:07:01.073][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-18 16:07:01.074][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-18 16:07:01.074][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:07:01.075][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:07:01.076][self$getBiodb()$getEntryFields()$get] Asked field names are: COFACTOR.
biodb.TRACE[2024-05-18 16:07:01.077][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-05-18 16:07:01.078][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:07:01.079][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:07:01.080][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-05-18 16:07:01.081][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-05-18 16:07:01.082][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:07:01.082][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:07:01.083][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-05-18 16:07:01.084][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-05-18 16:07:01.085][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:07:01.086][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:07:01.087][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-18 16:07:01.088][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-18 16:07:01.089][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:07:01.089][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:07:01.090][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-05-18 16:07:01.091][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-05-18 16:07:01.092][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:07:01.093][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:07:01.094][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-18 16:07:01.095][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-18 16:07:01.096][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:07:01.096][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:07:01.097][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-18 16:07:01.098][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-18 16:07:01.099][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:07:01.100][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:07:01.101][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-18 16:07:01.102][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-18 16:07:01.103][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:07:01.103][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:07:01.104][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-18 16:07:01.105][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-18 16:07:01.106][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:07:01.107][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:07:01.108][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-18 16:07:01.109][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-18 16:07:01.110][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:07:01.110][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:07:01.111][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-18 16:07:01.112][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-18 16:07:01.113][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:07:01.114][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-18 16:07:01.115][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 1.1.1.54.
biodb.TRACE[2024-05-18 16:07:01.133][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-05-18 16:07:01.134][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-05-18 16:07:01.135][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:07:01.135][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:07:01.136][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-05-18 16:07:01.137][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-05-18 16:07:01.138][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:07:01.139][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:07:01.140][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-05-18 16:07:01.141][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-05-18 16:07:01.142][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:07:01.142][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:07:01.143][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-05-18 16:07:01.144][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-05-18 16:07:01.145][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:07:01.146][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:07:01.147][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-18 16:07:01.148][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-18 16:07:01.149][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:07:01.150][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:07:01.154][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-05-18 16:07:01.155][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-05-18 16:07:01.156][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:07:01.156][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:07:01.164][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-18 16:07:01.165][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-18 16:07:01.166][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:07:01.166][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:07:01.167][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-18 16:07:01.168][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-18 16:07:01.169][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:07:01.170][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:07:01.171][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-18 16:07:01.172][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-18 16:07:01.173][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:07:01.173][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:07:01.175][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-18 16:07:01.176][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-18 16:07:01.177][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:07:01.178][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:07:01.179][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-18 16:07:01.180][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-18 16:07:01.181][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:07:01.182][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:07:01.182][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-18 16:07:01.183][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-18 16:07:01.184][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:07:01.185][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:07:01.186][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-05-18 16:07:01.187][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-05-18 16:07:01.188][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:07:01.189][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:07:01.190][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-05-18 16:07:01.191][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-05-18 16:07:01.191][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:07:01.192][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:07:01.193][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-05-18 16:07:01.194][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-05-18 16:07:01.195][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:07:01.196][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:07:01.210][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-18 16:07:01.211][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-18 16:07:01.212][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:07:01.213][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:07:01.214][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-18 16:07:01.215][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-18 16:07:01.215][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:07:01.216][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:07:01.217][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-18 16:07:01.218][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-18 16:07:01.219][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:07:01.220][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:07:01.221][ef$get] Asked field names are: accession.
biodb.TRACE[2024-05-18 16:07:01.222][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-18 16:07:01.222][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:07:01.223][ef$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:07:01.224][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-18 16:07:01.225][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-18 16:07:01.226][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:07:01.227][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:07:01.234][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-18 16:07:01.234][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-18 16:07:01.235][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:07:01.236][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:07:01.237][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-18 16:07:01.238][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-18 16:07:01.239][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:07:01.240][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:07:01.241][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-18 16:07:01.241][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-18 16:07:01.242][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:07:01.243][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:07:01.244][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-18 16:07:01.245][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-18 16:07:01.246][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:07:01.247][ef$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:07:01.247][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-18 16:07:01.248][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-18 16:07:01.249][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:07:01.250][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:07:01.257][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-05-18 16:07:01.258][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-05-18 16:07:01.259][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:07:01.260][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:07:01.261][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-05-18 16:07:01.262][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-05-18 16:07:01.262][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:07:01.263][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:07:01.264][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-05-18 16:07:01.265][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-05-18 16:07:01.266][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:07:01.267][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:07:01.268][ef$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-05-18 16:07:01.269][ef$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-05-18 16:07:01.269][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:07:01.270][ef$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:07:01.271][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-05-18 16:07:01.272][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-05-18 16:07:01.273][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:07:01.274][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:07:01.281][ef$get] Asked field names are: accession.
biodb.TRACE[2024-05-18 16:07:01.282][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-18 16:07:01.283][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:07:01.283][ef$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:07:01.287][ef$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-05-18 16:07:01.288][ef$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-05-18 16:07:01.289][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:07:01.290][ef$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:07:01.293][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-18 16:07:01.294][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-18 16:07:01.295][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:07:01.296][ef$get] fields variable is a list.
