Back to Long Tests report for BioC 3.17

This page was generated on 2023-10-14 21:30:02 -0400 (Sat, 14 Oct 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.2 LTS)x86_644.3.1 (2023-06-16) -- "Beagle Scouts" 4626
palomino3Windows Server 2022 Datacenterx644.3.1 (2023-06-16 ucrt) -- "Beagle Scouts" 4379
merida1macOS 12.6.4 Montereyx86_644.3.1 (2023-06-16) -- "Beagle Scouts" 4395
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 7/31HostnameOS / ArchCHECK
biodbExpasy 1.4.0  (landing page)
Pierrick Roger
Snapshot Date: 2023-10-14 09:55:02 -0400 (Sat, 14 Oct 2023)
git_url: https://git.bioconductor.org/packages/biodbExpasy
git_branch: RELEASE_3_17
git_last_commit: 6a2064e
git_last_commit_date: 2023-04-25 11:36:51 -0400 (Tue, 25 Apr 2023)
nebbiolo1Linux (Ubuntu 22.04.2 LTS) / x86_64  OK  
palomino3Windows Server 2022 Datacenter / x64  OK  
merida1macOS 12.6.4 Monterey / x86_64  OK  

CHECK results for biodbExpasy on merida1


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

raw results

Summary

Package: biodbExpasy
Version: 1.4.0
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_1.4.0.tar.gz
StartedAt: 2023-10-14 11:02:41 -0400 (Sat, 14 Oct 2023)
EndedAt: 2023-10-14 11:03:56 -0400 (Sat, 14 Oct 2023)
EllapsedTime: 75.2 seconds
RetCode: 0
Status:   OK  
CheckDir: biodbExpasy.Rcheck
Warnings: 0

Tests output

biodbExpasy.Rcheck/tests/testthat.Rout


R version 4.3.1 (2023-06-16) -- "Beagle Scouts"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20 (64-bit)

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

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Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'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 [2023-10-14 11:03:35.206][biodb::testContext]
biodb.INFO [2023-10-14 11:03:35.211][biodb::testContext] ********************************************************************************
biodb.INFO [2023-10-14 11:03:35.212][biodb::testContext] Test context - Generic long tests
biodb.INFO [2023-10-14 11:03:35.214][biodb::testContext] ********************************************************************************
biodb.INFO [2023-10-14 11:03:35.215][biodb::testContext]
biodb.INFO [2023-10-14 11:03:35.223][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.8.1.
biodb.DEBUG[2023-10-14 11:03:35.226][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2023-10-14 11:03:35.235][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-10-14 11:03:35.237][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2023-10-14 11:03:35.238][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2023-10-14 11:03:35.239][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:03:35.240][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:03:35.242][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:03:35.243][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2023-10-14 11:03:35.273][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2023-10-14 11:03:35.275][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:03:35.276][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:03:35.277][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[2023-10-14 11:03:35.279][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2023-10-14 11:03:35.281][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2023-10-14 11:03:35.282][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:03:35.283][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:03:35.285][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:03:35.286][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2023-10-14 11:03:35.288][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2023-10-14 11:03:35.290][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2023-10-14 11:03:35.291][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:03:35.292][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:03:35.294][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[2023-10-14 11:03:35.295][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2023-10-14 11:03:35.297][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2023-10-14 11:03:35.298][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2023-10-14 11:03:35.300][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:03:35.301][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:03:35.302][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:03:35.304][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2023-10-14 11:03:35.305][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2023-10-14 11:03:35.307][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:03:35.308][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:03:35.309][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:03:35.311][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2023-10-14 11:03:35.312][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2023-10-14 11:03:35.314][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2023-10-14 11:03:35.315][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:03:35.316][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:03:35.318][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:03:35.319][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2023-10-14 11:03:35.321][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2023-10-14 11:03:35.322][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:03:35.323][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:03:35.325][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:03:35.326][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2023-10-14 11:03:35.327][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2023-10-14 11:03:35.329][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2023-10-14 11:03:35.330][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:03:35.332][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:03:35.333][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:03:35.335][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2023-10-14 11:03:35.336][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2023-10-14 11:03:35.338][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2023-10-14 11:03:35.339][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2023-10-14 11:03:35.341][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2023-10-14 11:03:35.342][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2023-10-14 11:03:35.344][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:03:35.345][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:03:35.346][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:03:35.348][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2023-10-14 11:03:35.350][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2023-10-14 11:03:35.351][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:03:35.353][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:03:35.354][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:03:35.355][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2023-10-14 11:03:35.357][self$set] Set key entries.sep to "|".
biodb.DEBUG[2023-10-14 11:03:35.358][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:03:35.360][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:03:35.361][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:03:35.362][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2023-10-14 11:03:35.364][self$set] Set key offline to FALSE.
biodb.DEBUG[2023-10-14 11:03:35.365][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:03:35.367][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:03:35.368][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:03:35.369][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2023-10-14 11:03:35.371][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2023-10-14 11:03:35.372][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:03:35.374][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:03:35.375][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:03:35.376][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2023-10-14 11:03:35.378][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2023-10-14 11:03:35.379][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:03:35.381][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:03:35.382][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:03:35.383][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2023-10-14 11:03:35.385][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2023-10-14 11:03:35.397][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2023-10-14 11:03:35.399][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:03:35.400][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:03:35.402][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:03:35.403][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2023-10-14 11:03:35.405][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2023-10-14 11:03:35.406][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2023-10-14 11:03:35.408][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:03:35.409][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:03:35.410][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:03:35.415][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2023-10-14 11:03:35.471][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-10-14 11:03:35.503][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2023-10-14 11:03:35.504][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-10-14 11:03:35.505][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-10-14 11:03:35.507][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-10-14 11:03:35.508][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-10-14 11:03:35.509][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-10-14 11:03:35.510][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-10-14 11:03:35.511][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2023-10-14 11:03:35.513][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-10-14 11:03:35.514][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-10-14 11:03:35.515][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2023-10-14 11:03:35.516][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-10-14 11:03:35.517][self$setPropertyValue]
biodb.DEBUG[2023-10-14 11:03:35.519][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-10-14 11:03:35.520][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2023-10-14 11:03:35.520][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2023-10-14 11:03:35.520][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2023-10-14 11:03:35.520][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2023-10-14 11:03:35.520][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2023-10-14 11:03:35.521][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-10-14 11:03:35.522][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-10-14 11:03:35.523][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-10-14 11:03:35.525][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-10-14 11:03:35.526][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-10-14 11:03:35.527][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-10-14 11:03:35.528][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-10-14 11:03:35.529][self$setPropertyValue]
biodb.DEBUG[2023-10-14 11:03:35.530][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-10-14 11:03:35.531][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-10-14 11:03:35.532][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-10-14 11:03:35.534][self$setPropertyValue]
biodb.DEBUG[2023-10-14 11:03:35.535][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2023-10-14 11:03:35.537][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-10-14 11:03:35.538][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2023-10-14 11:03:35.540][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-10-14 11:03:35.541][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-10-14 11:03:35.542][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-10-14 11:03:35.544][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-10-14 11:03:35.545][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-10-14 11:03:35.546][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-10-14 11:03:35.547][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2023-10-14 11:03:35.549][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-10-14 11:03:35.550][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-10-14 11:03:35.551][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2023-10-14 11:03:35.552][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-10-14 11:03:35.554][self$setPropertyValue]
biodb.DEBUG[2023-10-14 11:03:35.555][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-10-14 11:03:35.556][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2023-10-14 11:03:35.556][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2023-10-14 11:03:35.556][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2023-10-14 11:03:35.556][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2023-10-14 11:03:35.556][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2023-10-14 11:03:35.557][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-10-14 11:03:35.559][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-10-14 11:03:35.560][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-10-14 11:03:35.561][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-10-14 11:03:35.562][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-10-14 11:03:35.563][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-10-14 11:03:35.565][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-10-14 11:03:35.566][self$setPropertyValue]
biodb.DEBUG[2023-10-14 11:03:35.567][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-10-14 11:03:35.568][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-10-14 11:03:35.569][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-10-14 11:03:35.571][self$setPropertyValue]
biodb.DEBUG[2023-10-14 11:03:35.572][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2023-10-14 11:03:35.574][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2023-10-14 11:03:35.575][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2023-10-14 11:03:35.577][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-10-14 11:03:35.578][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-10-14 11:03:35.579][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-10-14 11:03:35.580][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-10-14 11:03:35.582][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-10-14 11:03:35.583][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-10-14 11:03:35.584][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2023-10-14 11:03:35.585][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-10-14 11:03:35.587][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2023-10-14 11:03:35.588][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2023-10-14 11:03:35.589][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-10-14 11:03:35.590][self$setPropertyValue]
biodb.DEBUG[2023-10-14 11:03:35.591][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-10-14 11:03:35.593][self$setPropertyValue]
biodb.DEBUG[2023-10-14 11:03:35.594][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-10-14 11:03:35.595][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-10-14 11:03:35.596][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-10-14 11:03:35.597][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-10-14 11:03:35.599][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-10-14 11:03:35.600][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-10-14 11:03:35.601][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-10-14 11:03:35.602][self$setPropertyValue]
biodb.DEBUG[2023-10-14 11:03:35.603][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-10-14 11:03:35.604][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-10-14 11:03:35.606][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-10-14 11:03:35.607][self$setPropertyValue]
biodb.DEBUG[2023-10-14 11:03:35.608][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2023-10-14 11:03:35.611][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2023-10-14 11:03:35.612][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2023-10-14 11:03:35.613][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-10-14 11:03:35.615][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-10-14 11:03:35.616][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-10-14 11:03:35.617][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-10-14 11:03:35.618][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-10-14 11:03:35.619][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-10-14 11:03:35.621][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2023-10-14 11:03:35.623][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-10-14 11:03:35.624][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2023-10-14 11:03:35.626][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2023-10-14 11:03:35.627][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-10-14 11:03:35.628][self$setPropertyValue]
biodb.DEBUG[2023-10-14 11:03:35.629][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-10-14 11:03:35.630][self$setPropertyValue]
biodb.DEBUG[2023-10-14 11:03:35.632][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-10-14 11:03:35.633][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-10-14 11:03:35.634][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-10-14 11:03:35.635][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-10-14 11:03:35.636][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-10-14 11:03:35.637][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-10-14 11:03:35.638][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-10-14 11:03:35.640][self$setPropertyValue]
biodb.DEBUG[2023-10-14 11:03:35.641][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-10-14 11:03:35.642][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-10-14 11:03:35.643][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-10-14 11:03:35.644][self$setPropertyValue]
