Back to Long Tests report for BioC 3.20

This page was generated on 2024-06-03 18:33:27 -0400 (Mon, 03 Jun 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 RC (2024-04-16 r86468) -- "Puppy Cup" 4669
palomino4Windows Server 2022 Datacenterx644.4.0 RC (2024-04-16 r86468 ucrt) -- "Puppy Cup" 4404
merida1macOS 12.7.4 Montereyx86_644.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" 4431
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 7/32HostnameOS / ArchCHECK
biodbExpasy 1.9.0  (landing page)
Pierrick Roger
Snapshot Date: 2024-06-03 14:03:53 -0400 (Mon, 03 Jun 2024)
git_url: https://git.bioconductor.org/packages/biodbExpasy
git_branch: devel
git_last_commit: 25fc0fc
git_last_commit_date: 2024-04-30 11:41:12 -0400 (Tue, 30 Apr 2024)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  ERROR  
palomino4Windows Server 2022 Datacenter / x64  OK  
merida1macOS 12.7.4 Monterey / x86_64  ERROR  

CHECK results for biodbExpasy on merida1

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

raw results


Summary

Package: biodbExpasy
Version: 1.9.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --test-dir=longtests --no-stop-on-test-error --no-codoc --no-examples --no-manual --ignore-vignettes --check-subdirs=no biodbExpasy_1.9.0.tar.gz
StartedAt: 2024-06-03 14:22:19 -0400 (Mon, 03 Jun 2024)
EndedAt: 2024-06-03 14:23:23 -0400 (Mon, 03 Jun 2024)
EllapsedTime: 64.3 seconds
RetCode: 1
Status:   ERROR  
CheckDir: biodbExpasy.Rcheck
Warnings: NA