biodb.INFO [2024-05-18 16:07:01.302][biodb::testThat]
biodb.INFO [2024-05-18 16:07:01.303][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2024-05-18 16:07:01.303][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-18 16:07:01.304][biodb::testThat]
biodb.DEBUG[2024-05-18 16:07:01.306][private$loadEntries] Creating entries from ids [2]: "1.1.1.1, 1.1.1.54".
biodb.DEBUG[2024-05-18 16:07:01.313][conn$getEntryContent] Get Expasy ENZYME database. entry content(s) for 2 id(s)...
biodb.TRACE[2024-05-18 16:07:01.317][cch$loadFileContent] Trying to load 2 files from cache: [2]: "1.1.1.1, 1.1.1.54".
biodb.INFO [2024-05-18 16:07:01.318][self$getFolderPath] Create cache folder "/home/biocbuild/.cache/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280" for "expasy.enzyme-b59b84d962b6741050ba8f70ff4db280".
biodb.TRACE[2024-05-18 16:07:01.319][cch$loadFileContent] file.exist = [2]: "FALSE, FALSE".
biodb.TRACE[2024-05-18 16:07:01.320][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-05-18 16:07:01.321][conn$getEntryContent] 0 Expasy ENZYME database. entry content(s) loaded from cache.
biodb.DEBUG[2024-05-18 16:07:01.322][conn$getEntryContent] 2 entry content(s) need to be fetched from Expasy ENZYME database. database "https://enzyme.expasy.org/".
biodb.DEBUG[2024-05-18 16:07:01.323][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-05-18 16:07:01.324][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-05-18 16:07:01.329][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-18 16:07:01.329][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-18 16:07:01.330][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-18 16:07:01.334][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-18 16:07:01.335][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-18 16:07:01.336][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:07:01.336][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-18 16:07:01.337][scheduler$sendRequest] Getting content of get URL request "https://enzyme.expasy.org/EC/1.1.1.1.txt".
biodb.DEBUG[2024-05-18 16:07:01.361][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-18 16:07:01.362][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-18 16:07:01.363][private$doSendRequestOnce] Sent URL is "https://enzyme.expasy.org/EC/1.1.1.1.txt".
biodb.TRACE[2024-05-18 16:07:02.411][getRCurlRequestResult] Using RCurl package for sending request (https://enzyme.expasy.org/EC/1.1.1.1.txt).
biodb.DEBUG[2024-05-18 16:07:03.327][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-05-18 16:07:03.332][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280/a52675cfd2f0c2b41556caa64d9341e3.content"
biodb.TRACE[2024-05-18 16:07:03.362][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280/a52675cfd2f0c2b41556caa64d9341e3.request"
biodb.DEBUG[2024-05-18 16:07:03.366][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-18 16:07:03.368][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-18 16:07:03.369][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-18 16:07:03.376][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-18 16:07:03.378][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 16:07:03.379][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:07:03.380][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:07:03.406][scheduler$sendRequest] Getting content of get URL request "https://enzyme.expasy.org/EC/1.1.1.54.txt".
biodb.DEBUG[2024-05-18 16:07:03.420][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-18 16:07:03.421][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-18 16:07:03.445][private$doSendRequestOnce] Sent URL is "https://enzyme.expasy.org/EC/1.1.1.54.txt".
biodb.TRACE[2024-05-18 16:07:04.170][getRCurlRequestResult] Using RCurl package for sending request (https://enzyme.expasy.org/EC/1.1.1.54.txt).
biodb.DEBUG[2024-05-18 16:07:04.935][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-05-18 16:07:04.939][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280/a9b93566a091cbe35a06e4b3871f95c9.content"
biodb.TRACE[2024-05-18 16:07:04.946][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280/a9b93566a091cbe35a06e4b3871f95c9.request"
biodb.TRACE[2024-05-18 16:07:04.951][private$doSaveContentToFile] Saving to cache [2]: "/home/biocbuild/.cache/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280/1.1.1.1.txt, /home/biocbuild/.cache/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280/1.1.1.54.txt"
biodb.DEBUG[2024-05-18 16:07:04.954][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-05-18 16:07:04.957][self$createEntryFromContent] Creating Expasy ENZYME database. entries from 2 content(s).
biodb.DEBUG[2024-05-18 16:07:04.959][self$createEntryFromContent] Parsing 2 Expasy ENZYME database. entries.
biodb.DEBUG[2024-05-18 16:07:04.962][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-18 16:07:04.964][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-18 16:07:04.966][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-18 16:07:04.975][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-18 16:07:04.977][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-18 16:07:04.979][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:07:04.981][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-18 16:07:04.985][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-18 16:07:04.987][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-18 16:07:04.989][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:07:04.990][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:07:04.992][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-05-18 16:07:04.994][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-05-18 16:07:04.995][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:07:04.997][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:07:04.998][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-18 16:07:05.000][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-18 16:07:05.001][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:07:05.002][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:07:05.004][self$getBiodb()$getEntryFields()$get] Asked field names are: COFACTOR.