biodb.DEBUG[2023-10-14 11:03:35.649][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-10-14 11:03:35.650][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:03:35.651][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:03:35.652][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:03:35.653][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:03:35.654][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-14 11:03:35.655][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:03:35.657][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[2023-10-14 11:03:35.658][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:03:35.659][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:03:35.660][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-14 11:03:35.661][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:03:35.662][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:03:35.663][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:03:35.664][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:03:35.665][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-14 11:03:35.666][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:03:35.667][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:03:35.668][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:03:35.670][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:03:35.671][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-14 11:03:35.672][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:03:35.673][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:03:35.674][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:03:35.675][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:03:35.676][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-14 11:03:35.677][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:03:35.678][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:03:35.679][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:03:35.680][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:03:35.681][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-14 11:03:35.682][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:03:35.683][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:03:35.685][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:03:35.686][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:03:35.687][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-14 11:03:35.688][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:03:35.689][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:03:35.690][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:03:35.691][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:03:35.692][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-14 11:03:35.693][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:03:35.694][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:03:35.695][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:03:35.696][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:03:35.698][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-14 11:03:35.699][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:03:35.700][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:03:35.701][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:03:35.702][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:03:35.703][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-14 11:03:35.704][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:03:35.705][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:03:35.706][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:03:35.707][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:03:35.708][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-14 11:03:35.709][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:03:35.711][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:03:35.712][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:03:35.713][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:03:35.714][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-14 11:03:35.715][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:03:35.716][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:03:35.717][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:03:35.718][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:03:35.719][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-14 11:03:35.720][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:03:35.721][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:03:35.723][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:03:35.724][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:03:35.725][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-14 11:03:35.726][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:03:35.727][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:03:35.728][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:03:35.729][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:03:35.730][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-14 11:03:35.731][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:03:35.733][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:03:35.734][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:03:35.735][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:03:35.736][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-14 11:03:35.737][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:03:35.738][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:03:35.739][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:03:35.740][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:03:35.741][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-14 11:03:35.742][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:03:35.744][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:03:35.745][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2023-10-14 11:03:35.750][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2023-10-14 11:03:35.752][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2023-10-14 11:03:35.754][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2023-10-14 11:03:35.756][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2023-10-14 11:03:35.757][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2023-10-14 11:03:35.759][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2023-10-14 11:03:35.761][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2023-10-14 11:03:35.763][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2023-10-14 11:03:35.764][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2023-10-14 11:03:35.766][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2023-10-14 11:03:35.768][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2023-10-14 11:03:35.770][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2023-10-14 11:03:35.772][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2023-10-14 11:03:35.773][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2023-10-14 11:03:35.775][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2023-10-14 11:03:35.777][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2023-10-14 11:03:35.779][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2023-10-14 11:03:35.781][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2023-10-14 11:03:35.783][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2023-10-14 11:03:35.785][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2023-10-14 11:03:35.787][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2023-10-14 11:03:35.789][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2023-10-14 11:03:35.792][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2023-10-14 11:03:35.794][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2023-10-14 11:03:35.796][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2023-10-14 11:03:35.799][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2023-10-14 11:03:35.806][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2023-10-14 11:03:35.808][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2023-10-14 11:03:35.810][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2023-10-14 11:03:35.812][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2023-10-14 11:03:35.814][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2023-10-14 11:03:35.815][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2023-10-14 11:03:35.817][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2023-10-14 11:03:35.819][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2023-10-14 11:03:35.821][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2023-10-14 11:03:35.823][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2023-10-14 11:03:35.824][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2023-10-14 11:03:35.826][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2023-10-14 11:03:35.828][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2023-10-14 11:03:35.829][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2023-10-14 11:03:35.831][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2023-10-14 11:03:35.833][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2023-10-14 11:03:35.834][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2023-10-14 11:03:35.836][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2023-10-14 11:03:35.838][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2023-10-14 11:03:35.840][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2023-10-14 11:03:35.841][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2023-10-14 11:03:35.843][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2023-10-14 11:03:35.845][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2023-10-14 11:03:35.846][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2023-10-14 11:03:35.848][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2023-10-14 11:03:35.850][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2023-10-14 11:03:35.851][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2023-10-14 11:03:35.853][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2023-10-14 11:03:35.855][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2023-10-14 11:03:35.856][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2023-10-14 11:03:35.858][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2023-10-14 11:03:35.859][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2023-10-14 11:03:35.861][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2023-10-14 11:03:35.863][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2023-10-14 11:03:35.864][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2023-10-14 11:03:35.866][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2023-10-14 11:03:35.868][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2023-10-14 11:03:35.869][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2023-10-14 11:03:35.871][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2023-10-14 11:03:35.873][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2023-10-14 11:03:35.874][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2023-10-14 11:03:35.876][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2023-10-14 11:03:35.878][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2023-10-14 11:03:35.879][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2023-10-14 11:03:35.881][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2023-10-14 11:03:35.883][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2023-10-14 11:03:35.884][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2023-10-14 11:03:35.886][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2023-10-14 11:03:35.888][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2023-10-14 11:03:35.889][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2023-10-14 11:03:35.891][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2023-10-14 11:03:35.893][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2023-10-14 11:03:35.895][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2023-10-14 11:03:35.896][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2023-10-14 11:03:35.898][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2023-10-14 11:03:35.900][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2023-10-14 11:03:35.907][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2023-10-14 11:03:35.910][initialize] This is biodb version 1.8.1.
biodb.DEBUG[2023-10-14 11:03:35.914][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-10-14 11:03:35.915][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:03:35.916][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-14 11:03:35.917][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:03:35.918][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:03:35.924][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:03:35.925][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-14 11:03:35.926][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-14 11:03:35.927][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:03:35.928][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-14 11:03:35.929][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:03:35.930][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:03:35.931][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:03:35.932][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-14 11:03:35.933][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-14 11:03:35.934][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:03:35.936][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-14 11:03:35.937][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:03:35.938][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:03:35.939][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:03:35.940][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-14 11:03:35.941][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-14 11:03:35.942][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:03:35.943][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-14 11:03:35.944][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:03:35.945][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[2023-10-14 11:03:35.946][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:03:35.947][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-14 11:03:35.948][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-14 11:03:35.949][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:03:35.950][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-14 11:03:35.951][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:03:35.952][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:03:35.953][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:03:35.954][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-14 11:03:35.956][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-14 11:03:35.957][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:03:35.958][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-14 11:03:35.959][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:03:35.960][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:03:35.961][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:03:35.962][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-14 11:03:35.963][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-14 11:03:35.964][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:03:35.965][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-14 11:03:35.966][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:03:35.967][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:03:35.968][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:03:35.969][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-14 11:03:35.970][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-14 11:03:35.971][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:03:35.972][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-14 11:03:35.973][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:03:35.974][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:03:35.976][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:03:35.977][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-14 11:03:35.978][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-14 11:03:35.979][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:03:35.980][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-14 11:03:35.981][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:03:35.982][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:03:35.983][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:03:35.984][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-14 11:03:35.985][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-14 11:03:35.986][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:03:35.987][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-14 11:03:35.988][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:03:35.989][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:03:35.990][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:03:35.991][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-14 11:03:35.992][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-14 11:03:35.993][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:03:35.994][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-14 11:03:35.996][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:03:35.997][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:03:35.998][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:03:35.999][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-14 11:03:36.000][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-14 11:03:36.001][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:03:36.002][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-14 11:03:36.003][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:03:36.004][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:03:36.005][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:03:36.006][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-14 11:03:36.007][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-14 11:03:36.008][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:03:36.009][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-14 11:03:36.011][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:03:36.012][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:03:36.013][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:03:36.014][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-14 11:03:36.015][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-14 11:03:36.016][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:03:36.017][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-14 11:03:36.018][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:03:36.019][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[2023-10-14 11:03:36.020][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:03:36.021][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-14 11:03:36.023][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-14 11:03:36.024][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:03:36.025][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-14 11:03:36.026][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:03:36.027][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:03:36.028][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:03:36.029][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-14 11:03:36.030][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-14 11:03:36.031][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:03:36.032][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-14 11:03:36.033][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:03:36.034][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:03:36.035][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:03:36.036][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-14 11:03:36.037][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-14 11:03:36.038][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:03:36.040][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-14 11:03:36.041][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:03:36.042][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[2023-10-14 11:03:36.043][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:03:36.044][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-14 11:03:36.045][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-14 11:03:36.046][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:03:36.047][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-14 11:03:36.048][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:03:36.049][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:03:36.052][biodb$loadDefinitions] Load definitions from file "/Users/biocbuild/bbs-3.17-bioc-longtests/meat/biodbExpasy.Rcheck/biodbExpasy/definitions.yml".