Tests output

biodbExpasy.Rcheck/tests/testthat.Rout.fail


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

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

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

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

> # Script needed to run testthat automatically from ‘R CMD check’. See
> # testthat::test_dir documentation.
> library(testthat)
> library(biodbExpasy)
> Sys.setenv(TESTTHAT_REPORTER="summary")
> Sys.setenv(BIODB_LOG_DST="console")
> test_check("biodbExpasy")
biodb.INFO [2024-06-03 14:23:11.222][biodb::testContext]
biodb.INFO [2024-06-03 14:23:11.226][biodb::testContext] ********************************************************************************
biodb.INFO [2024-06-03 14:23:11.228][biodb::testContext] Test context - Generic long tests
biodb.INFO [2024-06-03 14:23:11.229][biodb::testContext] ********************************************************************************
biodb.INFO [2024-06-03 14:23:11.231][biodb::testContext]
biodb.INFO [2024-06-03 14:23:11.239][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.13.0.
biodb.DEBUG[2024-06-03 14:23:11.242][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2024-06-03 14:23:11.250][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-06-03 14:23:11.252][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-06-03 14:23:11.254][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-06-03 14:23:11.255][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-03 14:23:11.256][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-03 14:23:11.258][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-03 14:23:11.259][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-06-03 14:23:11.291][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-06-03 14:23:11.293][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-03 14:23:11.294][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-03 14:23:11.295][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-03 14:23:11.297][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-06-03 14:23:11.298][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-06-03 14:23:11.300][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-03 14:23:11.301][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-03 14:23:11.302][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-03 14:23:11.304][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-06-03 14:23:11.306][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-06-03 14:23:11.307][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-06-03 14:23:11.308][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-03 14:23:11.310][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-03 14:23:11.311][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-03 14:23:11.313][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-06-03 14:23:11.325][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-06-03 14:23:11.326][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-06-03 14:23:11.328][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-03 14:23:11.329][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-03 14:23:11.330][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-03 14:23:11.331][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-06-03 14:23:11.332][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-06-03 14:23:11.333][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-03 14:23:11.334][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-03 14:23:11.335][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-03 14:23:11.337][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-06-03 14:23:11.338][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-06-03 14:23:11.339][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-06-03 14:23:11.340][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-03 14:23:11.341][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-03 14:23:11.342][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-03 14:23:11.344][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-06-03 14:23:11.345][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-06-03 14:23:11.346][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-03 14:23:11.347][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-03 14:23:11.348][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-03 14:23:11.349][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-06-03 14:23:11.351][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-06-03 14:23:11.352][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-06-03 14:23:11.353][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-03 14:23:11.354][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-03 14:23:11.355][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-03 14:23:11.357][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-06-03 14:23:11.358][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-06-03 14:23:11.359][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-06-03 14:23:11.360][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-06-03 14:23:11.361][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-06-03 14:23:11.363][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-06-03 14:23:11.364][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-03 14:23:11.365][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-03 14:23:11.366][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-03 14:23:11.367][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-06-03 14:23:11.369][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-06-03 14:23:11.370][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-03 14:23:11.371][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-03 14:23:11.372][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-03 14:23:11.373][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-06-03 14:23:11.374][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-06-03 14:23:11.376][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-03 14:23:11.377][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-03 14:23:11.378][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-03 14:23:11.379][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-06-03 14:23:11.380][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-06-03 14:23:11.381][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-03 14:23:11.382][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-03 14:23:11.384][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-03 14:23:11.385][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-06-03 14:23:11.386][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-06-03 14:23:11.387][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-03 14:23:11.388][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-03 14:23:11.389][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-03 14:23:11.391][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-06-03 14:23:11.392][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-06-03 14:23:11.393][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-03 14:23:11.394][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-03 14:23:11.395][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-03 14:23:11.397][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-06-03 14:23:11.398][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-06-03 14:23:11.409][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-06-03 14:23:11.410][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-03 14:23:11.411][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-03 14:23:11.412][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-03 14:23:11.414][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-06-03 14:23:11.415][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-06-03 14:23:11.416][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-06-03 14:23:11.417][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-03 14:23:11.418][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-03 14:23:11.419][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-03 14:23:11.423][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-06-03 14:23:11.469][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-06-03 14:23:11.491][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2024-06-03 14:23:11.492][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-03 14:23:11.494][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-03 14:23:11.495][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-03 14:23:11.496][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-03 14:23:11.497][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-03 14:23:11.499][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-03 14:23:11.500][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-06-03 14:23:11.501][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-03 14:23:11.502][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-06-03 14:23:11.504][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-06-03 14:23:11.505][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-03 14:23:11.506][self$setPropertyValue]
biodb.DEBUG[2024-06-03 14:23:11.507][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-03 14:23:11.508][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-06-03 14:23:11.508][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-06-03 14:23:11.508][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-06-03 14:23:11.508][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-06-03 14:23:11.508][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-06-03 14:23:11.510][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-03 14:23:11.511][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-03 14:23:11.512][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-03 14:23:11.513][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-03 14:23:11.514][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-03 14:23:11.515][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-03 14:23:11.517][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-03 14:23:11.518][self$setPropertyValue]
biodb.DEBUG[2024-06-03 14:23:11.519][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-03 14:23:11.520][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-03 14:23:11.521][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-03 14:23:11.523][self$setPropertyValue]
biodb.DEBUG[2024-06-03 14:23:11.524][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-06-03 14:23:11.526][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-06-03 14:23:11.528][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-06-03 14:23:11.529][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-03 14:23:11.530][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-03 14:23:11.531][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-03 14:23:11.533][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-03 14:23:11.534][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-03 14:23:11.535][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-03 14:23:11.536][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-06-03 14:23:11.538][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-03 14:23:11.539][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-06-03 14:23:11.540][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-06-03 14:23:11.542][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-03 14:23:11.543][self$setPropertyValue]
biodb.DEBUG[2024-06-03 14:23:11.544][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-03 14:23:11.545][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-06-03 14:23:11.545][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-06-03 14:23:11.545][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-06-03 14:23:11.545][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-06-03 14:23:11.545][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-06-03 14:23:11.547][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-03 14:23:11.548][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-03 14:23:11.549][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-03 14:23:11.550][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-03 14:23:11.552][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-03 14:23:11.553][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-03 14:23:11.554][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-03 14:23:11.555][self$setPropertyValue]
biodb.DEBUG[2024-06-03 14:23:11.556][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-03 14:23:11.558][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-03 14:23:11.559][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-03 14:23:11.560][self$setPropertyValue]
biodb.DEBUG[2024-06-03 14:23:11.562][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-06-03 14:23:11.564][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-06-03 14:23:11.565][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2024-06-03 14:23:11.566][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-03 14:23:11.568][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-03 14:23:11.569][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-03 14:23:11.570][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-03 14:23:11.571][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-03 14:23:11.573][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-03 14:23:11.574][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-06-03 14:23:11.576][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-03 14:23:11.577][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-06-03 14:23:11.579][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-06-03 14:23:11.580][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-03 14:23:11.586][self$setPropertyValue]
biodb.DEBUG[2024-06-03 14:23:11.588][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-03 14:23:11.589][self$setPropertyValue]
biodb.DEBUG[2024-06-03 14:23:11.590][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-03 14:23:11.591][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-03 14:23:11.592][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-03 14:23:11.594][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-03 14:23:11.595][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-03 14:23:11.596][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-03 14:23:11.597][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-03 14:23:11.598][self$setPropertyValue]
biodb.DEBUG[2024-06-03 14:23:11.600][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-03 14:23:11.601][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-03 14:23:11.602][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-03 14:23:11.603][self$setPropertyValue]
biodb.DEBUG[2024-06-03 14:23:11.605][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-06-03 14:23:11.607][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-06-03 14:23:11.608][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-06-03 14:23:11.609][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-03 14:23:11.610][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-03 14:23:11.612][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-03 14:23:11.613][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-03 14:23:11.614][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-03 14:23:11.615][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-03 14:23:11.617][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-06-03 14:23:11.618][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-03 14:23:11.619][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-06-03 14:23:11.620][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-06-03 14:23:11.621][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-03 14:23:11.623][self$setPropertyValue]
biodb.DEBUG[2024-06-03 14:23:11.624][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-03 14:23:11.625][self$setPropertyValue]
biodb.DEBUG[2024-06-03 14:23:11.626][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-03 14:23:11.628][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-03 14:23:11.629][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-03 14:23:11.630][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-03 14:23:11.631][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-03 14:23:11.632][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-03 14:23:11.633][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-03 14:23:11.635][self$setPropertyValue]
biodb.DEBUG[2024-06-03 14:23:11.636][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-03 14:23:11.637][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-03 14:23:11.638][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-03 14:23:11.639][self$setPropertyValue]
biodb.DEBUG[2024-06-03 14:23:11.644][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-06-03 14:23:11.645][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-06-03 14:23:11.646][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-03 14:23:11.647][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-03 14:23:11.648][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-03 14:23:11.649][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-03 14:23:11.650][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-03 14:23:11.652][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-03 14:23:11.653][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-03 14:23:11.654][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-03 14:23:11.655][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-03 14:23:11.656][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-03 14:23:11.657][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-03 14:23:11.658][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-03 14:23:11.659][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-03 14:23:11.660][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-03 14:23:11.661][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-03 14:23:11.663][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-03 14:23:11.664][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-03 14:23:11.665][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-03 14:23:11.666][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-03 14:23:11.667][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-03 14:23:11.668][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-03 14:23:11.669][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-03 14:23:11.670][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-03 14:23:11.671][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-03 14:23:11.672][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-03 14:23:11.674][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-03 14:23:11.675][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-03 14:23:11.676][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-03 14:23:11.677][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-03 14:23:11.678][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-03 14:23:11.679][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-03 14:23:11.680][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-03 14:23:11.681][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-03 14:23:11.682][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-03 14:23:11.683][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-03 14:23:11.685][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-03 14:23:11.686][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-03 14:23:11.687][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-03 14:23:11.688][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-03 14:23:11.689][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-03 14:23:11.690][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-03 14:23:11.691][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-03 14:23:11.692][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-03 14:23:11.693][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-03 14:23:11.694][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-03 14:23:11.695][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-03 14:23:11.697][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-03 14:23:11.698][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-03 14:23:11.699][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-03 14:23:11.700][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-03 14:23:11.701][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-03 14:23:11.702][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-03 14:23:11.703][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-03 14:23:11.704][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-03 14:23:11.705][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-03 14:23:11.707][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-03 14:23:11.708][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-03 14:23:11.709][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-03 14:23:11.710][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-03 14:23:11.711][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-03 14:23:11.712][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-03 14:23:11.713][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-03 14:23:11.714][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-03 14:23:11.715][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-03 14:23:11.716][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-03 14:23:11.718][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-03 14:23:11.719][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-03 14:23:11.720][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-03 14:23:11.721][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-03 14:23:11.722][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-03 14:23:11.723][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-03 14:23:11.724][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-03 14:23:11.725][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-03 14:23:11.726][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-03 14:23:11.728][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-03 14:23:11.729][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-03 14:23:11.730][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-03 14:23:11.731][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-03 14:23:11.732][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-03 14:23:11.733][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-03 14:23:11.734][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-03 14:23:11.735][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-03 14:23:11.737][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-03 14:23:11.738][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-03 14:23:11.739][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-03 14:23:11.740][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-03 14:23:11.741][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-06-03 14:23:11.746][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-06-03 14:23:11.748][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-06-03 14:23:11.750][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-06-03 14:23:11.752][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-06-03 14:23:11.754][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-06-03 14:23:11.755][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-06-03 14:23:11.757][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-06-03 14:23:11.759][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-06-03 14:23:11.760][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-06-03 14:23:11.762][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-06-03 14:23:11.764][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-06-03 14:23:11.766][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-06-03 14:23:11.767][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-06-03 14:23:11.769][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-06-03 