biodb.TRACE[2024-05-18 16:07:05.005][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-05-18 16:07:05.006][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:07:05.007][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:07:05.009][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-18 16:07:05.010][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-18 16:07:05.011][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:07:05.012][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:07:05.013][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-18 16:07:05.014][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-18 16:07:05.015][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:07:05.016][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:07:05.018][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-18 16:07:05.019][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-18 16:07:05.020][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:07:05.021][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:07:05.022][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-18 16:07:05.023][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-18 16:07:05.023][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:07:05.024][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:07:05.025][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-18 16:07:05.026][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-18 16:07:05.027][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:07:05.028][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:07:05.029][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-05-18 16:07:05.030][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-05-18 16:07:05.031][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:07:05.032][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:07:05.033][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-05-18 16:07:05.034][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-05-18 16:07:05.034][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:07:05.035][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:07:05.036][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-18 16:07:05.037][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-18 16:07:05.038][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:07:05.039][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:07:05.040][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-05-18 16:07:05.041][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-05-18 16:07:05.041][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:07:05.042][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:07:05.043][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-18 16:07:05.044][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-18 16:07:05.045][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:07:05.046][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:07:05.047][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-18 16:07:05.048][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-18 16:07:05.048][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:07:05.049][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:07:05.050][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-18 16:07:05.051][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-18 16:07:05.052][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:07:05.053][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-18 16:07:05.054][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-18 16:07:05.055][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-18 16:07:05.055][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-18 16:07:05.059][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-18 16:07:05.060][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-18 16:07:05.061][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:07:05.062][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-18 16:07:05.063][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-18 16:07:05.064][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-18 16:07:05.065][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:07:05.066][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:07:05.067][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-05-18 16:07:05.068][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-05-18 16:07:05.069][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:07:05.070][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:07:05.071][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-18 16:07:05.072][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-18 16:07:05.072][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:07:05.073][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:07:05.074][self$getBiodb()$getEntryFields()$get] Asked field names are: COFACTOR.
biodb.TRACE[2024-05-18 16:07:05.075][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-05-18 16:07:05.076][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:07:05.077][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:07:05.078][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-05-18 16:07:05.079][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-05-18 16:07:05.080][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:07:05.080][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:07:05.081][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-05-18 16:07:05.082][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-05-18 16:07:05.083][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:07:05.084][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:07:05.085][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-18 16:07:05.086][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-18 16:07:05.087][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:07:05.087][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:07:05.088][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-05-18 16:07:05.089][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-05-18 16:07:05.090][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:07:05.091][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:07:05.092][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-18 16:07:05.093][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-18 16:07:05.094][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:07:05.094][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:07:05.095][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-18 16:07:05.096][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-18 16:07:05.097][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:07:05.098][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:07:05.099][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-18 16:07:05.100][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-18 16:07:05.101][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:07:05.101][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:07:05.102][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-18 16:07:05.103][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-18 16:07:05.104][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:07:05.105][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:07:05.106][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-18 16:07:05.107][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-18 16:07:05.108][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:07:05.108][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:07:05.109][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-18 16:07:05.110][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-18 16:07:05.111][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:07:05.112][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:07:05.113][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-18 16:07:05.114][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-18 16:07:05.115][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:07:05.115][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:07:05.116][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-18 16:07:05.117][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-18 16:07:05.118][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:07:05.119][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:07:05.120][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-18 16:07:05.121][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-18 16:07:05.122][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:07:05.122][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-18 16:07:05.123][self$createEntryFromContent] Accession numbers: 1.1.1.1, 1.1.1.54.
biodb.TRACE[2024-05-18 16:07:05.124][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2024-05-18 16:07:05.125][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2024-05-18 16:07:05.126][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:07:05.127][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:07:05.128][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2024-05-18 16:07:05.129][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2024-05-18 16:07:05.130][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:07:05.130][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:07:05.131][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2024-05-18 16:07:05.132][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2024-05-18 16:07:05.133][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:07:05.134][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:07:05.144][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2024-05-18 16:07:05.145][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2024-05-18 16:07:05.146][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:07:05.147][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:07:05.148][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2024-05-18 16:07:05.149][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2024-05-18 16:07:05.150][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:07:05.150][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:07:05.151][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2024-05-18 16:07:05.152][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2024-05-18 16:07:05.153][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:07:05.154][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-05-18 16:07:05.160][biodb::testThat]
biodb.INFO [2024-05-18 16:07:05.161][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2024-05-18 16:07:05.162][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-18 16:07:05.163][biodb::testThat]
biodb.TRACE[2024-05-18 16:07:05.165][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-18 16:07:05.166][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-18 16:07:05.167][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:07:05.168][ef$get] fields variable is a list.
biodb.DEBUG[2024-05-18 16:07:05.169][function(conn, opt)] Testing searchForEntries() with entry "1.1.1.1" and field "name".
biodb.TRACE[2024-05-18 16:07:05.190][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-18 16:07:05.191][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-18 16:07:05.192][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:07:05.193][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:07:05.193][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-18 16:07:05.194][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-18 16:07:05.195][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:07:05.196][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:07:05.197][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-18 16:07:05.198][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-18 16:07:05.199][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:07:05.200][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-18 16:07:05.203][function(conn, opt)] With value "alcohol dehydrogenase".
biodb.DEBUG[2024-05-18 16:07:05.204][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://enzyme.expasy.org/enzyme-byname.html?alcohol dehydrogenase".