biodb.DEBUG[2023-10-14 11:03:36.064][self$getDbsInfo()$define] Define connector expasy.enzyme.
biodb.DEBUG[2023-10-14 11:03:36.066][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-10-14 11:03:36.068][self$setPropertyValue] Setting property "description" to "Write here the description of this database.".
biodb.DEBUG[2023-10-14 11:03:36.069][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-10-14 11:03:36.070][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-10-14 11:03:36.071][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-10-14 11:03:36.072][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-10-14 11:03:36.074][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2023-10-14 11:03:36.075][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-10-14 11:03:36.076][self$setPropertyValue] Setting property "entry.content.type" to "txt".
biodb.DEBUG[2023-10-14 11:03:36.077][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-10-14 11:03:36.079][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-10-14 11:03:36.080][self$setPropertyValue] Setting property "name" to "Expasy ENZYME database.".
biodb.DEBUG[2023-10-14 11:03:36.081][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-10-14 11:03:36.082][self$setPropertyValue] Setting property "parsing.expr" to "^ID\s+([0-9.]+)$".
biodb.DEBUG[2023-10-14 11:03:36.082][self$setPropertyValue] Setting property "parsing.expr" to "^CA\s+(.+?)\.?$".
biodb.DEBUG[2023-10-14 11:03:36.082][self$setPropertyValue] Setting property "parsing.expr" to "^CF\s+(.+?)\.?$".
biodb.DEBUG[2023-10-14 11:03:36.082][self$setPropertyValue] Setting property "parsing.expr" to "^DE\s+(.+?)\.?$".
biodb.DEBUG[2023-10-14 11:03:36.084][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2023-10-14 11:03:36.085][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2023-10-14 11:03:36.086][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2023-10-14 11:03:36.087][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-10-14 11:03:36.088][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-10-14 11:03:36.089][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-10-14 11:03:36.091][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-10-14 11:03:36.092][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-10-14 11:03:36.093][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-10-14 11:03:36.094][self$setPropertyValue] Setting property "urls" to "https://enzyme.expasy.org/".
biodb.DEBUG[2023-10-14 11:03:36.095][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-10-14 11:03:36.101][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-10-14 11:03:36.102][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2023-10-14 11:03:36.103][self$setPropertyValue]
biodb.DEBUG[2023-10-14 11:03:36.110][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2023-10-14 11:03:36.135][super$initialize] Initialize connector expasy.enzyme.
biodb.DEBUG[2023-10-14 11:03:36.137][super$initialize] Register connector expasy.enzyme with the request scheduler
biodb.DEBUG[2023-10-14 11:03:36.142][private$bdb$getRequestScheduler()$re ...] Register connector expasy.enzyme.
biodb.DEBUG[2023-10-14 11:03:36.146][private$addConnectorRules] Create new rule for URL "enzyme.expasy.org" of connector "expasy.enzyme".
biodb.DEBUG[2023-10-14 11:03:36.151][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2023-10-14 11:03:36.153][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2023-10-14 11:03:36.154][biodb$getFactory()$createConn] Creating new connector expasy.enzyme for database class expasy.enzyme .
biodb.INFO [2023-10-14 11:03:36.165][biodb::testThat]
biodb.INFO [2023-10-14 11:03:36.166][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2023-10-14 11:03:36.167][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-10-14 11:03:36.168][biodb::testThat]
biodb.TRACE[2023-10-14 11:03:36.173][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/bbs-3.17-bioc-longtests/meat/biodbExpasy.Rcheck/biodbExpasy/testref/entry-expasy.enzyme-1.1.1.1-content.txt".
biodb.DEBUG[2023-10-14 11:03:36.175][biodb$getFactory()$createEntryFromCo ...] Creating Expasy ENZYME database. entries from 1 content(s).
biodb.DEBUG[2023-10-14 11:03:36.179][biodb$getFactory()$createEntryFromCo ...] Parsing 1 Expasy ENZYME database. entries.
biodb.DEBUG[2023-10-14 11:03:36.189][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-10-14 11:03:36.190][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-14 11:03:36.191][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-14 11:03:36.207][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:03:36.209][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-14 11:03:36.210][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:03:36.211][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-10-14 11:03:36.223][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-14 11:03:36.225][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-14 11:03:36.226][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:03:36.227][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:03:36.260][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2023-10-14 11:03:36.276][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2023-10-14 11:03:36.277][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:03:36.279][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:03:36.280][self$getBiodb()$getEntryFields()$get] Asked field names are: cofactor.
biodb.TRACE[2023-10-14 11:03:36.281][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2023-10-14 11:03:36.283][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:03:36.284][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:03:36.285][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-10-14 11:03:36.286][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-14 11:03:36.288][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:03:36.289][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:03:36.290][self$getBiodb()$getEntryFields()$get] Asked field names are: COFACTOR.
biodb.TRACE[2023-10-14 11:03:36.291][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2023-10-14 11:03:36.293][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:03:36.294][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:03:36.295][self$getBiodb()$getEntryFields()$get] Asked field names are: cofactor.
biodb.TRACE[2023-10-14 11:03:36.296][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2023-10-14 11:03:36.298][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:03:36.299][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:03:36.300][self$getBiodb()$getEntryFields()$get] Asked field names are: cofactor.
biodb.TRACE[2023-10-14 11:03:36.301][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2023-10-14 11:03:36.302][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:03:36.303][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:03:36.305][self$getBiodb()$getEntryFields()$get] Asked field names are: cofactor.
biodb.TRACE[2023-10-14 11:03:36.306][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2023-10-14 11:03:36.307][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:03:36.308][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:03:36.309][self$getBiodb()$getEntryFields()$get] Asked field names are: COFACTOR.
biodb.TRACE[2023-10-14 11:03:36.311][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2023-10-14 11:03:36.312][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:03:36.313][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:03:36.336][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-10-14 11:03:36.337][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-14 11:03:36.338][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:03:36.340][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:03:36.341][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-10-14 11:03:36.342][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-14 11:03:36.343][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:03:36.345][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:03:36.388][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-10-14 11:03:36.390][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-14 11:03:36.391][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:03:36.392][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:03:36.393][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-10-14 11:03:36.395][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-14 11:03:36.396][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:03:36.406][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:03:36.408][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-10-14 11:03:36.409][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-14 11:03:36.410][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:03:36.411][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:03:36.413][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2023-10-14 11:03:36.414][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2023-10-14 11:03:36.415][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:03:36.416][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:03:36.417][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2023-10-14 11:03:36.419][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2023-10-14 11:03:36.420][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:03:36.421][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:03:36.422][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-14 11:03:36.423][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-14 11:03:36.424][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:03:36.426][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:03:36.427][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2023-10-14 11:03:36.428][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2023-10-14 11:03:36.429][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:03:36.430][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:03:36.432][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-14 11:03:36.433][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-14 11:03:36.434][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:03:36.435][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:03:36.436][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-14 11:03:36.437][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-14 11:03:36.439][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:03:36.440][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:03:36.441][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-14 11:03:36.442][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-14 11:03:36.443][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:03:36.444][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:03:36.446][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-14 11:03:36.447][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-14 11:03:36.448][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:03:36.449][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:03:36.450][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-14 11:03:36.452][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-14 11:03:36.453][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:03:36.454][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:03:36.455][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-14 11:03:36.456][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-14 11:03:36.457][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:03:36.459][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-10-14 11:03:36.460][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 1.1.1.1.
biodb.TRACE[2023-10-14 11:03:36.463][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2023-10-14 11:03:36.464][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2023-10-14 11:03:36.465][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:03:36.466][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:03:36.467][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2023-10-14 11:03:36.469][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2023-10-14 11:03:36.470][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:03:36.471][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:03:36.472][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2023-10-14 11:03:36.473][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2023-10-14 11:03:36.474][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:03:36.476][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:03:36.477][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2023-10-14 11:03:36.478][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2023-10-14 11:03:36.479][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:03:36.480][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:03:36.499][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-14 11:03:36.500][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-14 11:03:36.501][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:03:36.502][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:03:36.520][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2023-10-14 11:03:36.521][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2023-10-14 11:03:36.523][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:03:36.524][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:03:36.531][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-14 11:03:36.533][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-14 11:03:36.534][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:03:36.535][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:03:36.536][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-14 11:03:36.537][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-14 11:03:36.539][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:03:36.540][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:03:36.541][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-14 11:03:36.542][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-14 11:03:36.543][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:03:36.545][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:03:36.548][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-14 11:03:36.549][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-14 11:03:36.550][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:03:36.552][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:03:36.553][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-14 11:03:36.554][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-14 11:03:36.555][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:03:36.556][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:03:36.557][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-14 11:03:36.559][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-14 11:03:36.560][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:03:36.561][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:03:36.562][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2023-10-14 11:03:36.563][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2023-10-14 11:03:36.565][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:03:36.566][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:03:36.567][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2023-10-14 11:03:36.568][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2023-10-14 11:03:36.569][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:03:36.570][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:03:36.572][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2023-10-14 11:03:36.573][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2023-10-14 11:03:36.574][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:03:36.575][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:03:36.586][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-14 11:03:36.587][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-14 11:03:36.588][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:03:36.589][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:03:36.590][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-14 11:03:36.592][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-14 11:03:36.593][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:03:36.594][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:03:36.595][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-14 11:03:36.597][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-14 11:03:36.598][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:03:36.599][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:03:36.600][ef$get] Asked field names are: accession.