14:23:11.771][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-06-03 14:23:11.772][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-06-03 14:23:11.774][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-06-03 14:23:11.776][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-06-03 14:23:11.778][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-06-03 14:23:11.779][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-06-03 14:23:11.781][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-06-03 14:23:11.783][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-06-03 14:23:11.785][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-06-03 14:23:11.786][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-06-03 14:23:11.788][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-06-03 14:23:11.790][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-06-03 14:23:11.792][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-06-03 14:23:11.793][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-06-03 14:23:11.795][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-06-03 14:23:11.797][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-06-03 14:23:11.799][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-06-03 14:23:11.800][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-06-03 14:23:11.802][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-06-03 14:23:11.804][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-06-03 14:23:11.806][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-06-03 14:23:11.807][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-06-03 14:23:11.809][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-06-03 14:23:11.811][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-06-03 14:23:11.813][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-06-03 14:23:11.814][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-06-03 14:23:11.816][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-06-03 14:23:11.818][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-06-03 14:23:11.820][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-06-03 14:23:11.821][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-06-03 14:23:11.823][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-06-03 14:23:11.825][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-06-03 14:23:11.832][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-06-03 14:23:11.834][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-06-03 14:23:11.836][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-06-03 14:23:11.838][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-06-03 14:23:11.839][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-06-03 14:23:11.841][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-06-03 14:23:11.843][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-06-03 14:23:11.844][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-06-03 14:23:11.846][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-06-03 14:23:11.848][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-06-03 14:23:11.849][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-06-03 14:23:11.851][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-06-03 14:23:11.853][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-06-03 14:23:11.855][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-06-03 14:23:11.856][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-06-03 14:23:11.858][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-06-03 14:23:11.860][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-06-03 14:23:11.861][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-06-03 14:23:11.863][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-06-03 14:23:11.865][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-06-03 14:23:11.866][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-06-03 14:23:11.868][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-06-03 14:23:11.870][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-06-03 14:23:11.872][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-06-03 14:23:11.873][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-06-03 14:23:11.875][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-06-03 14:23:11.877][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-06-03 14:23:11.879][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-06-03 14:23:11.881][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-06-03 14:23:11.883][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-06-03 14:23:11.884][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-06-03 14:23:11.886][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-06-03 14:23:11.888][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-06-03 14:23:11.889][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-06-03 14:23:11.891][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-06-03 14:23:11.893][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-06-03 14:23:11.901][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-06-03 14:23:11.903][initialize] This is biodb version 1.13.0.
biodb.DEBUG[2024-06-03 14:23:11.906][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-06-03 14:23:11.908][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-06-03 14:23:11.909][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-03 14:23:11.910][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-06-03 14:23:11.911][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-03 14:23:11.918][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-03 14:23:11.919][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-03 14:23:11.920][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-03 14:23:11.921][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-03 14:23:11.922][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-03 14:23:11.923][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-03 14:23:11.924][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-03 14:23:11.926][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-03 14:23:11.927][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-03 14:23:11.928][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-03 14:23:11.929][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-03 14:23:11.930][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-03 14:23:11.931][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-03 14:23:11.932][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-03 14:23:11.933][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-03 14:23:11.934][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-03 14:23:11.936][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-03 14:23:11.937][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-03 14:23:11.938][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-03 14:23:11.939][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-03 14:23:11.940][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[2024-06-03 14:23:11.941][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-03 14:23:11.942][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-03 14:23:11.943][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-03 14:23:11.944][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-03 14:23:11.946][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-03 14:23:11.947][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-03 14:23:11.948][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-03 14:23:11.949][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-03 14:23:11.950][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-03 14:23:11.951][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-03 14:23:11.952][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-03 14:23:11.953][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-03 14:23:11.954][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-03 14:23:11.956][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-03 14:23:11.957][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-03 14:23:11.958][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-03 14:23:11.959][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-03 14:23:11.960][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-03 14:23:11.961][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-03 14:23:11.962][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-03 14:23:11.963][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[2024-06-03 14:23:11.964][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-03 14:23:11.966][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-03 14:23:11.967][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-03 14:23:11.968][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-03 14:23:11.969][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-03 14:23:11.970][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-03 14:23:11.971][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-03 14:23:11.972][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-03 14:23:11.973][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-03 14:23:11.974][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-03 14:23:11.976][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-03 14:23:11.977][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-03 14:23:11.978][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-03 14:23:11.979][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-03 14:23:11.980][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-03 14:23:11.981][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-03 14:23:11.982][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-03 14:23:11.983][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-03 14:23:11.984][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-03 14:23:11.985][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-03 14:23:11.987][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-03 14:23:11.988][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-03 14:23:11.989][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-03 14:23:11.990][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-03 14:23:11.991][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-03 14:23:11.992][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-03 14:23:11.993][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-03 14:23:11.994][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-03 14:23:11.996][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-03 14:23:11.997][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-03 14:23:11.998][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-03 14:23:11.999][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-03 14:23:12.000][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-03 14:23:12.001][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-03 14:23:12.002][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-03 14:23:12.003][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-03 14:23:12.004][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-03 14:23:12.006][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-03 14:23:12.007][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-03 14:23:12.008][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-03 14:23:12.009][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-03 14:23:12.010][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-03 14:23:12.011][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-03 14:23:12.012][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-03 14:23:12.013][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-03 14:23:12.015][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-03 14:23:12.016][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-03 14:23:12.017][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-03 14:23:12.018][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-03 14:23:12.019][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-03 14:23:12.020][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-03 14:23:12.021][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-03 14:23:12.022][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-03 14:23:12.023][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-03 14:23:12.025][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-03 14:23:12.026][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[2024-06-03 14:23:12.027][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-03 14:23:12.028][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-03 14:23:12.029][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-03 14:23:12.030][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-03 14:23:12.031][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-03 14:23:12.032][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-03 14:23:12.033][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-03 14:23:12.035][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-03 14:23:12.036][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-03 14:23:12.037][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-03 14:23:12.038][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-03 14:23:12.039][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-03 14:23:12.040][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-03 14:23:12.042][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-03 14:23:12.043][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-03 14:23:12.044][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-03 14:23:12.045][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-03 14:23:12.046][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-03 14:23:12.047][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-03 14:23:12.049][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-03 14:23:12.050][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-03 14:23:12.053][biodb$loadDefinitions] Load definitions from file "/Users/biocbuild/bbs-3.20-bioc-longtests/meat/biodbExpasy.Rcheck/biodbExpasy/definitions.yml".
biodb.DEBUG[2024-06-03 14:23:12.066][self$getDbsInfo()$define] Define connector expasy.enzyme.
biodb.DEBUG[2024-06-03 14:23:12.068][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-06-03 14:23:12.074][self$setPropertyValue] Setting property "description" to "Write here the description of this database.".
biodb.DEBUG[2024-06-03 14:23:12.075][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-03 14:23:12.077][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-03 14:23:12.078][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-03 14:23:12.079][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-03 14:23:12.080][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-06-03 14:23:12.081][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-03 14:23:12.083][self$setPropertyValue] Setting property "entry.content.type" to "txt".
biodb.DEBUG[2024-06-03 14:23:12.084][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-03 14:23:12.085][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-06-03 14:23:12.086][self$setPropertyValue] Setting property "name" to "Expasy ENZYME database.".
biodb.DEBUG[2024-06-03 14:23:12.088][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-03 14:23:12.089][self$setPropertyValue] Setting property "parsing.expr" to "^ID\s+([0-9.]+)$".
biodb.DEBUG[2024-06-03 14:23:12.089][self$setPropertyValue] Setting property "parsing.expr" to "^CA\s+(.+?)\.?$".
biodb.DEBUG[2024-06-03 14:23:12.089][self$setPropertyValue] Setting property "parsing.expr" to "^CF\s+(.+?)\.?$".
biodb.DEBUG[2024-06-03 14:23:12.089][self$setPropertyValue] Setting property "parsing.expr" to "^DE\s+(.+?)\.?$".
biodb.DEBUG[2024-06-03 14:23:12.090][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-06-03 14:23:12.091][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-06-03 14:23:12.093][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2024-06-03 14:23:12.094][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-03 14:23:12.095][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-03 14:23:12.096][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-03 14:23:12.097][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-03 14:23:12.098][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-03 14:23:12.099][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-03 14:23:12.101][self$setPropertyValue] Setting property "urls" to "https://enzyme.expasy.org/".
biodb.DEBUG[2024-06-03 14:23:12.102][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-03 14:23:12.103][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-03 14:23:12.104][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-06-03 14:23:12.105][self$setPropertyValue]
biodb.DEBUG[2024-06-03 14:23:12.113][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-06-03 14:23:12.137][super$initialize] Initialize connector expasy.enzyme.
biodb.DEBUG[2024-06-03 14:23:12.139][super$initialize] Register connector expasy.enzyme with the request scheduler
biodb.DEBUG[2024-06-03 14:23:12.143][private$bdb$getRequestScheduler()$re ...] Register connector expasy.enzyme.
biodb.DEBUG[2024-06-03 14:23:12.148][private$addConnectorRules] Create new rule for URL "enzyme.expasy.org" of connector "expasy.enzyme".
biodb.DEBUG[2024-06-03 14:23:12.153][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-06-03 14:23:12.154][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-06-03 14:23:12.155][biodb$getFactory()$createConn] Creating new connector expasy.enzyme for database class expasy.enzyme .
biodb.INFO [2024-06-03 14:23:12.167][biodb::testThat]
biodb.INFO [2024-06-03 14:23:12.168][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2024-06-03 14:23:12.169][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-03 14:23:12.170][biodb::testThat]
biodb.TRACE[2024-06-03 14:23:12.175][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/bbs-3.20-bioc-longtests/meat/biodbExpasy.Rcheck/biodbExpasy/testref/entry-expasy.enzyme-1.1.1.1-content.txt".
biodb.DEBUG[2024-06-03 14:23:12.177][biodb$getFactory()$createEntryFromCo ...] Creating Expasy ENZYME database. entries from 1 content(s).
biodb.DEBUG[2024-06-03 14:23:12.181][biodb$getFactory()$createEntryFromCo ...] Parsing 1 Expasy ENZYME database. entries.
biodb.DEBUG[2024-06-03 14:23:12.190][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-03 14:23:12.191][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-03 14:23:12.192][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-03 14:23:12.208][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-03 14:23:12.209][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-03 14:23:12.210][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-03 14:23:12.212][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.TRACE[2024-06-03 14:23:12.223][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-03 14:23:12.225][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-03 14:23:12.226][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-03 14:23:12.227][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-03 14:23:12.263][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-06-03 14:23:12.281][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-06-03 14:23:12.282][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-03 14:23:12.283][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-03 14:23:12.285][self$getBiodb()$getEntryFields()$get] Asked field names are: cofactor.
biodb.TRACE[2024-06-03 14:23:12.286][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-06-03 14:23:12.287][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-03 14:23:12.289][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-03 14:23:12.290][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-03 14:23:12.292][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-03 14:23:12.293][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-03 14:23:12.294][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-03 14:23:12.295][self$getBiodb()$getEntryFields()$get] Asked field names are: COFACTOR.
biodb.TRACE[2024-06-03 14:23:12.297][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-06-03 14:23:12.298][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-03 14:23:12.299][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-03 14:23:12.300][self$getBiodb()$getEntryFields()$get] Asked field names are: cofactor.
biodb.TRACE[2024-06-03 14:23:12.302][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-06-03 14:23:12.303][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-03 14:23:12.304][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-03 14:23:12.305][self$getBiodb()$getEntryFields()$get] Asked field names are: cofactor.
biodb.TRACE[2024-06-03 14:23:12.307][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-06-03 14:23:12.308][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-03 14:23:12.309][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-03 14:23:12.311][self$getBiodb()$getEntryFields()$get] Asked field names are: cofactor.
biodb.TRACE[2024-06-03 14:23:12.312][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-06-03 14:23:12.313][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-03 14:23:12.314][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-03 14:23:12.316][self$getBiodb()$getEntryFields()$get] Asked field names are: COFACTOR.
biodb.TRACE[2024-06-03 14:23:12.317][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-06-03 14:23:12.318][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-03 14:23:12.319][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-03 14:23:12.353][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-03 14:23:12.354][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-03 14:23:12.355][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-03 14:23:12.356][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-03 14:23:12.358][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-03 14:23:12.359][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-03 14:23:12.360][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-03 14:23:12.361][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-03 14:23:12.408][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-03 14:23:12.410][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-03 14:23:12.411][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-03 14:23:12.412][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-03 14:23:12.413][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-03 14:23:12.415][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-03 14:23:12.416][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-03 14:23:12.417][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-03 14:23:12.418][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-03 14:23:12.419][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-03 14:23:12.421][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-03 14:23:12.422][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-03 14:23:12.423][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-06-03 14:23:12.424][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-06-03 14:23:12.426][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-03 14:23:12.427][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-03 14:23:12.428][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-06-03 14:23:12.429][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-06-03 14:23:12.430][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-03 14:23:12.432][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-03 14:23:12.433][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-03 14:23:12.434][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-03 14:23:12.435][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-03 14:23:12.436][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-03 14:23:12.438][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-06-03 14:23:12.439][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-06-03 14:23:12.440][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-03 14:23:12.441][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-03 14:23:12.443][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-03 14:23:12.444][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-03 14:23:12.445][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-03 14:23:12.446][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-03 14:23:12.447][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-03 14:23:12.449][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-03 14:23:12.450][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-03 14:23:12.451][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-03 14:23:12.452][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-03 14:23:12.454][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-03 14:23:12.455][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-03 14:23:12.456][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-03 14:23:12.457][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-03 14:23:12.459][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-03 14:23:12.460][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-03 14:23:12.461][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-03 14:23:12.462][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-03 14:23:12.464][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-03 14:23:12.465][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-03 14:23:12.466][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-03 14:23:12.467][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-03 14:23:12.468][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-03 14:23:12.470][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-03 14:23:12.471][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-03 14:23:12.472][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 1.1.1.1.