biodb.DEBUG[2024-05-18 16:07:05.207][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-18 16:07:05.208][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-18 16:07:05.209][private$doSendRequestOnce] Sent URL is "https://enzyme.expasy.org/enzyme-byname.html?alcohol%20dehydrogenase".
biodb.TRACE[2024-05-18 16:07:06.219][getRCurlRequestResult] Using RCurl package for sending request (https://enzyme.expasy.org/enzyme-byname.html?alcohol%20dehydrogenase).
biodb.DEBUG[2024-05-18 16:07:07.055][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-05-18 16:07:07.061][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280/f603fa2a57aec59588edc37541c6f6d5.content"
biodb.TRACE[2024-05-18 16:07:07.069][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280/f603fa2a57aec59588edc37541c6f6d5.request"
biodb.DEBUG[2024-05-18 16:07:07.084][function(conn, opt)] With found IDs [1]: "1.1.1.1".
biodb.INFO [2024-05-18 16:07:07.112][biodb::testThat]
biodb.INFO [2024-05-18 16:07:07.114][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2024-05-18 16:07:07.115][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-18 16:07:07.117][biodb::testThat]
biodb.TRACE[2024-05-18 16:07:07.145][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-18 16:07:07.146][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-18 16:07:07.147][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:07:07.148][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:07:07.149][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-18 16:07:07.150][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-18 16:07:07.151][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:07:07.152][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:07:07.153][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-18 16:07:07.154][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-18 16:07:07.155][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:07:07.156][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-18 16:07:07.183][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://enzyme.expasy.org/enzyme-byname.html?alcohol dehydrogenase".
biodb.DEBUG[2024-05-18 16:07:07.186][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-05-18 16:07:07.215][cch$loadFileContent] Trying to load 1 files from cache: [1]: "f603fa2a57aec59588edc37541c6f6d5".
biodb.TRACE[2024-05-18 16:07:07.217][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-05-18 16:07:07.218][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280/f603fa2a57aec59588edc37541c6f6d5.content".
biodb.INFO [2024-05-18 16:07:07.232][biodb::testThat]
biodb.INFO [2024-05-18 16:07:07.233][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2024-05-18 16:07:07.234][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-18 16:07:07.235][biodb::testThat]
biodb.TRACE[2024-05-18 16:07:07.244][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-05-18 16:07:07.245][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-05-18 16:07:07.246][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:07:07.247][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:07:07.248][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-05-18 16:07:07.249][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-05-18 16:07:07.250][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:07:07.250][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:07:07.251][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-05-18 16:07:07.252][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-05-18 16:07:07.253][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:07:07.254][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:07:07.255][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-05-18 16:07:07.256][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-05-18 16:07:07.257][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:07:07.258][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:07:07.289][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-05-18 16:07:07.290][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-05-18 16:07:07.291][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:07:07.292][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:07:07.293][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-05-18 16:07:07.294][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-05-18 16:07:07.295][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:07:07.295][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:07:07.296][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-05-18 16:07:07.297][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-05-18 16:07:07.298][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:07:07.299][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:07:07.300][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-05-18 16:07:07.301][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-05-18 16:07:07.302][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:07:07.303][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-05-18 16:07:07.308][biodb::testThat]
biodb.INFO [2024-05-18 16:07:07.308][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2024-05-18 16:07:07.309][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-18 16:07:07.310][biodb::testThat]
biodb.INFO [2024-05-18 16:07:07.318][biodb::testThat]
biodb.INFO [2024-05-18 16:07:07.318][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2024-05-18 16:07:07.319][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-18 16:07:07.320][biodb::testThat]
biodb.INFO [2024-05-18 16:07:07.327][biodb::testThat]
biodb.INFO [2024-05-18 16:07:07.327][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2024-05-18 16:07:07.328][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-18 16:07:07.329][biodb::testThat]
biodb.DEBUG[2024-05-18 16:07:07.341][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 16:07:08.118][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 16:07:08.951][biodb::testThat]
biodb.INFO [2024-05-18 16:07:08.953][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2024-05-18 16:07:08.955][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-18 16:07:08.957][biodb::testThat]
biodb.DEBUG[2024-05-18 16:07:10.475][getUrlContent] Use RCurl for downloading content of URL https://enzyme.expasy.org/images/1.1.1.1/image.png.
biodb.TRACE[2024-05-18 16:07:10.940][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-18 16:07:10.942][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-18 16:07:10.963][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:07:10.965][ef$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:07:10.968][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-18 16:07:10.970][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-18 16:07:10.972][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:07:10.974][ef$get] fields variable is a list.
biodb.INFO [2024-05-18 16:07:10.976][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-05-18 16:07:10.979][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector expasy.enzyme from the request scheduler
biodb.INFO [2024-05-18 16:07:10.981][self$deleteConn] Connector "expasy.enzyme" deleted.
biodb.DEBUG[2024-05-18 16:07:10.982][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-05-18 16:07:10.984][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-18 16:07:10.985][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-18 16:07:10.987][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-18 16:07:10.988][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-18 16:07:10.989][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:07:10.991][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2024-05-18 16:07:11.003][biodb::testContext]
biodb.INFO [2024-05-18 16:07:11.005][biodb::testContext] ********************************************************************************
biodb.INFO [2024-05-18 16:07:11.006][biodb::testContext] Test context - Example long tests
biodb.INFO [2024-05-18 16:07:11.007][biodb::testContext] ********************************************************************************
biodb.INFO [2024-05-18 16:07:11.008][biodb::testContext]
biodb.INFO [2024-05-18 16:07:11.010][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.13.0.