biodb.TRACE[2023-10-14 11:03:36.601][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-14 11:03:36.602][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:03:36.603][ef$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:03:36.605][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-14 11:03:36.606][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-14 11:03:36.607][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:03:36.608][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:03:36.620][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-10-14 11:03:36.622][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-14 11:03:36.623][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:03:36.624][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:03:36.625][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-10-14 11:03:36.626][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-14 11:03:36.627][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:03:36.628][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:03:36.630][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-10-14 11:03:36.631][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-14 11:03:36.632][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:03:36.633][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:03:36.634][ef$get] Asked field names are: name.
biodb.TRACE[2023-10-14 11:03:36.636][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-10-14 11:03:36.637][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:03:36.638][ef$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:03:36.639][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-10-14 11:03:36.640][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-14 11:03:36.641][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:03:36.643][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:03:36.655][self$getBiodb()$getEntryFields()$get] Asked field names are: cofactor.
biodb.TRACE[2023-10-14 11:03:36.656][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2023-10-14 11:03:36.657][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:03:36.658][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:03:36.659][self$getBiodb()$getEntryFields()$get] Asked field names are: cofactor.
biodb.TRACE[2023-10-14 11:03:36.661][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2023-10-14 11:03:36.662][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:03:36.668][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:03:36.669][self$getBiodb()$getEntryFields()$get] Asked field names are: cofactor.
biodb.TRACE[2023-10-14 11:03:36.670][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2023-10-14 11:03:36.671][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:03:36.672][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:03:36.674][ef$get] Asked field names are: cofactor.
biodb.TRACE[2023-10-14 11:03:36.675][ef$get] Realnames of fields are: cofactor.
biodb.TRACE[2023-10-14 11:03:36.676][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:03:36.677][ef$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:03:36.678][self$getBiodb()$getEntryFields()$get] Asked field names are: cofactor.
biodb.TRACE[2023-10-14 11:03:36.679][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2023-10-14 11:03:36.681][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:03:36.682][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:03:36.693][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2023-10-14 11:03:36.695][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2023-10-14 11:03:36.696][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:03:36.697][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:03:36.698][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2023-10-14 11:03:36.700][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2023-10-14 11:03:36.701][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:03:36.702][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:03:36.703][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2023-10-14 11:03:36.704][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2023-10-14 11:03:36.706][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:03:36.707][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:03:36.708][ef$get] Asked field names are: catalytic.activity.
biodb.TRACE[2023-10-14 11:03:36.709][ef$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2023-10-14 11:03:36.710][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:03:36.711][ef$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:03:36.713][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2023-10-14 11:03:36.714][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2023-10-14 11:03:36.715][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:03:36.716][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:03:36.728][ef$get] Asked field names are: accession.
biodb.TRACE[2023-10-14 11:03:36.729][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-14 11:03:36.731][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:03:36.732][ef$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:03:36.739][ef$get] Asked field names are: catalytic.activity.
biodb.TRACE[2023-10-14 11:03:36.740][ef$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2023-10-14 11:03:36.741][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:03:36.742][ef$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:03:36.749][ef$get] Asked field names are: cofactor.
biodb.TRACE[2023-10-14 11:03:36.751][ef$get] Realnames of fields are: cofactor.
biodb.TRACE[2023-10-14 11:03:36.752][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:03:36.753][ef$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:03:36.760][ef$get] Asked field names are: name.
biodb.TRACE[2023-10-14 11:03:36.761][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-10-14 11:03:36.762][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:03:36.763][ef$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:03:36.785][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/bbs-3.17-bioc-longtests/meat/biodbExpasy.Rcheck/biodbExpasy/testref/entry-expasy.enzyme-1.1.1.54-content.txt".
biodb.DEBUG[2023-10-14 11:03:36.829][biodb$getFactory()$createEntryFromCo ...] Creating Expasy ENZYME database. entries from 1 content(s).
biodb.DEBUG[2023-10-14 11:03:36.830][biodb$getFactory()$createEntryFromCo ...] Parsing 1 Expasy ENZYME database. entries.
biodb.DEBUG[2023-10-14 11:03:36.832][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-10-14 11:03:36.833][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-14 11:03:36.834][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-14 11:03:36.841][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:03:36.843][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-14 11:03:36.844][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:03:36.845][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-10-14 11:03:36.847][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-14 11:03:36.848][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-14 11:03:36.849][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:03:36.851][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:03:36.852][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2023-10-14 11:03:36.853][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2023-10-14 11:03:36.854][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:03:36.855][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:03:36.857][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-10-14 11:03:36.858][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-14 11:03:36.859][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:03:36.860][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:03:36.862][self$getBiodb()$getEntryFields()$get] Asked field names are: COFACTOR.
biodb.TRACE[2023-10-14 11:03:36.863][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2023-10-14 11:03:36.864][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:03:36.865][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:03:36.867][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2023-10-14 11:03:36.868][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2023-10-14 11:03:36.869][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:03:36.870][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:03:36.871][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2023-10-14 11:03:36.872][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2023-10-14 11:03:36.874][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:03:36.875][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:03:36.876][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-14 11:03:36.877][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-14 11:03:36.878][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:03:36.879][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:03:36.881][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2023-10-14 11:03:36.882][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2023-10-14 11:03:36.883][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:03:36.884][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:03:36.885][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-14 11:03:36.887][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-14 11:03:36.888][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:03:36.889][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:03:36.890][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-14 11:03:36.891][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-14 11:03:36.892][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:03:36.893][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:03:36.895][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-14 11:03:36.896][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-14 11:03:36.897][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:03:36.898][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:03:36.899][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-14 11:03:36.901][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-14 11:03:36.902][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:03:36.925][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:03:36.927][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-14 11:03:36.928][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-14 11:03:36.929][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:03:36.930][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:03:36.931][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-14 11:03:36.933][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-14 11:03:36.934][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:03:36.935][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-10-14 11:03:36.936][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 1.1.1.54.
biodb.TRACE[2023-10-14 11:03:36.962][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2023-10-14 11:03:36.963][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2023-10-14 11:03:36.964][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:03:36.966][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:03:36.967][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2023-10-14 11:03:36.968][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2023-10-14 11:03:36.969][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:03:36.971][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:03:36.972][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2023-10-14 11:03:36.973][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2023-10-14 11:03:36.974][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:03:36.976][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:03:36.977][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2023-10-14 11:03:36.978][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2023-10-14 11:03:36.979][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:03:36.981][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:03:36.983][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-14 11:03:36.985][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-14 11:03:36.987][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:03:36.988][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:03:36.996][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2023-10-14 11:03:36.997][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2023-10-14 11:03:36.999][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:03:37.000][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:03:37.007][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-14 11:03:37.009][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-14 11:03:37.010][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:03:37.011][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:03:37.012][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-14 11:03:37.014][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-14 11:03:37.015][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:03:37.016][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:03:37.017][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-14 11:03:37.019][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-14 11:03:37.020][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:03:37.021][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:03:37.024][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-14 11:03:37.026][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-14 11:03:37.027][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:03:37.028][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:03:37.030][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-14 11:03:37.031][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-14 11:03:37.032][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:03:37.033][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:03:37.035][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-14 11:03:37.036][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-14 11:03:37.037][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:03:37.038][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:03:37.040][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2023-10-14 11:03:37.041][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2023-10-14 11:03:37.043][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:03:37.044][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:03:37.045][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2023-10-14 11:03:37.046][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2023-10-14 11:03:37.048][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:03:37.050][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:03:37.051][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2023-10-14 11:03:37.053][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2023-10-14 11:03:37.054][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:03:37.055][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:03:37.078][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-14 11:03:37.079][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-14 11:03:37.081][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:03:37.082][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:03:37.083][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-14 11:03:37.084][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-14 11:03:37.086][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:03:37.087][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:03:37.088][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-14 11:03:37.089][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-14 11:03:37.090][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:03:37.092][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:03:37.093][ef$get] Asked field names are: accession.
biodb.TRACE[2023-10-14 11:03:37.094][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-14 11:03:37.095][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:03:37.096][ef$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:03:37.098][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-14 11:03:37.100][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-14 11:03:37.102][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:03:37.104][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:03:37.117][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-10-14 11:03:37.119][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-14 11:03:37.120][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:03:37.121][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:03:37.122][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-10-14 11:03:37.124][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-14 11:03:37.125][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:03:37.126][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:03:37.127][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-10-14 11:03:37.129][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-14 11:03:37.130][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:03:37.131][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:03:37.133][ef$get] Asked field names are: name.
biodb.TRACE[2023-10-14 11:03:37.134][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-10-14 11:03:37.135][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:03:37.136][ef$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:03:37.138][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-10-14 11:03:37.139][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-14 11:03:37.140][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:03:37.141][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:03:37.155][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2023-10-14 11:03:37.157][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2023-10-14 11:03:37.158][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:03:37.159][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:03:37.161][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2023-10-14 11:03:37.162][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2023-10-14 11:03:37.163][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:03:37.164][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:03:37.166][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2023-10-14 11:03:37.167][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2023-10-14 11:03:37.168][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:03:37.169][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:03:37.171][ef$get] Asked field names are: catalytic.activity.