biodb.TRACE[2024-06-03 14:23:12.475][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-06-03 14:23:12.476][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-06-03 14:23:12.477][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-03 14:23:12.479][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-03 14:23:12.480][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-06-03 14:23:12.481][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-06-03 14:23:12.482][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-03 14:23:12.483][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-03 14:23:12.485][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-06-03 14:23:12.486][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-06-03 14:23:12.487][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-03 14:23:12.489][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-03 14:23:12.490][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-06-03 14:23:12.491][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-06-03 14:23:12.492][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-03 14:23:12.494][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-03 14:23:12.512][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-03 14:23:12.513][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-03 14:23:12.515][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-03 14:23:12.516][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-03 14:23:12.563][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-06-03 14:23:12.565][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-06-03 14:23:12.566][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-03 14:23:12.567][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-03 14:23:12.574][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-03 14:23:12.575][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-03 14:23:12.576][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-03 14:23:12.577][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-03 14:23:12.579][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-03 14:23:12.580][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-03 14:23:12.581][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-03 14:23:12.582][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-03 14:23:12.583][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-03 14:23:12.585][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-03 14:23:12.586][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-03 14:23:12.587][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-03 14:23:12.590][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-03 14:23:12.592][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-03 14:23:12.593][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-03 14:23:12.594][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-03 14:23:12.595][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-03 14:23:12.597][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-03 14:23:12.598][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-03 14:23:12.599][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-03 14:23:12.600][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-03 14:23:12.602][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-03 14:23:12.603][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-03 14:23:12.604][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-03 14:23:12.606][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-06-03 14:23:12.607][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-06-03 14:23:12.608][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-03 14:23:12.609][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-03 14:23:12.611][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-06-03 14:23:12.612][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-06-03 14:23:12.613][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-03 14:23:12.614][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-03 14:23:12.616][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-06-03 14:23:12.617][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-06-03 14:23:12.618][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-03 14:23:12.619][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-03 14:23:12.629][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-03 14:23:12.631][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-03 14:23:12.632][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-03 14:23:12.633][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-03 14:23:12.635][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-03 14:23:12.636][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-03 14:23:12.637][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-03 14:23:12.638][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-03 14:23:12.640][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-03 14:23:12.641][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-03 14:23:12.642][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-03 14:23:12.643][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-03 14:23:12.644][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-03 14:23:12.646][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-03 14:23:12.647][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-03 14:23:12.648][ef$get] fields variable is a list.
biodb.TRACE[2024-06-03 14:23:12.649][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-03 14:23:12.651][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-03 14:23:12.652][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-03 14:23:12.653][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-03 14:23:12.665][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-03 14:23:12.666][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-03 14:23:12.667][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-03 14:23:12.669][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-03 14:23:12.670][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-03 14:23:12.671][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-03 14:23:12.672][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-03 14:23:12.674][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-03 14:23:12.675][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-03 14:23:12.676][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-03 14:23:12.677][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-03 14:23:12.678][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-03 14:23:12.680][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-03 14:23:12.681][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-03 14:23:12.682][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-03 14:23:12.683][ef$get] fields variable is a list.
biodb.TRACE[2024-06-03 14:23:12.685][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-03 14:23:12.686][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-03 14:23:12.687][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-03 14:23:12.688][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-03 14:23:12.700][self$getBiodb()$getEntryFields()$get] Asked field names are: cofactor.
biodb.TRACE[2024-06-03 14:23:12.702][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-06-03 14:23:12.703][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-03 14:23:12.704][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-03 14:23:12.705][self$getBiodb()$getEntryFields()$get] Asked field names are: cofactor.
biodb.TRACE[2024-06-03 14:23:12.707][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-06-03 14:23:12.708][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-03 14:23:12.709][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-03 14:23:12.710][self$getBiodb()$getEntryFields()$get] Asked field names are: cofactor.
biodb.TRACE[2024-06-03 14:23:12.712][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-06-03 14:23:12.713][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-03 14:23:12.714][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-03 14:23:12.716][ef$get] Asked field names are: cofactor.
biodb.TRACE[2024-06-03 14:23:12.717][ef$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-06-03 14:23:12.718][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-03 14:23:12.719][ef$get] fields variable is a list.
biodb.TRACE[2024-06-03 14:23:12.721][self$getBiodb()$getEntryFields()$get] Asked field names are: cofactor.
biodb.TRACE[2024-06-03 14:23:12.722][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-06-03 14:23:12.723][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-03 14:23:12.724][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-03 14:23:12.736][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-06-03 14:23:12.737][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-06-03 14:23:12.738][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-03 14:23:12.740][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-03 14:23:12.741][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-06-03 14:23:12.742][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-06-03 14:23:12.743][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-03 14:23:12.744][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-03 14:23:12.746][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-06-03 14:23:12.747][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-06-03 14:23:12.748][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-03 14:23:12.749][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-03 14:23:12.751][ef$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-06-03 14:23:12.752][ef$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-06-03 14:23:12.753][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-03 14:23:12.754][ef$get] fields variable is a list.
biodb.TRACE[2024-06-03 14:23:12.756][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-06-03 14:23:12.757][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-06-03 14:23:12.758][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-03 14:23:12.759][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-03 14:23:12.775][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-03 14:23:12.777][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-03 14:23:12.778][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-03 14:23:12.779][ef$get] fields variable is a list.
biodb.TRACE[2024-06-03 14:23:12.786][ef$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-06-03 14:23:12.787][ef$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-06-03 14:23:12.788][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-03 14:23:12.789][ef$get] fields variable is a list.
biodb.TRACE[2024-06-03 14:23:12.796][ef$get] Asked field names are: cofactor.
biodb.TRACE[2024-06-03 14:23:12.797][ef$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-06-03 14:23:12.798][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-03 14:23:12.800][ef$get] fields variable is a list.
biodb.TRACE[2024-06-03 14:23:12.806][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-03 14:23:12.808][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-03 14:23:12.809][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-03 14:23:12.810][ef$get] fields variable is a list.
biodb.TRACE[2024-06-03 14:23:12.834][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/bbs-3.20-bioc-longtests/meat/biodbExpasy.Rcheck/biodbExpasy/testref/entry-expasy.enzyme-1.1.1.54-content.txt".
biodb.DEBUG[2024-06-03 14:23:12.883][biodb$getFactory()$createEntryFromCo ...] Creating Expasy ENZYME database. entries from 1 content(s).
biodb.DEBUG[2024-06-03 14:23:12.884][biodb$getFactory()$createEntryFromCo ...] Parsing 1 Expasy ENZYME database. entries.
biodb.DEBUG[2024-06-03 14:23:12.886][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-03 14:23:12.888][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-03 14:23:12.889][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-03 14:23:12.895][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-03 14:23:12.896][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-03 14:23:12.897][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-03 14:23:12.898][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-03 14:23:12.901][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-03 14:23:12.902][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-03 14:23:12.903][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-03 14:23:12.905][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-03 14:23:12.906][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-06-03 14:23:12.908][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-06-03 14:23:12.909][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-03 14:23:12.910][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-03 14:23:12.912][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-03 14:23:12.913][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-03 14:23:12.914][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-03 14:23:12.915][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-03 14:23:12.917][self$getBiodb()$getEntryFields()$get] Asked field names are: COFACTOR.
biodb.TRACE[2024-06-03 14:23:12.918][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-06-03 14:23:12.919][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-03 14:23:12.920][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-03 14:23:12.922][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-06-03 14:23:12.923][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-06-03 14:23:12.924][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-03 14:23:12.925][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-03 14:23:12.927][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-06-03 14:23:12.928][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-06-03 14:23:12.929][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-03 14:23:12.930][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-03 14:23:12.932][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-03 14:23:12.933][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-03 14:23:12.934][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-03 14:23:12.935][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-03 14:23:12.937][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-06-03 14:23:12.938][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-06-03 14:23:12.939][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-03 14:23:12.940][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-03 14:23:12.942][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-03 14:23:12.943][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-03 14:23:12.944][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-03 14:23:12.945][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-03 14:23:12.947][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-03 14:23:12.948][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-03 14:23:12.949][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-03 14:23:12.950][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-03 14:23:12.951][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-03 14:23:12.953][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-03 14:23:12.954][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-03 14:23:12.955][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-03 14:23:12.957][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-03 14:23:12.958][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-03 14:23:12.959][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-03 14:23:12.960][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-03 14:23:12.962][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-03 14:23:12.963][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-03 14:23:12.969][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-03 14:23:12.970][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-03 14:23:12.971][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-03 14:23:12.973][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-03 14:23:12.974][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-03 14:23:12.975][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-03 14:23:12.976][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 1.1.1.54.
biodb.TRACE[2024-06-03 14:23:13.004][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-06-03 14:23:13.006][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-06-03 14:23:13.007][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-03 14:23:13.009][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-03 14:23:13.010][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-06-03 14:23:13.012][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-06-03 14:23:13.013][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-03 14:23:13.014][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-03 14:23:13.015][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-06-03 14:23:13.017][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-06-03 14:23:13.018][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-03 14:23:13.020][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-03 14:23:13.021][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-06-03 14:23:13.022][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-06-03 14:23:13.024][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-03 14:23:13.025][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-03 14:23:13.027][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-03 14:23:13.029][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-03 14:23:13.030][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-03 14:23:13.031][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-03 14:23:13.038][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-06-03 14:23:13.039][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-06-03 14:23:13.041][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-03 14:23:13.042][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-03 14:23:13.049][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-03 14:23:13.050][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-03 14:23:13.051][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-03 14:23:13.052][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-03 14:23:13.054][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-03 14:23:13.055][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-03 14:23:13.056][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-03 14:23:13.057][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-03 14:23:13.059][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-03 14:23:13.060][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-03 14:23:13.061][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-03 14:23:13.062][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-03 14:23:13.065][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-03 14:23:13.067][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-03 14:23:13.068][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-03 14:23:13.069][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-03 14:23:13.070][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-03 14:23:13.072][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-03 14:23:13.073][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-03 14:23:13.074][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-03 14:23:13.075][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-03 14:23:13.077][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-03 14:23:13.078][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-03 14:23:13.079][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-03 14:23:13.081][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-06-03 14:23:13.082][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-06-03 14:23:13.083][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-03 14:23:13.084][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-03 14:23:13.086][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-06-03 14:23:13.087][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-06-03 14:23:13.088][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-03 14:23:13.090][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-03 14:23:13.091][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-06-03 14:23:13.092][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-06-03 14:23:13.093][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-03 14:23:13.094][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-03 14:23:13.117][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-03 14:23:13.119][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-03 14:23:13.120][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-03 14:23:13.121][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-03 14:23:13.122][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-03 14:23:13.124][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-03 14:23:13.125][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-03 14:23:13.126][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-03 14:23:13.127][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-03 14:23:13.128][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-03 14:23:13.130][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-03 14:23:13.131][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-03 14:23:13.132][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-03 14:23:13.133][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-03 14:23:13.135][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-03 14:23:13.136][ef$get] fields variable is a list.