biodb.DEBUG[2024-05-18 16:07:11.012][self$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.20-bioc/R/site-library/biodb/definitions.yml".
biodb.DEBUG[2024-05-18 16:07:11.017][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-05-18 16:07:11.018][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-05-18 16:07:11.019][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-05-18 16:07:11.020][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:07:11.020][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:07:11.021][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:07:11.022][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-05-18 16:07:11.023][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-05-18 16:07:11.024][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:07:11.025][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:07:11.026][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-18 16:07:11.027][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-05-18 16:07:11.028][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-05-18 16:07:11.029][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:07:11.029][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:07:11.030][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 16:07:11.031][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-05-18 16:07:11.032][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-05-18 16:07:11.033][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-05-18 16:07:11.034][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:07:11.034][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:07:11.035][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-18 16:07:11.036][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-05-18 16:07:11.037][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-05-18 16:07:11.038][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-05-18 16:07:11.039][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:07:11.039][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:07:11.040][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-18 16:07:11.041][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-05-18 16:07:11.042][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-05-18 16:07:11.043][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:07:11.044][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:07:11.044][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-18 16:07:11.045][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-05-18 16:07:11.046][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-05-18 16:07:11.047][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-05-18 16:07:11.048][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:07:11.049][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:07:11.049][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:07:11.050][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-05-18 16:07:11.051][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-05-18 16:07:11.052][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:07:11.053][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:07:11.054][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-18 16:07:11.054][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-05-18 16:07:11.055][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-05-18 16:07:11.056][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-05-18 16:07:11.057][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:07:11.058][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:07:11.059][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 16:07:11.059][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-05-18 16:07:11.060][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-05-18 16:07:11.061][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-05-18 16:07:11.062][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-05-18 16:07:11.063][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-05-18 16:07:11.064][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-05-18 16:07:11.065][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:07:11.065][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:07:11.066][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-18 16:07:11.067][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-05-18 16:07:11.068][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-05-18 16:07:11.069][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:07:11.070][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:07:11.070][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-18 16:07:11.071][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-05-18 16:07:11.072][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-05-18 16:07:11.073][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:07:11.074][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:07:11.075][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-18 16:07:11.075][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-05-18 16:07:11.076][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-05-18 16:07:11.077][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:07:11.078][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:07:11.079][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:07:11.080][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-05-18 16:07:11.080][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-05-18 16:07:11.081][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:07:11.082][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:07:11.083][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-18 16:07:11.084][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-05-18 16:07:11.085][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-05-18 16:07:11.085][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:07:11.086][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:07:11.087][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:07:11.088][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-05-18 16:07:11.089][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-05-18 16:07:11.092][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-05-18 16:07:11.092][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:07:11.093][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:07:11.094][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-18 16:07:11.095][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-05-18 16:07:11.096][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-05-18 16:07:11.097][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-05-18 16:07:11.097][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:07:11.098][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:07:11.099][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-18 16:07:11.100][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-05-18 16:07:11.102][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-05-18 16:07:11.103][self$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 16:07:11.103][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-18 16:07:11.104][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-18 16:07:11.105][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-18 16:07:11.106][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-18 16:07:11.107][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-05-18 16:07:11.108][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-18 16:07:11.109][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-05-18 16:07:11.110][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-18 16:07:11.111][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-05-18 16:07:11.111][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-05-18 16:07:11.112][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-18 16:07:11.113][self$setPropertyValue]
biodb.DEBUG[2024-05-18 16:07:11.114][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-05-18 16:07:11.115][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-05-18 16:07:11.115][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-05-18 16:07:11.115][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-05-18 16:07:11.115][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-05-18 16:07:11.115][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-05-18 16:07:11.116][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-05-18 16:07:11.117][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-18 16:07:11.118][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-18 16:07:11.118][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-18 16:07:11.119][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-18 16:07:11.120][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-18 16:07:11.121][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-18 16:07:11.122][self$setPropertyValue]
biodb.DEBUG[2024-05-18 16:07:11.123][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-18 16:07:11.123][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-18 16:07:11.124][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-05-18 16:07:11.125][self$setPropertyValue]
biodb.DEBUG[2024-05-18 16:07:11.126][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-05-18 16:07:11.128][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-05-18 16:07:11.129][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-05-18 16:07:11.130][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-18 16:07:11.131][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-18 16:07:11.131][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-18 16:07:11.132][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-18 16:07:11.133][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-05-18 16:07:11.134][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-18 16:07:11.135][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-05-18 16:07:11.136][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-18 16:07:11.137][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-05-18 16:07:11.138][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-05-18 16:07:11.139][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-18 16:07:11.140][self$setPropertyValue]
biodb.DEBUG[2024-05-18 16:07:11.140][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-05-18 16:07:11.141][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-05-18 16:07:11.141][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-05-18 16:07:11.141][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-05-18 16:07:11.141][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-05-18 16:07:11.141][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-05-18 16:07:11.142][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-05-18 16:07:11.143][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-18 16:07:11.144][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-18 16:07:11.145][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-18 16:07:11.146][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-18 16:07:11.147][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-18 16:07:11.147][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-18 16:07:11.153][self$setPropertyValue]
biodb.DEBUG[2024-05-18 16:07:11.154][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-18 16:07:11.154][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-18 16:07:11.155][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-05-18 16:07:11.156][self$setPropertyValue]
biodb.DEBUG[2024-05-18 16:07:11.157][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-05-18 16:07:11.159][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-05-18 16:07:11.160][self$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 16:07:11.161][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-18 16:07:11.162][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-18 16:07:11.162][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-18 16:07:11.163][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-18 16:07:11.164][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-05-18 16:07:11.165][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-18 16:07:11.166][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-05-18 16:07:11.167][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-18 16:07:11.168][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-05-18 16:07:11.169][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-05-18 16:07:11.170][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-18 16:07:11.171][self$setPropertyValue]