biodb.TRACE[2023-10-14 11:03:37.172][ef$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2023-10-14 11:03:37.173][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:03:37.174][ef$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:03:37.176][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2023-10-14 11:03:37.177][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2023-10-14 11:03:37.178][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:03:37.179][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:03:37.197][ef$get] Asked field names are: accession.
biodb.TRACE[2023-10-14 11:03:37.199][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-14 11:03:37.200][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:03:37.202][ef$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:03:37.209][ef$get] Asked field names are: catalytic.activity.
biodb.TRACE[2023-10-14 11:03:37.210][ef$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2023-10-14 11:03:37.212][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:03:37.213][ef$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:03:37.220][ef$get] Asked field names are: name.
biodb.TRACE[2023-10-14 11:03:37.222][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-10-14 11:03:37.223][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:03:37.225][ef$get] fields variable is a list.
biodb.INFO [2023-10-14 11:03:37.240][biodb::testThat]
biodb.INFO [2023-10-14 11:03:37.242][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2023-10-14 11:03:37.243][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-10-14 11:03:37.244][biodb::testThat]
biodb.DEBUG[2023-10-14 11:03:37.247][private$loadEntries] Creating entries from ids [2]: "1.1.1.1, 1.1.1.54".
biodb.DEBUG[2023-10-14 11:03:37.256][conn$getEntryContent] Get Expasy ENZYME database. entry content(s) for 2 id(s)...
biodb.TRACE[2023-10-14 11:03:37.260][cch$loadFileContent] Trying to load 2 files from cache: [2]: "1.1.1.1, 1.1.1.54".
biodb.INFO [2023-10-14 11:03:37.261][self$getFolderPath] Create cache folder "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280" for "expasy.enzyme-b59b84d962b6741050ba8f70ff4db280".
biodb.TRACE[2023-10-14 11:03:37.263][cch$loadFileContent] file.exist = [2]: "FALSE, FALSE".
biodb.TRACE[2023-10-14 11:03:37.264][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2023-10-14 11:03:37.266][conn$getEntryContent] 0 Expasy ENZYME database. entry content(s) loaded from cache.
biodb.DEBUG[2023-10-14 11:03:37.267][conn$getEntryContent] 2 entry content(s) need to be fetched from Expasy ENZYME database. database "https://enzyme.expasy.org/".
biodb.DEBUG[2023-10-14 11:03:37.268][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2023-10-14 11:03:37.270][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2023-10-14 11:03:37.276][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-10-14 11:03:37.277][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-14 11:03:37.278][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-14 11:03:37.285][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:03:37.286][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-14 11:03:37.287][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:03:37.288][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:03:37.290][scheduler$sendRequest] Getting content of get URL request "https://enzyme.expasy.org/EC/1.1.1.1.txt".
biodb.DEBUG[2023-10-14 11:03:37.315][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-10-14 11:03:37.316][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-10-14 11:03:37.318][private$doSendRequestOnce] Sent URL is "https://enzyme.expasy.org/EC/1.1.1.1.txt".
biodb.TRACE[2023-10-14 11:03:38.435][getRCurlRequestResult] Using RCurl package for sending request (https://enzyme.expasy.org/EC/1.1.1.1.txt).
biodb.DEBUG[2023-10-14 11:03:39.493][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2023-10-14 11:03:39.495][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280/a52675cfd2f0c2b41556caa64d9341e3.content"
biodb.TRACE[2023-10-14 11:03:39.513][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280/a52675cfd2f0c2b41556caa64d9341e3.request"
biodb.DEBUG[2023-10-14 11:03:39.516][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-10-14 11:03:39.517][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-14 11:03:39.518][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-14 11:03:39.525][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:03:39.526][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-14 11:03:39.527][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:03:39.528][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:03:39.555][scheduler$sendRequest] Getting content of get URL request "https://enzyme.expasy.org/EC/1.1.1.54.txt".
biodb.DEBUG[2023-10-14 11:03:39.575][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-10-14 11:03:39.576][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-10-14 11:03:39.595][private$doSendRequestOnce] Sent URL is "https://enzyme.expasy.org/EC/1.1.1.54.txt".
biodb.TRACE[2023-10-14 11:03:40.603][getRCurlRequestResult] Using RCurl package for sending request (https://enzyme.expasy.org/EC/1.1.1.54.txt).
biodb.DEBUG[2023-10-14 11:03:41.626][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2023-10-14 11:03:41.628][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280/a9b93566a091cbe35a06e4b3871f95c9.content"
biodb.TRACE[2023-10-14 11:03:41.633][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280/a9b93566a091cbe35a06e4b3871f95c9.request"
biodb.TRACE[2023-10-14 11:03:41.636][private$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[2023-10-14 11:03:41.638][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2023-10-14 11:03:41.640][self$createEntryFromContent] Creating Expasy ENZYME database. entries from 2 content(s).
biodb.DEBUG[2023-10-14 11:03:41.641][self$createEntryFromContent] Parsing 2 Expasy ENZYME database. entries.
biodb.DEBUG[2023-10-14 11:03:41.643][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-10-14 11:03:41.644][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-14 11:03:41.645][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-14 11:03:41.653][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:03:41.654][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-14 11:03:41.655][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:03:41.656][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-10-14 11:03:41.659][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-14 11:03:41.660][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-14 11:03:41.661][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:03:41.662][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:03:41.664][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2023-10-14 11:03:41.665][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2023-10-14 11:03:41.666][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:03:41.667][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:03:41.669][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-10-14 11:03:41.670][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-14 11:03:41.671][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:03:41.673][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:03:41.674][self$getBiodb()$getEntryFields()$get] Asked field names are: COFACTOR.
biodb.TRACE[2023-10-14 11:03:41.675][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2023-10-14 11:03:41.676][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:03:41.677][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:03:41.679][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-10-14 11:03:41.680][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-14 11:03:41.681][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:03:41.682][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:03:41.683][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-10-14 11:03:41.685][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-14 11:03:41.686][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:03:41.687][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:03:41.688][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-10-14 11:03:41.689][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-14 11:03:41.690][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:03:41.692][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:03:41.693][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-10-14 11:03:41.694][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-14 11:03:41.695][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:03:41.696][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:03:41.697][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-10-14 11:03:41.699][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-14 11:03:41.700][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:03:41.701][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:03:41.702][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2023-10-14 11:03:41.703][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2023-10-14 11:03:41.705][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:03:41.706][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:03:41.707][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2023-10-14 11:03:41.708][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2023-10-14 11:03:41.709][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:03:41.710][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:03:41.711][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-14 11:03:41.713][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-14 11:03:41.714][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:03:41.715][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:03:41.716][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2023-10-14 11:03:41.717][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2023-10-14 11:03:41.719][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:03:41.726][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:03:41.728][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-14 11:03:41.729][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-14 11:03:41.730][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:03:41.731][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:03:41.733][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-14 11:03:41.734][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-14 11:03:41.735][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:03:41.736][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:03:41.737][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-14 11:03:41.739][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-14 11:03:41.740][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:03:41.741][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-10-14 11:03:41.742][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-10-14 11:03:41.743][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-14 11:03:41.744][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-14 11:03:41.751][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:03:41.752][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-14 11:03:41.753][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:03:41.754][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-10-14 11:03:41.757][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-14 11:03:41.758][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-14 11:03:41.759][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:03:41.760][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:03:41.762][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2023-10-14 11:03:41.763][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2023-10-14 11:03:41.764][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:03:41.765][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:03:41.767][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-10-14 11:03:41.768][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-14 11:03:41.769][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:03:41.770][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:03:41.771][self$getBiodb()$getEntryFields()$get] Asked field names are: COFACTOR.
biodb.TRACE[2023-10-14 11:03:41.773][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2023-10-14 11:03:41.774][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:03:41.775][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:03:41.776][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2023-10-14 11:03:41.778][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2023-10-14 11:03:41.779][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:03:41.780][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:03:41.781][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2023-10-14 11:03:41.782][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2023-10-14 11:03:41.783][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:03:41.785][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:03:41.786][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-14 11:03:41.787][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-14 11:03:41.788][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:03:41.789][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:03:41.790][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2023-10-14 11:03:41.792][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2023-10-14 11:03:41.793][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:03:41.794][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:03:41.795][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-14 11:03:41.797][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-14 11:03:41.798][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:03:41.799][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:03:41.800][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-14 11:03:41.801][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-14 11:03:41.803][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:03:41.804][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:03:41.805][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-14 11:03:41.806][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-14 11:03:41.807][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:03:41.809][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:03:41.810][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-14 11:03:41.811][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-14 11:03:41.812][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:03:41.813][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:03:41.815][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-14 11:03:41.816][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-14 11:03:41.817][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:03:41.818][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:03:41.819][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-14 11:03:41.821][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-14 11:03:41.822][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:03:41.823][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:03:41.824][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-14 11:03:41.826][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-14 11:03:41.827][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:03:41.828][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:03:41.829][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-14 11:03:41.830][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-14 11:03:41.832][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:03:41.833][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:03:41.834][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-14 11:03:41.835][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-14 11:03:41.836][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:03:41.837][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-10-14 11:03:41.839][self$createEntryFromContent] Accession numbers: 1.1.1.1, 1.1.1.54.