biodb.TRACE[2024-06-03 14:23:13.137][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-03 14:23:13.138][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-03 14:23:13.139][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-03 14:23:13.141][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-03 14:23:13.152][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-03 14:23:13.154][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-03 14:23:13.155][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-03 14:23:13.156][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-03 14:23:13.157][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-03 14:23:13.159][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-03 14:23:13.160][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-03 14:23:13.161][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-03 14:23:13.162][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-03 14:23:13.163][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-03 14:23:13.165][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-03 14:23:13.166][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-03 14:23:13.167][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-03 14:23:13.173][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-03 14:23:13.174][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-03 14:23:13.175][ef$get] fields variable is a list.
biodb.TRACE[2024-06-03 14:23:13.176][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-03 14:23:13.178][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-03 14:23:13.179][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-03 14:23:13.180][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-03 14:23:13.191][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-06-03 14:23:13.193][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-06-03 14:23:13.194][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-03 14:23:13.195][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-03 14:23:13.196][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-06-03 14:23:13.198][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-06-03 14:23:13.199][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-03 14:23:13.200][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-03 14:23:13.201][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-06-03 14:23:13.203][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-06-03 14:23:13.204][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-03 14:23:13.205][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-03 14:23:13.206][ef$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-06-03 14:23:13.208][ef$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-06-03 14:23:13.209][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-03 14:23:13.210][ef$get] fields variable is a list.
biodb.TRACE[2024-06-03 14:23:13.211][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-06-03 14:23:13.212][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-06-03 14:23:13.214][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-03 14:23:13.215][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-03 14:23:13.226][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-03 14:23:13.228][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-03 14:23:13.229][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-03 14:23:13.230][ef$get] fields variable is a list.
biodb.TRACE[2024-06-03 14:23:13.236][ef$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-06-03 14:23:13.238][ef$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-06-03 14:23:13.239][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-03 14:23:13.240][ef$get] fields variable is a list.
biodb.TRACE[2024-06-03 14:23:13.247][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-03 14:23:13.248][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-03 14:23:13.249][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-03 14:23:13.251][ef$get] fields variable is a list.
biodb.INFO [2024-06-03 14:23:13.262][biodb::testThat]
biodb.INFO [2024-06-03 14:23:13.263][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2024-06-03 14:23:13.264][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-03 14:23:13.266][biodb::testThat]
biodb.DEBUG[2024-06-03 14:23:13.268][private$loadEntries] Creating entries from ids [2]: "1.1.1.1, 1.1.1.54".
biodb.DEBUG[2024-06-03 14:23:13.276][conn$getEntryContent] Get Expasy ENZYME database. entry content(s) for 2 id(s)...
biodb.TRACE[2024-06-03 14:23:13.283][cch$loadFileContent] Trying to load 2 files from cache: [2]: "1.1.1.1, 1.1.1.54".
biodb.INFO [2024-06-03 14:23:13.285][self$getFolderPath] Create cache folder "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280" for "expasy.enzyme-b59b84d962b6741050ba8f70ff4db280".
biodb.TRACE[2024-06-03 14:23:13.287][cch$loadFileContent] file.exist = [2]: "FALSE, FALSE".
biodb.TRACE[2024-06-03 14:23:13.288][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-06-03 14:23:13.289][conn$getEntryContent] 0 Expasy ENZYME database. entry content(s) loaded from cache.
biodb.DEBUG[2024-06-03 14:23:13.290][conn$getEntryContent] 2 entry content(s) need to be fetched from Expasy ENZYME database. database "https://enzyme.expasy.org/".
biodb.DEBUG[2024-06-03 14:23:13.292][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-06-03 14:23:13.293][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-06-03 14:23:13.299][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-03 14:23:13.300][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-03 14:23:13.301][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-03 14:23:13.308][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-03 14:23:13.309][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-03 14:23:13.310][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-03 14:23:13.311][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-03 14:23:13.312][scheduler$sendRequest] Getting content of get URL request "https://enzyme.expasy.org/EC/1.1.1.1.txt".
biodb.DEBUG[2024-06-03 14:23:13.340][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-03 14:23:13.341][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-03 14:23:13.343][private$doSendRequestOnce] Sent URL is "https://enzyme.expasy.org/EC/1.1.1.1.txt".
biodb.TRACE[2024-06-03 14:23:15.996][getRCurlRequestResult] Using RCurl package for sending request (https://enzyme.expasy.org/EC/1.1.1.1.txt).
biodb.DEBUG[2024-06-03 14:23:16.882][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-06-03 14:23:16.884][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280/a52675cfd2f0c2b41556caa64d9341e3.content"
biodb.TRACE[2024-06-03 14:23:16.904][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280/a52675cfd2f0c2b41556caa64d9341e3.request"
biodb.DEBUG[2024-06-03 14:23:16.907][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-03 14:23:16.908][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-03 14:23:16.909][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-03 14:23:16.916][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-03 14:23:16.917][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-03 14:23:16.918][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-03 14:23:16.919][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[2024-06-03 14:23:16.959][scheduler$sendRequest] Getting content of get URL request "https://enzyme.expasy.org/EC/1.1.1.54.txt".
biodb.DEBUG[2024-06-03 14:23:16.980][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-03 14:23:16.981][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-03 14:23:17.002][private$doSendRequestOnce] Sent URL is "https://enzyme.expasy.org/EC/1.1.1.54.txt".
biodb.TRACE[2024-06-03 14:23:17.632][getRCurlRequestResult] Using RCurl package for sending request (https://enzyme.expasy.org/EC/1.1.1.54.txt).
biodb.DEBUG[2024-06-03 14:23:18.292][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-06-03 14:23:18.295][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280/a9b93566a091cbe35a06e4b3871f95c9.content"
biodb.TRACE[2024-06-03 14:23:18.299][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280/a9b93566a091cbe35a06e4b3871f95c9.request"
biodb.TRACE[2024-06-03 14:23:18.302][private$doSaveContentToFile] Saving to cache [2]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280/1.1.1.1.txt, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280/1.1.1.54.txt"
biodb.DEBUG[2024-06-03 14:23:18.305][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-06-03 14:23:18.306][self$createEntryFromContent] Creating Expasy ENZYME database. entries from 2 content(s).
biodb.DEBUG[2024-06-03 14:23:18.307][self$createEntryFromContent] Parsing 2 Expasy ENZYME database. entries.
biodb.DEBUG[2024-06-03 14:23:18.309][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-03 14:23:18.311][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-03 14:23:18.312][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-03 14:23:18.318][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-03 14:23:18.319][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-03 14:23:18.320][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-03 14:23:18.321][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-03 14:23:18.324][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-03 14:23:18.326][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-03 14:23:18.327][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-03 14:23:18.328][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-03 14:23:18.330][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-06-03 14:23:18.331][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-06-03 14:23:18.332][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-03 14:23:18.334][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-03 14:23:18.335][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-03 14:23:18.337][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-03 14:23:18.338][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-03 14:23:18.339][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-03 14:23:18.340][self$getBiodb()$getEntryFields()$get] Asked field names are: COFACTOR.
biodb.TRACE[2024-06-03 14:23:18.342][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-06-03 14:23:18.343][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-03 14:23:18.344][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-03 14:23:18.346][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-03 14:23:18.347][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-03 14:23:18.348][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-03 14:23:18.349][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-03 14:23:18.351][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-03 14:23:18.352][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-03 14:23:18.353][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-03 14:23:18.355][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-03 14:23:18.356][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-03 14:23:18.357][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-03 14:23:18.358][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-03 14:23:18.360][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-03 14:23:18.361][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-03 14:23:18.362][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-03 14:23:18.363][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-03 14:23:18.365][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-03 14:23:18.366][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-03 14:23:18.367][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-03 14:23:18.368][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-03 14:23:18.370][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-03 14:23:18.371][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-06-03 14:23:18.372][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-06-03 14:23:18.374][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-03 14:23:18.375][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-03 14:23:18.376][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-06-03 14:23:18.378][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-06-03 14:23:18.379][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-03 14:23:18.380][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-03 14:23:18.381][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-03 14:23:18.383][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-03 14:23:18.384][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-03 14:23:18.385][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-03 14:23:18.386][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-06-03 14:23:18.388][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-06-03 14:23:18.389][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-03 14:23:18.390][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-03 14:23:18.391][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-03 14:23:18.393][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-03 14:23:18.394][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-03 14:23:18.395][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-03 14:23:18.404][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-03 14:23:18.405][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-03 14:23:18.406][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-03 14:23:18.407][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-03 14:23:18.409][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-03 14:23:18.410][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-03 14:23:18.411][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-03 14:23:18.412][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-03 14:23:18.414][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-03 14:23:18.415][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-03 14:23:18.416][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-03 14:23:18.422][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-03 14:23:18.423][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-03 14:23:18.424][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-03 14:23:18.426][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-03 14:23:18.428][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-03 14:23:18.429][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-03 14:23:18.431][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-03 14:23:18.432][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-03 14:23:18.433][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-06-03 14:23:18.435][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-06-03 14:23:18.436][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-03 14:23:18.437][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-03 14:23:18.439][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-03 14:23:18.440][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-03 14:23:18.441][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-03 14:23:18.442][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-03 14:23:18.444][self$getBiodb()$getEntryFields()$get] Asked field names are: COFACTOR.
biodb.TRACE[2024-06-03 14:23:18.445][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-06-03 14:23:18.446][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-03 14:23:18.447][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-03 14:23:18.449][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-06-03 14:23:18.450][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-06-03 14:23:18.451][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-03 14:23:18.453][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-03 14:23:18.454][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-06-03 14:23:18.455][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-06-03 14:23:18.456][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-03 14:23:18.458][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-03 14:23:18.459][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-03 14:23:18.460][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-03 14:23:18.461][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-03 14:23:18.463][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-03 14:23:18.464][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-06-03 14:23:18.465][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-06-03 14:23:18.466][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-03 14:23:18.467][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-03 14:23:18.469][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-03 14:23:18.470][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-03 14:23:18.471][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-03 14:23:18.472][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-03 14:23:18.474][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-03 14:23:18.475][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-03 14:23:18.476][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-03 14:23:18.477][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-03 14:23:18.479][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-03 14:23:18.480][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-03 14:23:18.481][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-03 14:23:18.482][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-03 14:23:18.484][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-03 14:23:18.485][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-03 14:23:18.486][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-03 14:23:18.487][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-03 14:23:18.488][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-03 14:23:18.490][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-03 14:23:18.491][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-03 14:23:18.492][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-03 14:23:18.493][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-03 14:23:18.495][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-03 14:23:18.496][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-03 14:23:18.497][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-03 14:23:18.498][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-03 14:23:18.500][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-03 14:23:18.501][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-03 14:23:18.502][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-03 14:23:18.503][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-03 14:23:18.504][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-03 14:23:18.506][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-03 14:23:18.507][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-03 14:23:18.508][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-03 14:23:18.509][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-03 14:23:18.511][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-03 14:23:18.512][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-03 14:23:18.513][self$createEntryFromContent] Accession numbers: 1.1.1.1, 1.1.1.54.
biodb.TRACE[2024-06-03 14:23:18.514][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2024-06-03 14:23:18.516][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2024-06-03 14:23:18.517][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-03 14:23:18.518][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-03 14:23:18.519][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2024-06-03 14:23:18.521][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2024-06-03 14:23:18.522][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-03 14:23:18.523][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-03 14:23:18.524][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2024-06-03 14:23:18.526][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2024-06-03 14:23:18.527][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-03 14:23:18.528][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-03 14:23:18.535][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2024-06-03 14:23:18.536][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2024-06-03 14:23:18.537][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-03 14:23:18.539][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-03 14:23:18.540][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2024-06-03 14:23:18.541][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2024-06-03 14:23:18.543][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-03 14:23:18.544][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-03 14:23:18.545][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2024-06-03 14:23:18.546][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2024-06-03 14:23:18.548][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-03 14:23:18.549][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-06-03 14:23:18.560][biodb::testThat]
biodb.INFO [2024-06-03 14:23:18.561][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2024-06-03 14:23:18.562][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-03 14:23:18.567][biodb::testThat]
biodb.TRACE[2024-06-03 14:23:18.571][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-03 14:23:18.572][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-03 14:23:18.573][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-03 14:23:18.575][ef$get] fields variable is a list.
biodb.DEBUG[2024-06-03 14:23:18.576][function(conn, opt)] Testing searchForEntries() with entry "1.1.1.1" and field "name".
biodb.TRACE[2024-06-03 14:23:18.611][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-03 14:23:18.612][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-03 14:23:18.614][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-03 14:23:18.615][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-03 14:23:18.616][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-03 14:23:18.617][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-03 14:23:18.619][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-03 14:23:18.620][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-03 14:23:18.621][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-03 14:23:18.622][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-03 14:23:18.624][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-03 14:23:18.625][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-03 14:23:18.630][function(conn, opt)] With value "alcohol dehydrogenase".
biodb.DEBUG[2024-06-03 14:23:18.632][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://enzyme.expasy.org/enzyme-byname.html?alcohol dehydrogenase".
biodb.DEBUG[2024-06-03 14:23:18.636][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-03 14:23:18.637][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-03 14:23:18.638][private$doSendRequestOnce] Sent URL is "https://enzyme.expasy.org/enzyme-byname.html?alcohol%20dehydrogenase".
biodb.TRACE[2024-06-03 14:23:19.116][getRCurlRequestResult] Using RCurl package for sending request (https://enzyme.expasy.org/enzyme-byname.html?alcohol%20dehydrogenase).
biodb.DEBUG[2024-06-03 14:23:19.586][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-06-03 14:23:19.589][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280/f603fa2a57aec59588edc37541c6f6d5.content"
biodb.TRACE[2024-06-03 14:23:19.593][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280/f603fa2a57aec59588edc37541c6f6d5.request"
biodb.DEBUG[2024-06-03 14:23:19.601][function(conn, opt)] With found IDs [1]: "1.1.1.1".
biodb.INFO [2024-06-03 14:23:19.621][biodb::testThat]
biodb.INFO [2024-06-03 14:23:19.622][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2024-06-03 14:23:19.623][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-03 14:23:19.624][biodb::testThat]
biodb.TRACE[2024-06-03 14:23:19.658][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-03 14:23:19.659][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-03 14:23:19.660][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-03 14:23:19.662][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-03 14:23:19.663][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-03 14:23:19.664][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-03 14:23:19.666][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-03 14:23:19.667][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-03 14:23:19.668][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-03 14:23:19.670][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-03 14:23:19.671][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-03 14:23:19.672][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-03 14:23:19.716][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://enzyme.expasy.org/enzyme-byname.html?alcohol dehydrogenase".