biodb.DEBUG[2024-05-18 16:07:11.171][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-05-18 16:07:11.172][self$setPropertyValue]
biodb.DEBUG[2024-05-18 16:07:11.173][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-05-18 16:07:11.174][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-18 16:07:11.175][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-18 16:07:11.176][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-18 16:07:11.177][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-18 16:07:11.177][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-18 16:07:11.178][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-18 16:07:11.179][self$setPropertyValue]
biodb.DEBUG[2024-05-18 16:07:11.180][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-18 16:07:11.181][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-18 16:07:11.182][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-05-18 16:07:11.183][self$setPropertyValue]
biodb.DEBUG[2024-05-18 16:07:11.184][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-05-18 16:07:11.185][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-05-18 16:07:11.186][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-05-18 16:07:11.187][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-18 16:07:11.188][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-18 16:07:11.189][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-18 16:07:11.190][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-18 16:07:11.191][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-05-18 16:07:11.192][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-18 16:07:11.192][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-05-18 16:07:11.193][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-18 16:07:11.194][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-05-18 16:07:11.195][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-05-18 16:07:11.196][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-18 16:07:11.197][self$setPropertyValue]
biodb.DEBUG[2024-05-18 16:07:11.198][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-05-18 16:07:11.199][self$setPropertyValue]
biodb.DEBUG[2024-05-18 16:07:11.200][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-05-18 16:07:11.200][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-18 16:07:11.201][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-18 16:07:11.202][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-18 16:07:11.203][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-18 16:07:11.204][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-18 16:07:11.205][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-18 16:07:11.205][self$setPropertyValue]
biodb.DEBUG[2024-05-18 16:07:11.206][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-18 16:07:11.207][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-18 16:07:11.208][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-05-18 16:07:11.209][self$setPropertyValue]
biodb.DEBUG[2024-05-18 16:07:11.210][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-05-18 16:07:11.211][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:07:11.212][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:07:11.212][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:07:11.213][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-18 16:07:11.214][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 16:07:11.215][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:07:11.216][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:07:11.216][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:07:11.217][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-18 16:07:11.218][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 16:07:11.219][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:07:11.220][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:07:11.220][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:07:11.221][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-18 16:07:11.222][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-18 16:07:11.223][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:07:11.224][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-18 16:07:11.225][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:07:11.225][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-18 16:07:11.226][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 16:07:11.227][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:07:11.228][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:07:11.228][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:07:11.229][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-18 16:07:11.230][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 16:07:11.231][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:07:11.232][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:07:11.232][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:07:11.233][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-18 16:07:11.234][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 16:07:11.235][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:07:11.236][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:07:11.236][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:07:11.237][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-18 16:07:11.238][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-18 16:07:11.239][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:07:11.239][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:07:11.240][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:07:11.241][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-18 16:07:11.242][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 16:07:11.243][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:07:11.243][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:07:11.244][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:07:11.245][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-18 16:07:11.246][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 16:07:11.247][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:07:11.247][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-18 16:07:11.248][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:07:11.249][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-18 16:07:11.250][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 16:07:11.250][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:07:11.251][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-18 16:07:11.252][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:07:11.253][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-18 16:07:11.254][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-18 16:07:11.254][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:07:11.255][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:07:11.256][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:07:11.257][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-18 16:07:11.258][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 16:07:11.258][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:07:11.259][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:07:11.260][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:07:11.261][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-18 16:07:11.261][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 16:07:11.262][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:07:11.263][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:07:11.264][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:07:11.265][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-18 16:07:11.265][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-18 16:07:11.266][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:07:11.267][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-18 16:07:11.268][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:07:11.269][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-18 16:07:11.269][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 16:07:11.270][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:07:11.271][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:07:11.272][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:07:11.272][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-18 16:07:11.273][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 16:07:11.274][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:07:11.275][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-18 16:07:11.276][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:07:11.276][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-18 16:07:11.277][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 16:07:11.278][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:07:11.279][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:07:11.280][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-05-18 16:07:11.281][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-05-18 16:07:11.282][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-05-18 16:07:11.284][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-05-18 16:07:11.285][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-05-18 16:07:11.286][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-05-18 16:07:11.287][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-05-18 16:07:11.288][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-05-18 16:07:11.290][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-05-18 16:07:11.291][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-05-18 16:07:11.292][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-05-18 16:07:11.293][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-05-18 16:07:11.295][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-05-18 16:07:11.296][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-05-18 16:07:11.297][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-05-18 16:07:11.298][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-05-18 16:07:11.300][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-05-18 16:07:11.301][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-05-18 16:07:11.302][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-05-18 16:07:11.303][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-05-18 16:07:11.305][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-05-18 16:07:11.306][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-05-18 16:07:11.307][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-05-18 16:07:11.308][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-05-18 16:07:11.310][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-05-18 16:07:11.315][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-05-18 16:07:11.316][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-05-18 16:07:11.317][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-05-18 16:07:11.318][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-05-18 16:07:11.320][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-05-18 16:07:11.321][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-05-18 16:07:11.322][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-05-18 16:07:11.323][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-05-18 16:07:11.325][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-05-18 16:07:11.326][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-05-18 16:07:11.327][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-05-18 16:07:11.328][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-05-18 