biodb.TRACE[2023-10-14 11:03:41.840][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2023-10-14 11:03:41.841][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2023-10-14 11:03:41.842][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:03:41.844][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:03:41.845][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2023-10-14 11:03:41.846][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2023-10-14 11:03:41.847][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:03:41.848][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:03:41.850][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2023-10-14 11:03:41.851][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2023-10-14 11:03:41.852][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:03:41.853][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:03:41.861][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2023-10-14 11:03:41.862][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2023-10-14 11:03:41.863][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:03:41.864][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:03:41.865][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2023-10-14 11:03:41.867][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2023-10-14 11:03:41.868][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:03:41.869][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:03:41.870][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2023-10-14 11:03:41.872][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2023-10-14 11:03:41.873][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:03:41.874][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2023-10-14 11:03:41.889][biodb::testThat]
biodb.INFO [2023-10-14 11:03:41.890][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2023-10-14 11:03:41.891][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-10-14 11:03:41.892][biodb::testThat]
biodb.TRACE[2023-10-14 11:03:41.896][ef$get] Asked field names are: name.
biodb.TRACE[2023-10-14 11:03:41.897][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-10-14 11:03:41.898][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:03:41.899][ef$get] fields variable is a list.
biodb.DEBUG[2023-10-14 11:03:41.901][function(conn, opt)] Testing searchForEntries() with entry "1.1.1.1" and field "name".
biodb.TRACE[2023-10-14 11:03:41.935][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-10-14 11:03:41.941][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-14 11:03:41.942][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:03:41.943][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:03:41.944][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-10-14 11:03:41.945][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-14 11:03:41.946][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:03:41.947][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:03:41.949][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-10-14 11:03:41.950][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-14 11:03:41.951][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:03:41.952][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-10-14 11:03:41.956][function(conn, opt)] With value "alcohol dehydrogenase".
biodb.DEBUG[2023-10-14 11:03:41.959][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://enzyme.expasy.org/enzyme-byname.html?alcohol dehydrogenase".
biodb.DEBUG[2023-10-14 11:03:41.962][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-10-14 11:03:41.963][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-10-14 11:03:41.965][private$doSendRequestOnce] Sent URL is "https://enzyme.expasy.org/enzyme-byname.html?alcohol%20dehydrogenase".
biodb.TRACE[2023-10-14 11:03:43.045][getRCurlRequestResult] Using RCurl package for sending request (https://enzyme.expasy.org/enzyme-byname.html?alcohol%20dehydrogenase).
biodb.DEBUG[2023-10-14 11:03:44.184][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2023-10-14 11:03:44.187][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280/f603fa2a57aec59588edc37541c6f6d5.content"
biodb.TRACE[2023-10-14 11:03:44.191][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280/f603fa2a57aec59588edc37541c6f6d5.request"
biodb.DEBUG[2023-10-14 11:03:44.198][function(conn, opt)] With found IDs [1]: "1.1.1.1".
biodb.INFO [2023-10-14 11:03:44.221][biodb::testThat]
biodb.INFO [2023-10-14 11:03:44.222][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2023-10-14 11:03:44.223][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-10-14 11:03:44.224][biodb::testThat]
biodb.TRACE[2023-10-14 11:03:44.260][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-10-14 11:03:44.261][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-14 11:03:44.262][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:03:44.263][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:03:44.265][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-10-14 11:03:44.266][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-14 11:03:44.267][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:03:44.268][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:03:44.269][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-10-14 11:03:44.271][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-14 11:03:44.272][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:03:44.273][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-10-14 11:03:44.313][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://enzyme.expasy.org/enzyme-byname.html?alcohol dehydrogenase".
biodb.DEBUG[2023-10-14 11:03:44.317][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-10-14 11:03:44.336][cch$loadFileContent] Trying to load 1 files from cache: [1]: "f603fa2a57aec59588edc37541c6f6d5".
biodb.TRACE[2023-10-14 11:03:44.337][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-10-14 11:03:44.339][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280/f603fa2a57aec59588edc37541c6f6d5.content".
biodb.INFO [2023-10-14 11:03:44.372][biodb::testThat]
biodb.INFO [2023-10-14 11:03:44.373][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2023-10-14 11:03:44.374][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-10-14 11:03:44.375][biodb::testThat]
biodb.TRACE[2023-10-14 11:03:44.388][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2023-10-14 11:03:44.390][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2023-10-14 11:03:44.391][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:03:44.392][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:03:44.393][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2023-10-14 11:03:44.394][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2023-10-14 11:03:44.395][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:03:44.396][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:03:44.398][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2023-10-14 11:03:44.399][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2023-10-14 11:03:44.400][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:03:44.401][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:03:44.402][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2023-10-14 11:03:44.404][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2023-10-14 11:03:44.405][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:03:44.406][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:03:44.446][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2023-10-14 11:03:44.448][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2023-10-14 11:03:44.449][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:03:44.450][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:03:44.451][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2023-10-14 11:03:44.452][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2023-10-14 11:03:44.453][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:03:44.455][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:03:44.456][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2023-10-14 11:03:44.457][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2023-10-14 11:03:44.458][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:03:44.459][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:03:44.461][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2023-10-14 11:03:44.462][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2023-10-14 11:03:44.463][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:03:44.464][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2023-10-14 11:03:44.497][biodb::testThat]
biodb.INFO [2023-10-14 11:03:44.499][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2023-10-14 11:03:44.500][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-10-14 11:03:44.501][biodb::testThat]
biodb.INFO [2023-10-14 11:03:44.514][biodb::testThat]
biodb.INFO [2023-10-14 11:03:44.515][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2023-10-14 11:03:44.516][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-10-14 11:03:44.517][biodb::testThat]
biodb.INFO [2023-10-14 11:03:44.528][biodb::testThat]
biodb.INFO [2023-10-14 11:03:44.529][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2023-10-14 11:03:44.531][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-10-14 11:03:44.532][biodb::testThat]
biodb.DEBUG[2023-10-14 11:03:44.550][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[2023-10-14 11:03:45.615][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 [2023-10-14 11:03:46.664][biodb::testThat]
biodb.INFO [2023-10-14 11:03:46.665][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2023-10-14 11:03:46.666][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-10-14 11:03:46.667][biodb::testThat]
biodb.DEBUG[2023-10-14 11:03:54.357][getUrlContent] Use RCurl for downloading content of URL https://enzyme.expasy.org/images/1.1.1.1/image.png.
biodb.TRACE[2023-10-14 11:03:55.029][ef$get] Asked field names are: name.
biodb.TRACE[2023-10-14 11:03:55.031][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-10-14 11:03:55.037][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:03:55.044][ef$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:03:55.045][ef$get] Asked field names are: name.
biodb.TRACE[2023-10-14 11:03:55.046][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-10-14 11:03:55.047][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:03:55.048][ef$get] fields variable is a list.
biodb.INFO [2023-10-14 11:03:55.050][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2023-10-14 11:03:55.051][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector expasy.enzyme from the request scheduler
biodb.INFO [2023-10-14 11:03:55.052][self$deleteConn] Connector "expasy.enzyme" deleted.
biodb.DEBUG[2023-10-14 11:03:55.053][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2023-10-14 11:03:55.054][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-14 11:03:55.055][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-14 11:03:55.056][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:03:55.057][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-14 11:03:55.059][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:03:55.060][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2023-10-14 11:03:55.071][biodb::testContext]
biodb.INFO [2023-10-14 11:03:55.073][biodb::testContext] ********************************************************************************
biodb.INFO [2023-10-14 11:03:55.074][biodb::testContext] Test context - Example long tests
biodb.INFO [2023-10-14 11:03:55.075][biodb::testContext] ********************************************************************************
biodb.INFO [2023-10-14 11:03:55.076][biodb::testContext]
biodb.INFO [2023-10-14 11:03:55.078][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.8.1.
biodb.DEBUG[2023-10-14 11:03:55.080][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2023-10-14 11:03:55.084][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-10-14 11:03:55.086][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2023-10-14 11:03:55.087][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2023-10-14 11:03:55.088][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:03:55.089][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:03:55.090][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:03:55.091][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2023-10-14 11:03:55.092][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2023-10-14 11:03:55.093][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:03:55.094][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:03:55.095][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:03:55.096][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2023-10-14 11:03:55.098][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2023-10-14 11:03:55.099][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:03:55.100][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:03:55.101][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:03:55.102][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2023-10-14 11:03:55.103][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2023-10-14 11:03:55.104][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2023-10-14 11:03:55.105][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:03:55.106][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:03:55.107][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:03:55.109][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2023-10-14 11:03:55.110][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2023-10-14 11:03:55.111][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2023-10-14 11:03:55.112][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:03:55.113][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:03:55.114][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:03:55.115][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2023-10-14 11:03:55.116][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2023-10-14 11:03:55.117][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:03:55.118][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:03:55.119][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:03:55.121][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2023-10-14 11:03:55.122][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2023-10-14 11:03:55.123][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2023-10-14 11:03:55.124][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:03:55.125][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:03:55.126][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:03:55.127][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2023-10-14 11:03:55.128][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2023-10-14 11:03:55.130][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:03:55.131][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:03:55.132][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:03:55.133][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2023-10-14 11:03:55.134][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2023-10-14 11:03:55.135][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2023-10-14 11:03:55.136][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:03:55.137][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:03:55.138][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:03:55.139][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2023-10-14 11:03:55.141][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2023-10-14 11:03:55.142][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2023-10-14 11:03:55.143][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2023-10-14 11:03:55.144][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2023-10-14 11:03:55.145][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2023-10-14 11:03:55.146][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:03:55.147][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:03:55.148][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:03:55.150][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2023-10-14 11:03:55.151][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2023-10-14 11:03:55.152][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:03:55.153][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:03:55.154][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:03:55.155][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2023-10-14 11:03:55.156][self$set] Set key entries.sep to "|".