biodb.DEBUG[2024-06-03 14:23:19.719][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-06-03 14:23:19.741][cch$loadFileContent] Trying to load 1 files from cache: [1]: "f603fa2a57aec59588edc37541c6f6d5".
biodb.TRACE[2024-06-03 14:23:19.743][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-06-03 14:23:19.744][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280/f603fa2a57aec59588edc37541c6f6d5.content".
biodb.INFO [2024-06-03 14:23:19.767][biodb::testThat]
biodb.INFO [2024-06-03 14:23:19.768][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2024-06-03 14:23:19.769][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-03 14:23:19.770][biodb::testThat]
biodb.TRACE[2024-06-03 14:23:19.783][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-06-03 14:23:19.785][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-06-03 14:23:19.786][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-03 14:23:19.787][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-03 14:23:19.789][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-06-03 14:23:19.790][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-06-03 14:23:19.791][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-03 14:23:19.792][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-03 14:23:19.794][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-06-03 14:23:19.795][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-06-03 14:23:19.796][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-03 14:23:19.797][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-03 14:23:19.799][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-06-03 14:23:19.800][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-06-03 14:23:19.801][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-03 14:23:19.802][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-03 14:23:19.854][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-06-03 14:23:19.855][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-06-03 14:23:19.856][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-03 14:23:19.858][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-03 14:23:19.859][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-06-03 14:23:19.860][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-06-03 14:23:19.861][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-03 14:23:19.863][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-03 14:23:19.864][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-06-03 14:23:19.865][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-06-03 14:23:19.866][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-03 14:23:19.868][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-03 14:23:19.869][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-06-03 14:23:19.870][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-06-03 14:23:19.872][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-03 14:23:19.873][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-06-03 14:23:19.881][biodb::testThat]
biodb.INFO [2024-06-03 14:23:19.882][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2024-06-03 14:23:19.883][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-03 14:23:19.884][biodb::testThat]
biodb.INFO [2024-06-03 14:23:19.896][biodb::testThat]
biodb.INFO [2024-06-03 14:23:19.897][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2024-06-03 14:23:19.898][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-03 14:23:19.900][biodb::testThat]
biodb.INFO [2024-06-03 14:23:19.910][biodb::testThat]
biodb.INFO [2024-06-03 14:23:19.911][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2024-06-03 14:23:19.913][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-03 14:23:19.914][biodb::testThat]
biodb.DEBUG[2024-06-03 14:23:19.933][function(conn, opt)] Trying to download "https://enzyme.expasy.org/cgi-bin/enzyme/enzyme-search-ec?field1=1&field2=1&field3=1&field4=1".
biodb.DEBUG[2024-06-03 14:23:20.398][getUrlContent] Use RCurl for downloading content of URL https://enzyme.expasy.org/cgi-bin/enzyme/enzyme-search-ec?field1=1&field2=1&field3=1&field4=1.
biodb.INFO [2024-06-03 14:23:20.878][biodb::testThat]
biodb.INFO [2024-06-03 14:23:20.880][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2024-06-03 14:23:20.881][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-03 14:23:20.882][biodb::testThat]
biodb.DEBUG[2024-06-03 14:23:21.230][getUrlContent] Use base::url() for downloading content of URL https://enzyme.expasy.org/images/1.1.1.1/image.png.
biodb.TRACE[2024-06-03 14:23:21.877][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-03 14:23:21.879][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-03 14:23:21.880][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-03 14:23:21.881][ef$get] fields variable is a list.
biodb.TRACE[2024-06-03 14:23:21.882][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-03 14:23:21.884][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-03 14:23:21.885][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-03 14:23:21.886][ef$get] fields variable is a list.
biodb.INFO [2024-06-03 14:23:21.887][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-06-03 14:23:21.893][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector expasy.enzyme from the request scheduler
biodb.INFO [2024-06-03 14:23:21.899][self$deleteConn] Connector "expasy.enzyme" deleted.
biodb.DEBUG[2024-06-03 14:23:21.900][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-06-03 14:23:21.901][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-03 14:23:21.902][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-03 14:23:21.903][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-03 14:23:21.904][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-03 14:23:21.906][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-06-03 14:23:21.907][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2024-06-03 14:23:21.919][biodb::testContext]
biodb.INFO [2024-06-03 14:23:21.921][biodb::testContext] ********************************************************************************
biodb.INFO [2024-06-03 14:23:21.922][biodb::testContext] Test context - Example long tests
biodb.INFO [2024-06-03 14:23:21.923][biodb::testContext] ********************************************************************************
biodb.INFO [2024-06-03 14:23:21.924][biodb::testContext]
biodb.INFO [2024-06-03 14:23:21.927][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.13.0.
biodb.DEBUG[2024-06-03 14:23:21.929][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2024-06-03 14:23:21.933][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-06-03 14:23:21.934][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-06-03 14:23:21.936][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-06-03 14:23:21.937][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-03 14:23:21.938][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-03 14:23:21.939][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-03 14:23:21.940][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-06-03 14:23:21.941][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-06-03 14:23:21.942][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-03 14:23:21.944][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-03 14:23:21.945][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-03 14:23:21.946][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-06-03 14:23:21.947][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-06-03 14:23:21.948][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-03 14:23:21.949][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-03 14:23:21.951][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-03 14:23:21.952][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-06-03 14:23:21.953][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-06-03 14:23:21.954][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-06-03 14:23:21.956][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-03 14:23:21.957][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-03 14:23:21.958][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-03 14:23:21.959][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-06-03 14:23:21.960][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-06-03 14:23:21.962][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-06-03 14:23:21.963][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-03 14:23:21.964][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-03 14:23:21.965][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-03 14:23:21.966][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-06-03 14:23:21.967][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-06-03 14:23:21.968][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-03 14:23:21.970][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-03 14:23:21.971][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-03 14:23:21.972][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-06-03 14:23:21.973][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-06-03 14:23:21.974][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-06-03 14:23:21.975][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-03 14:23:21.977][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-03 14:23:21.978][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-03 14:23:21.979][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-06-03 14:23:21.980][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-06-03 14:23:21.981][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-03 14:23:21.982][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-03 14:23:21.983][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-03 14:23:21.985][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-06-03 14:23:21.986][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-06-03 14:23:21.987][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-06-03 14:23:21.988][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-03 14:23:21.989][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-03 14:23:21.991][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[2024-06-03 14:23:21.992][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-06-03 14:23:21.993][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-06-03 14:23:21.994][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-06-03 14:23:21.996][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-06-03 14:23:21.997][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-06-03 14:23:21.998][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-06-03 14:23:21.999][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-03 14:23:22.000][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-03 14:23:22.002][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-03 14:23:22.003][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-06-03 14:23:22.004][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-06-03 14:23:22.005][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-03 14:23:22.006][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-03 14:23:22.007][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-03 14:23:22.009][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-06-03 14:23:22.010][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-06-03 14:23:22.011][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-03 14:23:22.012][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-03 14:23:22.013][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-03 14:23:22.015][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-06-03 14:23:22.016][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-06-03 14:23:22.017][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-03 14:23:22.018][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-03 14:23:22.019][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-03 14:23:22.021][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-06-03 14:23:22.022][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-06-03 14:23:22.023][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-03 14:23:22.024][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-03 14:23:22.025][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-03 14:23:22.027][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-06-03 14:23:22.028][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-06-03 14:23:22.029][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-03 14:23:22.030][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-03 14:23:22.031][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-03 14:23:22.033][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-06-03 14:23:22.034][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-06-03 14:23:22.045][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-06-03 14:23:22.046][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-03 14:23:22.047][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-03 14:23:22.048][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-03 14:23:22.049][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-06-03 14:23:22.051][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-06-03 14:23:22.052][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-06-03 14:23:22.053][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-03 14:23:22.054][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-03 14:23:22.060][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-03 14:23:22.061][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-06-03 14:23:22.064][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-06-03 14:23:22.065][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2024-06-03 14:23:22.066][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-03 14:23:22.067][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-03 14:23:22.069][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-03 14:23:22.070][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-03 14:23:22.071][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-03 14:23:22.072][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-03 14:23:22.074][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-06-03 14:23:22.075][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-03 14:23:22.076][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-06-03 14:23:22.077][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-06-03 14:23:22.079][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-03 14:23:22.080][self$setPropertyValue]
biodb.DEBUG[2024-06-03 14:23:22.081][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-03 14:23:22.082][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-06-03 14:23:22.082][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-06-03 14:23:22.082][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-06-03 14:23:22.082][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-06-03 14:23:22.082][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-06-03 14:23:22.084][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-03 14:23:22.085][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-03 14:23:22.086][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-03 14:23:22.087][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-03 14:23:22.088][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-03 14:23:22.089][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-03 14:23:22.091][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-03 14:23:22.092][self$setPropertyValue]
biodb.DEBUG[2024-06-03 14:23:22.093][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-03 14:23:22.095][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-03 14:23:22.096][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-03 14:23:22.097][self$setPropertyValue]
biodb.DEBUG[2024-06-03 14:23:22.099][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-06-03 14:23:22.101][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-06-03 14:23:22.102][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-06-03 14:23:22.103][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-03 14:23:22.105][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-03 14:23:22.106][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-03 14:23:22.107][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-03 14:23:22.108][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-03 14:23:22.110][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-03 14:23:22.111][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-06-03 14:23:22.112][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-03 14:23:22.113][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-06-03 14:23:22.115][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-06-03 14:23:22.116][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-03 14:23:22.117][self$setPropertyValue]
biodb.DEBUG[2024-06-03 14:23:22.118][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-03 14:23:22.120][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-06-03 14:23:22.120][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-06-03 14:23:22.120][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-06-03 14:23:22.120][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-06-03 14:23:22.120][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-06-03 14:23:22.121][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-03 14:23:22.122][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-03 14:23:22.123][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-03 14:23:22.125][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-03 14:23:22.126][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-03 14:23:22.127][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-03 14:23:22.128][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-03 14:23:22.130][self$setPropertyValue]
biodb.DEBUG[2024-06-03 14:23:22.131][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-03 14:23:22.132][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-03 14:23:22.133][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-03 14:23:22.135][self$setPropertyValue]
biodb.DEBUG[2024-06-03 14:23:22.137][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-06-03 14:23:22.139][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-06-03 14:23:22.140][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2024-06-03 14:23:22.141][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-03 14:23:22.143][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-03 14:23:22.144][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-03 14:23:22.145][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-03 14:23:22.146][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-03 14:23:22.148][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-03 14:23:22.149][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-06-03 14:23:22.150][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-03 14:23:22.151][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-06-03 14:23:22.153][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-06-03 14:23:22.154][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-03 14:23:22.155][self$setPropertyValue]
biodb.DEBUG[2024-06-03 14:23:22.156][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-03 14:23:22.158][self$setPropertyValue]
biodb.DEBUG[2024-06-03 14:23:22.159][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-03 14:23:22.160][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-03 14:23:22.161][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-03 14:23:22.162][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-03 14:23:22.164][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-03 14:23:22.165][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-03 14:23:22.166][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-03 14:23:22.167][self$setPropertyValue]
biodb.DEBUG[2024-06-03 14:23:22.168][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-03 14:23:22.170][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-03 14:23:22.171][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-03 14:23:22.172][self$setPropertyValue]
biodb.DEBUG[2024-06-03 14:23:22.174][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-06-03 14:23:22.176][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-06-03 14:23:22.177][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-06-03 14:23:22.178][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-03 14:23:22.180][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-03 14:23:22.181][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-03 14:23:22.182][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-03 14:23:22.183][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-03 14:23:22.185][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-03 14:23:22.186][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-06-03 14:23:22.187][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-03 14:23:22.188][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-06-03 14:23:22.190][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-06-03 14:23:22.191][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-03 14:23:22.192][self$setPropertyValue]
biodb.DEBUG[2024-06-03 14:23:22.193][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-03 14:23:22.195][self$setPropertyValue]
biodb.DEBUG[2024-06-03 14:23:22.196][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-03 14:23:22.197][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-03 14:23:22.198][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-03 14:23:22.200][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-03 14:23:22.201][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-03 14:23:22.202][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-03 14:23:22.203][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-03 14:23:22.204][self$setPropertyValue]
biodb.DEBUG[2024-06-03 14:23:22.206][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-03 14:23:22.207][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-03 14:23:22.212][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-03 14:23:22.213][self$setPropertyValue]