16:07:11.330][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-05-18 16:07:11.331][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-05-18 16:07:11.332][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-05-18 16:07:11.333][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-05-18 16:07:11.335][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-05-18 16:07:11.336][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-05-18 16:07:11.337][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-05-18 16:07:11.338][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-05-18 16:07:11.340][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-05-18 16:07:11.341][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-05-18 16:07:11.342][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-05-18 16:07:11.343][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-05-18 16:07:11.345][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-05-18 16:07:11.346][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-05-18 16:07:11.347][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-05-18 16:07:11.348][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-05-18 16:07:11.349][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-05-18 16:07:11.351][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-05-18 16:07:11.352][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-05-18 16:07:11.353][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-05-18 16:07:11.354][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-05-18 16:07:11.356][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-05-18 16:07:11.357][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-05-18 16:07:11.358][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-05-18 16:07:11.359][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-05-18 16:07:11.361][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-05-18 16:07:11.362][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-05-18 16:07:11.363][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-05-18 16:07:11.364][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-05-18 16:07:11.365][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-05-18 16:07:11.367][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-05-18 16:07:11.368][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-05-18 16:07:11.369][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-05-18 16:07:11.370][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-05-18 16:07:11.372][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-05-18 16:07:11.373][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-05-18 16:07:11.374][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-05-18 16:07:11.375][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-05-18 16:07:11.376][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-05-18 16:07:11.378][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-05-18 16:07:11.379][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-05-18 16:07:11.380][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-05-18 16:07:11.381][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-05-18 16:07:11.383][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-05-18 16:07:11.384][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-05-18 16:07:11.385][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-05-18 16:07:11.386][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-05-18 16:07:11.388][initialize] This is biodb version 1.13.0.
biodb.DEBUG[2024-05-18 16:07:11.389][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-05-18 16:07:11.390][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-05-18 16:07:11.390][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 16:07:11.391][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:07:11.392][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:07:11.393][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:07:11.393][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-18 16:07:11.394][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-18 16:07:11.395][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-18 16:07:11.396][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-18 16:07:11.397][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:07:11.397][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:07:11.398][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:07:11.399][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-18 16:07:11.400][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-18 16:07:11.400][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-18 16:07:11.401][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 16:07:11.402][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:07:11.403][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:07:11.404][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:07:11.404][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-18 16:07:11.405][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-18 16:07:11.406][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-18 16:07:11.407][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 16:07:11.408][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:07:11.408][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:07:11.409][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:07:11.410][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-18 16:07:11.411][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-18 16:07:11.411][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-18 16:07:11.412][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 16:07:11.413][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:07:11.414][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:07:11.415][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:07:11.415][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-18 16:07:11.416][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-18 16:07:11.417][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-18 16:07:11.418][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 16:07:11.418][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:07:11.419][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:07:11.420][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:07:11.421][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-18 16:07:11.422][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-18 16:07:11.422][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-18 16:07:11.423][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 16:07:11.424][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:07:11.425][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:07:11.425][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:07:11.426][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-18 16:07:11.427][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-18 16:07:11.428][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-18 16:07:11.429][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 16:07:11.429][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:07:11.430][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:07:11.431][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:07:11.432][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-18 16:07:11.433][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-18 16:07:11.433][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-18 16:07:11.434][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 16:07:11.435][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:07:11.436][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:07:11.436][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:07:11.437][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-18 16:07:11.438][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-18 16:07:11.439][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-18 16:07:11.440][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 16:07:11.440][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:07:11.441][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:07:11.442][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:07:11.443][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-18 16:07:11.443][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-18 16:07:11.444][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-18 16:07:11.445][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 16:07:11.446][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:07:11.447][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:07:11.447][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:07:11.448][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-18 16:07:11.449][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-18 16:07:11.450][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-18 16:07:11.451][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 16:07:11.451][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:07:11.452][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:07:11.453][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:07:11.454][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-18 16:07:11.454][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-18 16:07:11.455][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-18 16:07:11.456][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 16:07:11.457][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:07:11.458][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:07:11.458][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:07:11.459][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-18 16:07:11.460][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-18 16:07:11.461][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-18 16:07:11.461][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 16:07:11.462][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:07:11.463][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-18 16:07:11.464][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:07:11.465][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-18 16:07:11.465][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-18 16:07:11.466][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-18 16:07:11.467][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-18 16:07:11.468][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:07:11.469][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:07:11.473][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:07:11.474][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-18 16:07:11.475][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-18 16:07:11.476][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-18 16:07:11.477][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-18 16:07:11.478][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:07:11.478][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:07:11.479][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:07:11.480][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-18 16:07:11.481][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-18 16:07:11.481][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-18 16:07:11.482][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 16:07:11.483][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:07:11.484][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:07:11.485][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:07:11.485][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-18 16:07:11.486][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-18 16:07:11.487][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-18 16:07:11.488][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 16:07:11.489][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:07:11.489][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:07:11.491][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.20-bioc-longtests/meat/biodbExpasy.Rcheck/biodbExpasy/definitions.yml".