biodb.DEBUG[2023-10-14 11:03:55.157][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:03:55.158][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:03:55.159][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:03:55.161][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2023-10-14 11:03:55.162][self$set] Set key offline to FALSE.
biodb.DEBUG[2023-10-14 11:03:55.163][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:03:55.164][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:03:55.165][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:03:55.166][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2023-10-14 11:03:55.167][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2023-10-14 11:03:55.168][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:03:55.169][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:03:55.170][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:03:55.172][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2023-10-14 11:03:55.173][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2023-10-14 11:03:55.174][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:03:55.175][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:03:55.176][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:03:55.177][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2023-10-14 11:03:55.178][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2023-10-14 11:03:55.189][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2023-10-14 11:03:55.190][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:03:55.191][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:03:55.192][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:03:55.194][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2023-10-14 11:03:55.195][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2023-10-14 11:03:55.196][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2023-10-14 11:03:55.197][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:03:55.198][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:03:55.199][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:03:55.201][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2023-10-14 11:03:55.203][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-10-14 11:03:55.204][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2023-10-14 11:03:55.205][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-10-14 11:03:55.206][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-10-14 11:03:55.208][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-10-14 11:03:55.209][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-10-14 11:03:55.210][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-10-14 11:03:55.211][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-10-14 11:03:55.212][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2023-10-14 11:03:55.213][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-10-14 11:03:55.215][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-10-14 11:03:55.216][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2023-10-14 11:03:55.217][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-10-14 11:03:55.218][self$setPropertyValue]
biodb.DEBUG[2023-10-14 11:03:55.219][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-10-14 11:03:55.220][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2023-10-14 11:03:55.220][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2023-10-14 11:03:55.220][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2023-10-14 11:03:55.220][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2023-10-14 11:03:55.220][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2023-10-14 11:03:55.222][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-10-14 11:03:55.223][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-10-14 11:03:55.224][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-10-14 11:03:55.225][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-10-14 11:03:55.226][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-10-14 11:03:55.227][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-10-14 11:03:55.228][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-10-14 11:03:55.230][self$setPropertyValue]
biodb.DEBUG[2023-10-14 11:03:55.231][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-10-14 11:03:55.232][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-10-14 11:03:55.233][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-10-14 11:03:55.234][self$setPropertyValue]
biodb.DEBUG[2023-10-14 11:03:55.236][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2023-10-14 11:03:55.238][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-10-14 11:03:55.239][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2023-10-14 11:03:55.240][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-10-14 11:03:55.241][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-10-14 11:03:55.243][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-10-14 11:03:55.244][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-10-14 11:03:55.245][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-10-14 11:03:55.246][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-10-14 11:03:55.247][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2023-10-14 11:03:55.249][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-10-14 11:03:55.250][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-10-14 11:03:55.251][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2023-10-14 11:03:55.252][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-10-14 11:03:55.253][self$setPropertyValue]
biodb.DEBUG[2023-10-14 11:03:55.254][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-10-14 11:03:55.260][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2023-10-14 11:03:55.260][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2023-10-14 11:03:55.260][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2023-10-14 11:03:55.260][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2023-10-14 11:03:55.260][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2023-10-14 11:03:55.262][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-10-14 11:03:55.263][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-10-14 11:03:55.264][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-10-14 11:03:55.265][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-10-14 11:03:55.266][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-10-14 11:03:55.268][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-10-14 11:03:55.269][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-10-14 11:03:55.270][self$setPropertyValue]
biodb.DEBUG[2023-10-14 11:03:55.271][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-10-14 11:03:55.272][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-10-14 11:03:55.273][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-10-14 11:03:55.274][self$setPropertyValue]
biodb.DEBUG[2023-10-14 11:03:55.276][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2023-10-14 11:03:55.278][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2023-10-14 11:03:55.279][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2023-10-14 11:03:55.280][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-10-14 11:03:55.281][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-10-14 11:03:55.282][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-10-14 11:03:55.283][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-10-14 11:03:55.285][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-10-14 11:03:55.286][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-10-14 11:03:55.287][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2023-10-14 11:03:55.288][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-10-14 11:03:55.289][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2023-10-14 11:03:55.290][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2023-10-14 11:03:55.292][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-10-14 11:03:55.293][self$setPropertyValue]
biodb.DEBUG[2023-10-14 11:03:55.294][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-10-14 11:03:55.295][self$setPropertyValue]
biodb.DEBUG[2023-10-14 11:03:55.296][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-10-14 11:03:55.297][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-10-14 11:03:55.298][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-10-14 11:03:55.299][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-10-14 11:03:55.301][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-10-14 11:03:55.302][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-10-14 11:03:55.303][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-10-14 11:03:55.304][self$setPropertyValue]
biodb.DEBUG[2023-10-14 11:03:55.305][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-10-14 11:03:55.306][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-10-14 11:03:55.307][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-10-14 11:03:55.308][self$setPropertyValue]
biodb.DEBUG[2023-10-14 11:03:55.310][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2023-10-14 11:03:55.312][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2023-10-14 11:03:55.313][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2023-10-14 11:03:55.314][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-10-14 11:03:55.315][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-10-14 11:03:55.316][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-10-14 11:03:55.318][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-10-14 11:03:55.319][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-10-14 11:03:55.320][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-10-14 11:03:55.321][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2023-10-14 11:03:55.322][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-10-14 11:03:55.323][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2023-10-14 11:03:55.325][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2023-10-14 11:03:55.326][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-10-14 11:03:55.327][self$setPropertyValue]
biodb.DEBUG[2023-10-14 11:03:55.328][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-10-14 11:03:55.329][self$setPropertyValue]
biodb.DEBUG[2023-10-14 11:03:55.330][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-10-14 11:03:55.332][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-10-14 11:03:55.333][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-10-14 11:03:55.334][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-10-14 11:03:55.335][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-10-14 11:03:55.336][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-10-14 11:03:55.337][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-10-14 11:03:55.338][self$setPropertyValue]
biodb.DEBUG[2023-10-14 11:03:55.339][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-10-14 11:03:55.340][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-10-14 11:03:55.341][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-10-14 11:03:55.343][self$setPropertyValue]
biodb.DEBUG[2023-10-14 11:03:55.344][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-10-14 11:03:55.345][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:03:55.346][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:03:55.347][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:03:55.348][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:03:55.349][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-14 11:03:55.350][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:03:55.351][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:03:55.352][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:03:55.353][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:03:55.354][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-14 11:03:55.355][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:03:55.356][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:03:55.357][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:03:55.358][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:03:55.359][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-14 11:03:55.360][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:03:55.361][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:03:55.362][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:03:55.363][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:03:55.364][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-14 11:03:55.365][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:03:55.367][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:03:55.368][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:03:55.369][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:03:55.370][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-14 11:03:55.371][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:03:55.372][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[2023-10-14 11:03:55.373][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:03:55.374][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:03:55.375][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-14 11:03:55.376][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:03:55.377][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:03:55.378][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:03:55.379][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:03:55.380][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-14 11:03:55.381][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:03:55.382][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:03:55.383][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:03:55.384][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:03:55.385][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-14 11:03:55.386][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:03:55.387][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:03:55.388][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:03:55.389][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:03:55.390][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-14 11:03:55.391][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:03:55.392][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:03:55.393][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:03:55.394][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:03:55.395][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-14 11:03:55.396][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:03:55.397][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:03:55.398][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:03:55.399][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:03:55.400][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-14 11:03:55.401][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:03:55.403][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:03:55.404][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:03:55.405][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:03:55.406][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-14 11:03:55.407][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:03:55.408][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:03:55.409][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:03:55.410][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:03:55.411][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-14 11:03:55.412][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:03:55.413][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:03:55.414][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:03:55.415][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:03:55.416][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-14 11:03:55.417][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:03:55.418][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:03:55.419][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:03:55.420][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:03:55.421][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-14 11:03:55.422][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:03:55.423][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:03:55.424][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:03:55.425][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:03:55.426][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-14 11:03:55.427][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:03:55.428][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:03:55.429][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:03:55.430][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:03:55.431][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-14 11:03:55.432][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:03:55.433][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:03:55.434][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2023-10-14 11:03:55.436][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2023-10-14 11:03:55.437][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2023-10-14 11:03:55.439][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2023-10-14 11:03:55.441][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2023-10-14 11:03:55.442][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2023-10-14 11:03:55.444][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2023-10-14 11:03:55.446][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2023-10-14 11:03:55.447][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2023-10-14 11:03:55.449][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2023-10-14 11:03:55.451][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2023-10-14 11:03:55.452][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2023-10-14 11:03:55.454][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2023-10-14 11:03:55.456][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2023-10-14 11:03:55.461][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2023-10-14 11:03:55.463][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2023-10-14 11:03:55.464][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2023-10-14 11:03:55.466][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2023-10-14 11:03:55.468][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2023-10-14 11:03:55.469][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2023-10-14 11:03:55.471][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2023-10-14 11:03:55.472][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2023-10-14 11:03:55.474][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2023-10-14 11:03:55.476][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2023-10-14 11:03:55.477][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2023-10-14 11:03:55.479][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2023-10-14 11:03:55.480][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2023-10-14 11:03:55.482][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2023-10-14 11:03:55.483][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2023-10-14 11:03:55.485][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2023-10-14 11:03:55.487][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2023-10-14 11:03:55.488][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2023-10-14 11:03:55.490][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2023-10-14 11:03:55.491][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2023-10-14 11:03:55.493][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2023-10-14 11:03:55.495][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2023-10-14 11:03:55.496][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2023-10-14 11:03:55.498][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2023-10-14 11:03:55.499][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2023-10-14 11:03:55.501][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2023-10-14 11:03:55.503][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2023-10-14 11:03:55.504][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2023-10-14 11:03:55.506][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2023-10-14 11:03:55.507][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2023-10-14 11:03:55.509][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2023-10-14 11:03:55.511][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2023-10-14 11:03:55.512][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2023-10-14 11:03:55.514][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2023-10-14 11:03:55.515][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2023-10-14 11:03:55.517][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2023-10-14 11:03:55.519][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2023-10-14 11:03:55.520][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2023-10-14 11:03:55.522][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2023-10-14 11:03:55.523][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2023-10-14 11:03:55.525][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2023-10-14 11:03:55.526][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2023-10-14 11:03:55.528][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2023-10-14 11:03:55.530][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2023-10-14 11:03:55.531][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2023-10-14 11:03:55.533][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2023-10-14 11:03:55.534][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2023-10-14 11:03:55.536][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2023-10-14 11:03:55.538][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2023-10-14 11:03:55.539][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2023-10-14 11:03:55.541][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2023-10-14 11:03:55.542][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2023-10-14 11:03:55.544][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2023-10-14 11:03:55.545][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2023-10-14 11:03:55.547][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2023-10-14 11:03:55.549][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2023-10-14 11:03:55.550][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2023-10-14 11:03:55.552][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2023-10-14 11:03:55.553][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2023-10-14 11:03:55.555][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2023-10-14 11:03:55.556][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2023-10-14 11:03:55.558][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2023-10-14 11:03:55.560][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2023-10-14 11:03:55.561][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2023-10-14 11:03:55.563][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2023-10-14 11:03:55.564][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2023-10-14 11:03:55.566][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2023-10-14 11:03:55.568][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2023-10-14 11:03:55.569][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2023-10-14 11:03:55.571][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2023-10-14 11:03:55.573][initialize] This is biodb version 1.8.1.