biodb.DEBUG[2024-06-03 14:23:22.215][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-06-03 14:23:22.216][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-06-03 14:23:22.217][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-03 14:23:22.218][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-03 14:23:22.219][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-03 14:23:22.220][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-03 14:23:22.222][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-03 14:23:22.223][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-03 14:23:22.224][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-03 14:23:22.225][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-03 14:23:22.226][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-03 14:23:22.227][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-03 14:23:22.228][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[2024-06-03 14:23:22.229][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-03 14:23:22.230][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-03 14:23:22.231][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-03 14:23:22.232][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-03 14:23:22.233][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[2024-06-03 14:23:22.235][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-03 14:23:22.236][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-03 14:23:22.237][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-03 14:23:22.238][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-03 14:23:22.239][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[2024-06-03 14:23:22.240][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-03 14:23:22.241][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-03 14:23:22.242][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-03 14:23:22.243][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-03 14:23:22.244][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-03 14:23:22.245][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-03 14:23:22.247][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-03 14:23:22.248][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-03 14:23:22.249][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-03 14:23:22.250][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-03 14:23:22.251][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-03 14:23:22.252][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-03 14:23:22.253][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-03 14:23:22.254][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-03 14:23:22.255][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[2024-06-03 14:23:22.256][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-03 14:23:22.258][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-03 14:23:22.259][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-03 14:23:22.260][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-03 14:23:22.261][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-03 14:23:22.262][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-03 14:23:22.263][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-03 14:23:22.264][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-03 14:23:22.265][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-03 14:23:22.266][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-03 14:23:22.267][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-03 14:23:22.268][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-03 14:23:22.270][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-03 14:23:22.271][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-03 14:23:22.272][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-03 14:23:22.273][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-03 14:23:22.274][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-03 14:23:22.275][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-03 14:23:22.276][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-03 14:23:22.277][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-03 14:23:22.278][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-03 14:23:22.279][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-03 14:23:22.281][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-03 14:23:22.282][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-03 14:23:22.283][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-03 14:23:22.284][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-03 14:23:22.285][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-03 14:23:22.286][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-03 14:23:22.287][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-03 14:23:22.288][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-03 14:23:22.289][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-03 14:23:22.290][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-03 14:23:22.291][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-03 14:23:22.292][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-03 14:23:22.294][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-03 14:23:22.295][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-03 14:23:22.296][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-03 14:23:22.297][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-03 14:23:22.298][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-03 14:23:22.299][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-03 14:23:22.300][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-03 14:23:22.301][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-03 14:23:22.302][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-03 14:23:22.303][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-03 14:23:22.304][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-03 14:23:22.306][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-03 14:23:22.307][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-03 14:23:22.308][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-03 14:23:22.309][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-03 14:23:22.310][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-03 14:23:22.311][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-06-03 14:23:22.313][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-06-03 14:23:22.315][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-06-03 14:23:22.316][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-06-03 14:23:22.318][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-06-03 14:23:22.320][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-06-03 14:23:22.322][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-06-03 14:23:22.323][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-06-03 14:23:22.325][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-06-03 14:23:22.327][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-06-03 14:23:22.328][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-06-03 14:23:22.330][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-06-03 14:23:22.332][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-06-03 14:23:22.334][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-06-03 14:23:22.335][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-06-03 14:23:22.337][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-06-03 14:23:22.339][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-06-03 14:23:22.341][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-06-03 14:23:22.342][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-06-03 14:23:22.344][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-06-03 14:23:22.346][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-06-03 14:23:22.348][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-06-03 14:23:22.349][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-06-03 14:23:22.351][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-06-03 14:23:22.357][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-06-03 14:23:22.359][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-06-03 14:23:22.361][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-06-03 14:23:22.363][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-06-03 14:23:22.364][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-06-03 14:23:22.366][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-06-03 14:23:22.368][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-06-03 14:23:22.369][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-06-03 14:23:22.371][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-06-03 14:23:22.373][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-06-03 14:23:22.374][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-06-03 14:23:22.376][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-06-03 14:23:22.378][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-06-03 14:23:22.379][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-06-03 14:23:22.381][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-06-03 14:23:22.383][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-06-03 14:23:22.384][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-06-03 14:23:22.386][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-06-03 14:23:22.388][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-06-03 14:23:22.390][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-06-03 14:23:22.391][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-06-03 14:23:22.393][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-06-03 14:23:22.395][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-06-03 14:23:22.397][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-06-03 14:23:22.398][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-06-03 14:23:22.400][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-06-03 14:23:22.402][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-06-03 14:23:22.403][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-06-03 14:23:22.405][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-06-03 14:23:22.407][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-06-03 14:23:22.408][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-06-03 14:23:22.410][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-06-03 14:23:22.412][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-06-03 14:23:22.413][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-06-03 14:23:22.415][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-06-03 14:23:22.417][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-06-03 14:23:22.419][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-06-03 14:23:22.420][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-06-03 14:23:22.422][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-06-03 14:23:22.424][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-06-03 14:23:22.425][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-06-03 14:23:22.427][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-06-03 14:23:22.429][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-06-03 14:23:22.430][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-06-03 14:23:22.432][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-06-03 14:23:22.434][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-06-03 14:23:22.435][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-06-03 14:23:22.437][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-06-03 14:23:22.439][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-06-03 14:23:22.440][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-06-03 14:23:22.442][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-06-03 14:23:22.444][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-06-03 14:23:22.445][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-06-03 14:23:22.447][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-06-03 14:23:22.449][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-06-03 14:23:22.450][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-06-03 14:23:22.452][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-06-03 14:23:22.454][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-06-03 14:23:22.456][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-06-03 14:23:22.457][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-06-03 14:23:22.459][initialize] This is biodb version 1.13.0.
biodb.DEBUG[2024-06-03 14:23:22.460][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-06-03 14:23:22.462][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-06-03 14:23:22.463][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-03 14:23:22.464][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-06-03 14:23:22.465][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[2024-06-03 14:23:22.466][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-03 14:23:22.467][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-03 14:23:22.468][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-03 14:23:22.469][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-03 14:23:22.470][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-03 14:23:22.471][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-03 14:23:22.472][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-03 14:23:22.474][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-03 14:23:22.475][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-03 14:23:22.476][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-03 14:23:22.477][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-03 14:23:22.478][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-03 14:23:22.479][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-03 14:23:22.480][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-03 14:23:22.481][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-03 14:23:22.482][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-03 14:23:22.483][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-03 14:23:22.484][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-03 14:23:22.486][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-03 14:23:22.487][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-03 14:23:22.488][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-03 14:23:22.489][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-03 14:23:22.490][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-03 14:23:22.491][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-03 14:23:22.492][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-03 14:23:22.493][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-03 14:23:22.494][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-03 14:23:22.500][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-03 14:23:22.501][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-03 14:23:22.502][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-03 14:23:22.503][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-03 14:23:22.504][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-03 14:23:22.506][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-03 14:23:22.507][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-03 14:23:22.508][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-03 14:23:22.509][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-03 14:23:22.510][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-03 14:23:22.511][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-03 14:23:22.512][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-03 14:23:22.513][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-03 14:23:22.514][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-03 14:23:22.515][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-03 14:23:22.516][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-03 14:23:22.517][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-03 14:23:22.519][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-03 14:23:22.520][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-03 14:23:22.521][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-03 14:23:22.522][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-03 14:23:22.523][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-03 14:23:22.524][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-03 14:23:22.525][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-03 14:23:22.526][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-03 14:23:22.527][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-03 14:23:22.528][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-03 14:23:22.529][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-03 14:23:22.531][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-03 14:23:22.532][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-03 14:23:22.533][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-03 14:23:22.534][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-03 14:23:22.535][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-03 14:23:22.536][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-03 14:23:22.537][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-03 14:23:22.538][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-03 14:23:22.539][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-03 14:23:22.540][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-03 14:23:22.541][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-03 14:23:22.543][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-03 14:23:22.544][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-03 14:23:22.545][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-03 14:23:22.546][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-03 14:23:22.547][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-03 14:23:22.548][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-03 14:23:22.549][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-03 14:23:22.550][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-03 14:23:22.551][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-03 14:23:22.552][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-03 14:23:22.554][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-03 14:23:22.555][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-03 14:23:22.556][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-03 14:23:22.557][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-03 14:23:22.558][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-03 14:23:22.559][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-03 14:23:22.560][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-03 14:23:22.561][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-03 14:23:22.562][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-03 14:23:22.563][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-03 14:23:22.565][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-03 14:23:22.566][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-03 14:23:22.567][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-03 14:23:22.568][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-03 14:23:22.569][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-03 14:23:22.570][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-03 14:23:22.571][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-03 14:23:22.572][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-03 14:23:22.573][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-03 14:23:22.574][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-03 14:23:22.575][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-03 14:23:22.576][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-03 14:23:22.577][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-03 14:23:22.578][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-03 14:23:22.580][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-03 14:23:22.581][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-03 14:23:22.582][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-03 14:23:22.583][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-03 14:23:22.584][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-03 14:23:22.585][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-03 14:23:22.586][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-03 14:23:22.587][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-03 14:23:22.588][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-03 14:23:22.589][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-03 14:23:22.590][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-03 14:23:22.591][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-03 14:23:22.592][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-03 14:23:22.594][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-03 14:23:22.595][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-03 14:23:22.596][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-03 14:23:22.597][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-03 14:23:22.598][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-03 14:23:22.599][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-03 14:23:22.601][biodb$loadDefinitions] Load definitions from file "/Users/biocbuild/bbs-3.20-bioc-longtests/meat/biodbExpasy.Rcheck/biodbExpasy/definitions.yml".
biodb.DEBUG[2024-06-03 14:23:22.603][self$getDbsInfo()$define] Define connector expasy.enzyme.
biodb.DEBUG[2024-06-03 14:23:22.605][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-06-03 14:23:22.607][self$setPropertyValue] Setting property "description" to "Write here the description of this database.".
biodb.DEBUG[2024-06-03 14:23:22.608][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-03 14:23:22.609][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-03 14:23:22.610][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-03 14:23:22.611][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-03 14:23:22.613][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-06-03 14:23:22.614][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-03 14:23:22.615][self$setPropertyValue] Setting property "entry.content.type" to "txt".
biodb.DEBUG[2024-06-03 14:23:22.616][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-03 14:23:22.618][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-06-03 14:23:22.619][self$setPropertyValue] Setting property "name" to "Expasy ENZYME database.".
biodb.DEBUG[2024-06-03 14:23:22.620][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-03 14:23:22.621][self$setPropertyValue] Setting property "parsing.expr" to "^ID\s+([0-9.]+)$".
biodb.DEBUG[2024-06-03 14:23:22.621][self$setPropertyValue] Setting property "parsing.expr" to "^CA\s+(.+?)\.?$".
biodb.DEBUG[2024-06-03 14:23:22.621][self$setPropertyValue] Setting property "parsing.expr" to "^CF\s+(.+?)\.?$".
biodb.DEBUG[2024-06-03 14:23:22.621][self$setPropertyValue] Setting property "parsing.expr" to "^DE\s+(.+?)\.?$".
biodb.DEBUG[2024-06-03 14:23:22.622][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-06-03 14:23:22.624][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-06-03 14:23:22.625][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2024-06-03 14:23:22.626][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-03 14:23:22.627][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-03 14:23:22.628][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-03 14:23:22.630][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-03 14:23:22.631][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-03 14:23:22.632][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-03 14:23:22.633][self$setPropertyValue] Setting property "urls" to "https://enzyme.expasy.org/".
biodb.DEBUG[2024-06-03 14:23:22.634][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-03 14:23:22.636][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-03 14:23:22.637][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-06-03 14:23:22.638][self$setPropertyValue]
biodb.DEBUG[2024-06-03 14:23:22.644][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-06-03 14:23:22.648][super$initialize] Initialize connector expasy.enzyme.
biodb.DEBUG[2024-06-03 14:23:22.649][super$initialize] Register connector expasy.enzyme with the request scheduler
biodb.DEBUG[2024-06-03 14:23:22.651][private$bdb$getRequestScheduler()$re ...] Register connector expasy.enzyme.
biodb.DEBUG[2024-06-03 14:23:22.652][private$addConnectorRules] Create new rule for URL "enzyme.expasy.org" of connector "expasy.enzyme".
biodb.DEBUG[2024-06-03 14:23:22.654][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-06-03 14:23:22.655][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-06-03 14:23:22.656][biodb$getFactory()$createConn] Creating new connector expasy.enzyme for database class expasy.enzyme .
biodb.INFO [2024-06-03 14:23:22.657][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-06-03 14:23:22.659][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector expasy.enzyme from the request scheduler
biodb.INFO [2024-06-03 14:23:22.660][self$deleteConn] Connector "expasy.enzyme" deleted.
biodb.DEBUG[2024-06-03 14:23:22.661][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-06-03 14:23:22.662][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-03 14:23:22.663][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-03 14:23:22.664][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-03 14:23:22.665][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-03 14:23:22.667][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-06-03 14:23:22.668][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
[ FAIL 1 | WARN 0 | SKIP 0 | PASS 85 ]