biodb.DEBUG[2024-05-18 16:07:11.499][self$getDbsInfo()$define] Define connector expasy.enzyme.
biodb.DEBUG[2024-05-18 16:07:11.501][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-05-18 16:07:11.502][self$setPropertyValue] Setting property "description" to "Write here the description of this database.".
biodb.DEBUG[2024-05-18 16:07:11.503][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-18 16:07:11.504][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-18 16:07:11.505][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-18 16:07:11.506][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-18 16:07:11.506][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-05-18 16:07:11.507][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-18 16:07:11.508][self$setPropertyValue] Setting property "entry.content.type" to "txt".
biodb.DEBUG[2024-05-18 16:07:11.509][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-18 16:07:11.510][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-05-18 16:07:11.511][self$setPropertyValue] Setting property "name" to "Expasy ENZYME database.".
biodb.DEBUG[2024-05-18 16:07:11.512][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-18 16:07:11.513][self$setPropertyValue] Setting property "parsing.expr" to "^ID\s+([0-9.]+)$".
biodb.DEBUG[2024-05-18 16:07:11.513][self$setPropertyValue] Setting property "parsing.expr" to "^CA\s+(.+?)\.?$".
biodb.DEBUG[2024-05-18 16:07:11.513][self$setPropertyValue] Setting property "parsing.expr" to "^CF\s+(.+?)\.?$".
biodb.DEBUG[2024-05-18 16:07:11.513][self$setPropertyValue] Setting property "parsing.expr" to "^DE\s+(.+?)\.?$".
biodb.DEBUG[2024-05-18 16:07:11.514][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-05-18 16:07:11.514][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-05-18 16:07:11.515][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2024-05-18 16:07:11.516][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-18 16:07:11.517][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-18 16:07:11.518][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-18 16:07:11.519][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-18 16:07:11.519][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-18 16:07:11.520][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-18 16:07:11.521][self$setPropertyValue] Setting property "urls" to "https://enzyme.expasy.org/".
biodb.DEBUG[2024-05-18 16:07:11.522][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-18 16:07:11.523][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-18 16:07:11.524][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-05-18 16:07:11.524][self$setPropertyValue]
biodb.DEBUG[2024-05-18 16:07:11.526][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-05-18 16:07:11.529][super$initialize] Initialize connector expasy.enzyme.
biodb.DEBUG[2024-05-18 16:07:11.530][super$initialize] Register connector expasy.enzyme with the request scheduler
biodb.DEBUG[2024-05-18 16:07:11.531][private$bdb$getRequestScheduler()$re ...] Register connector expasy.enzyme.
biodb.DEBUG[2024-05-18 16:07:11.532][private$addConnectorRules] Create new rule for URL "enzyme.expasy.org" of connector "expasy.enzyme".
biodb.DEBUG[2024-05-18 16:07:11.533][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-05-18 16:07:11.534][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-05-18 16:07:11.535][biodb$getFactory()$createConn] Creating new connector expasy.enzyme for database class expasy.enzyme .
biodb.INFO [2024-05-18 16:07:11.536][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-05-18 16:07:11.537][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector expasy.enzyme from the request scheduler
biodb.INFO [2024-05-18 16:07:11.538][self$deleteConn] Connector "expasy.enzyme" deleted.
biodb.DEBUG[2024-05-18 16:07:11.538][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-05-18 16:07:11.539][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-18 16:07:11.540][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-18 16:07:11.541][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-18 16:07:11.541][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 16:07:11.542][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:07:11.543][FUN] Functions in observer 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 
  5.382   0.186  13.391

'R CMD check' output

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


* using log directory ‘/home/biocbuild/bbs-3.20-bioc-longtests/meat/biodbExpasy.Rcheck’
* using R version 4.4.0 RC (2024-04-16 r86468)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
    GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* using options ‘--no-codoc --no-examples --no-manual --ignore-vignettes --no-stop-on-test-error’
* checking for file ‘biodbExpasy/DESCRIPTION’ ... OK
* this is package ‘biodbExpasy’ version ‘1.9.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘biodbExpasy’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Title field: should not end in a period.
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... SKIPPED
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... SKIPPED
* checking examples ... SKIPPED
* checking for unstated dependencies in ‘longtests’ ... OK
* checking tests in ‘longtests’ ...
  Running ‘testthat.R’
 OK
* DONE

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

Installation output

biodbExpasy.Rcheck/00install.out

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