biodb.DEBUG[2023-10-14 11:03:55.574][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-10-14 11:03:55.575][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:03:55.576][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-14 11:03:55.577][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:03:55.578][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:03:55.579][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:03:55.580][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-14 11:03:55.581][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-14 11:03:55.582][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:03:55.583][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-14 11:03:55.584][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:03:55.585][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:03:55.586][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:03:55.587][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-14 11:03:55.588][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-14 11:03:55.589][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:03:55.590][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-14 11:03:55.591][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:03:55.592][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:03:55.593][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:03:55.594][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-14 11:03:55.595][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-14 11:03:55.596][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:03:55.597][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-14 11:03:55.598][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:03:55.599][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[2023-10-14 11:03:55.600][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:03:55.601][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-14 11:03:55.602][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-14 11:03:55.603][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:03:55.604][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-14 11:03:55.605][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:03:55.606][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:03:55.607][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:03:55.608][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-14 11:03:55.609][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-14 11:03:55.610][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:03:55.611][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-14 11:03:55.612][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:03:55.613][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:03:55.614][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:03:55.615][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-14 11:03:55.616][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-14 11:03:55.617][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:03:55.618][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-14 11:03:55.619][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:03:55.620][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:03:55.621][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:03:55.622][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-14 11:03:55.623][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-14 11:03:55.624][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:03:55.625][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-14 11:03:55.626][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:03:55.627][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:03:55.628][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:03:55.629][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-14 11:03:55.630][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-14 11:03:55.631][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:03:55.632][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-14 11:03:55.633][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:03:55.634][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:03:55.636][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:03:55.637][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-14 11:03:55.638][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-14 11:03:55.639][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:03:55.640][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-14 11:03:55.641][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:03:55.642][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:03:55.643][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:03:55.644][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-14 11:03:55.645][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-14 11:03:55.646][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:03:55.647][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-14 11:03:55.648][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:03:55.649][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:03:55.650][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:03:55.655][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-14 11:03:55.656][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-14 11:03:55.657][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:03:55.658][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-14 11:03:55.659][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:03:55.660][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:03:55.661][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:03:55.662][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-14 11:03:55.663][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-14 11:03:55.664][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:03:55.665][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-14 11:03:55.666][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:03:55.667][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:03:55.668][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:03:55.669][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-14 11:03:55.670][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-14 11:03:55.671][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:03:55.672][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-14 11:03:55.673][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:03:55.675][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:03:55.676][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:03:55.677][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-14 11:03:55.678][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-14 11:03:55.700][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:03:55.701][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-14 11:03:55.702][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:03:55.703][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:03:55.704][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:03:55.705][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-14 11:03:55.706][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-14 11:03:55.707][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:03:55.708][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-14 11:03:55.709][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:03:55.710][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:03:55.711][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:03:55.712][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-14 11:03:55.713][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-14 11:03:55.715][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:03:55.716][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-14 11:03:55.717][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:03:55.718][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[2023-10-14 11:03:55.719][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:03:55.720][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-14 11:03:55.721][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-14 11:03:55.722][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:03:55.723][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-14 11:03:55.724][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:03:55.725][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:03:55.728][biodb$loadDefinitions] Load definitions from file "/Users/biocbuild/bbs-3.17-bioc-longtests/meat/biodbExpasy.Rcheck/biodbExpasy/definitions.yml".
biodb.DEBUG[2023-10-14 11:03:55.729][self$getDbsInfo()$define] Define connector expasy.enzyme.
biodb.DEBUG[2023-10-14 11:03:55.731][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-10-14 11:03:55.733][self$setPropertyValue] Setting property "description" to "Write here the description of this database.".
biodb.DEBUG[2023-10-14 11:03:55.734][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-10-14 11:03:55.735][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-10-14 11:03:55.736][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-10-14 11:03:55.737][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-10-14 11:03:55.738][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2023-10-14 11:03:55.744][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-10-14 11:03:55.745][self$setPropertyValue] Setting property "entry.content.type" to "txt".
biodb.DEBUG[2023-10-14 11:03:55.746][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-10-14 11:03:55.747][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-10-14 11:03:55.749][self$setPropertyValue] Setting property "name" to "Expasy ENZYME database.".
biodb.DEBUG[2023-10-14 11:03:55.750][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-10-14 11:03:55.751][self$setPropertyValue] Setting property "parsing.expr" to "^ID\s+([0-9.]+)$".
biodb.DEBUG[2023-10-14 11:03:55.751][self$setPropertyValue] Setting property "parsing.expr" to "^CA\s+(.+?)\.?$".
biodb.DEBUG[2023-10-14 11:03:55.751][self$setPropertyValue] Setting property "parsing.expr" to "^CF\s+(.+?)\.?$".
biodb.DEBUG[2023-10-14 11:03:55.751][self$setPropertyValue] Setting property "parsing.expr" to "^DE\s+(.+?)\.?$".
biodb.DEBUG[2023-10-14 11:03:55.752][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2023-10-14 11:03:55.753][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2023-10-14 11:03:55.755][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2023-10-14 11:03:55.756][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-10-14 11:03:55.757][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-10-14 11:03:55.758][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-10-14 11:03:55.759][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-10-14 11:03:55.760][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-10-14 11:03:55.761][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-10-14 11:03:55.762][self$setPropertyValue] Setting property "urls" to "https://enzyme.expasy.org/".
biodb.DEBUG[2023-10-14 11:03:55.764][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-10-14 11:03:55.765][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-10-14 11:03:55.766][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2023-10-14 11:03:55.767][self$setPropertyValue]
biodb.DEBUG[2023-10-14 11:03:55.769][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2023-10-14 11:03:55.772][super$initialize] Initialize connector expasy.enzyme.
biodb.DEBUG[2023-10-14 11:03:55.774][super$initialize] Register connector expasy.enzyme with the request scheduler
biodb.DEBUG[2023-10-14 11:03:55.775][private$bdb$getRequestScheduler()$re ...] Register connector expasy.enzyme.
biodb.DEBUG[2023-10-14 11:03:55.777][private$addConnectorRules] Create new rule for URL "enzyme.expasy.org" of connector "expasy.enzyme".
biodb.DEBUG[2023-10-14 11:03:55.778][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2023-10-14 11:03:55.779][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2023-10-14 11:03:55.781][biodb$getFactory()$createConn] Creating new connector expasy.enzyme for database class expasy.enzyme .
biodb.INFO [2023-10-14 11:03:55.782][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2023-10-14 11:03:55.783][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector expasy.enzyme from the request scheduler
biodb.INFO [2023-10-14 11:03:55.784][self$deleteConn] Connector "expasy.enzyme" deleted.
biodb.DEBUG[2023-10-14 11:03:55.786][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2023-10-14 11:03:55.787][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-14 11:03:55.788][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-14 11:03:55.789][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:03:55.790][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-14 11:03:55.791][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:03:55.792][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 86 ]
> 
> proc.time()
   user  system elapsed 
  5.984   0.358  22.909

'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_1.4.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.17-bioc-longtests/meat/biodbExpasy.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: x86_64-apple-darwin20 (64-bit)
* R was compiled by
    Apple clang version 14.0.3 (clang-1403.0.22.14.1)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.6.4
* 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 ‘1.4.0’
* 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 R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... SKIPPED
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... SKIPPED
* checking examples ... SKIPPED
* checking for unstated dependencies in ‘longtests’ ... OK
* checking tests in ‘longtests’ ...
  Running ‘testthat.R’
 OK
* DONE

Status: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.17-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)