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

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

'R CMD check' output

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


* using log directory ‘/Users/biocbuild/bbs-3.20-bioc-longtests/meat/biodbExpasy.Rcheck’
* using R version 4.4.0 Patched (2024-04-24 r86482)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.4
* using session charset: UTF-8
* using options ‘--no-codoc --no-examples --no-manual --ignore-vignettes --no-stop-on-test-error’
* checking for file ‘biodbExpasy/DESCRIPTION’ ... OK
* this is package ‘biodbExpasy’ version ‘1.9.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘biodbExpasy’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Title field: should not end in a period.
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... SKIPPED
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... SKIPPED
* checking examples ... SKIPPED
* checking for unstated dependencies in ‘longtests’ ... OK
* checking tests in ‘longtests’ ...
  Running ‘testthat.R’
 ERROR
Running the tests in ‘longtests/testthat.R’ failed.
Last 13 lines of output:
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test_long_100_generic.R:37:1'): The entry image URL can be downloaded. ──
  Error in `charToRaw(content)`: argument must be a character vector of length 1
  Backtrace:
      ▆
   1. ├─base::do.call(fct, params)
   2. └─biodb (local) `<fn>`(conn = `<ExpsyEnC>`, opt = `<named list>`)
   3.   └─biodb:::getUrlContent(url, binary = TRUE)
   4.     └─biodb:::getBaseUrlContent(u, binary = binary)
   5.       └─base::charToRaw(content)
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 85 ]
  Error: Test failures
  Execution halted
* DONE

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

Installation output

biodbExpasy.Rcheck/00install.out

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