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 palomino3


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: F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --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 11:04:37 -0400 (Sat, 14 Oct 2023)
EndedAt: 2023-10-14 11:05:31 -0400 (Sat, 14 Oct 2023)
EllapsedTime: 54.1 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 ucrt) -- "Beagle Scouts"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)

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

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

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

> # Script needed to run testthat automatically from ‘R CMD check’. See
> # testthat::test_dir documentation.
> library(testthat)
> library(biodbExpasy)
> Sys.setenv(TESTTHAT_REPORTER="summary")
> Sys.setenv(BIODB_LOG_DST="console")
> test_check("biodbExpasy")
biodb.INFO [2023-10-14 11:05:19.985][biodb::testContext]
biodb.INFO [2023-10-14 11:05:19.989][biodb::testContext] ********************************************************************************
biodb.INFO [2023-10-14 11:05:19.990][biodb::testContext] Test context - Generic long tests
biodb.INFO [2023-10-14 11:05:19.991][biodb::testContext] ********************************************************************************
biodb.INFO [2023-10-14 11:05:19.993][biodb::testContext]
biodb.INFO [2023-10-14 11:05:20.000][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.8.1.
biodb.DEBUG[2023-10-14 11:05:20.003][self$loadDefinitions] Load definitions from file "F:/biocbuild/bbs-3.17-bioc/R/library/biodb/definitions.yml".
biodb.DEBUG[2023-10-14 11:05:20.042][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-10-14 11:05:20.045][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2023-10-14 11:05:20.047][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2023-10-14 11:05:20.048][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:05:20.050][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:05:20.052][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:05:20.054][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2023-10-14 11:05:20.076][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2023-10-14 11:05:20.078][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:05:20.079][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:05:20.080][FUN] Functions in observer BiodbConfig: [21]: ".__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 11:05:20.082][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2023-10-14 11:05:20.083][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2023-10-14 11:05:20.084][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:05:20.086][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:05:20.087][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:05:20.088][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2023-10-14 11:05:20.089][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2023-10-14 11:05:20.091][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2023-10-14 11:05:20.092][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:05:20.093][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:05:20.095][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 11:05:20.096][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2023-10-14 11:05:20.097][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2023-10-14 11:05:20.099][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2023-10-14 11:05:20.100][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:05:20.101][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:05:20.103][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:05:20.104][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2023-10-14 11:05:20.105][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2023-10-14 11:05:20.106][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:05:20.108][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:05:20.109][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:05:20.110][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2023-10-14 11:05:20.111][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2023-10-14 11:05:20.113][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2023-10-14 11:05:20.114][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:05:20.115][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:05:20.117][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:05:20.118][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2023-10-14 11:05:20.119][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2023-10-14 11:05:20.120][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:05:20.122][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:05:20.123][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:05:20.124][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2023-10-14 11:05:20.126][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2023-10-14 11:05:20.127][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2023-10-14 11:05:20.128][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:05:20.129][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:05:20.131][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:05:20.132][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2023-10-14 11:05:20.133][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2023-10-14 11:05:20.135][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2023-10-14 11:05:20.136][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2023-10-14 11:05:20.137][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2023-10-14 11:05:20.139][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2023-10-14 11:05:20.140][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:05:20.141][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:05:20.143][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:05:20.144][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2023-10-14 11:05:20.145][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2023-10-14 11:05:20.146][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:05:20.148][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:05:20.149][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:05:20.150][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2023-10-14 11:05:20.152][self$set] Set key entries.sep to "|".
biodb.DEBUG[2023-10-14 11:05:20.153][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:05:20.154][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:05:20.155][FUN] Functions in observer BiodbConfig: [21]: ".__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 11:05:20.157][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2023-10-14 11:05:20.158][self$set] Set key offline to FALSE.
biodb.DEBUG[2023-10-14 11:05:20.159][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:05:20.160][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:05:20.162][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:05:20.163][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2023-10-14 11:05:20.164][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2023-10-14 11:05:20.166][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:05:20.167][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:05:20.168][FUN] Functions in observer BiodbConfig: [21]: ".__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 11:05:20.169][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2023-10-14 11:05:20.171][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2023-10-14 11:05:20.172][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:05:20.173][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:05:20.175][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:05:20.176][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2023-10-14 11:05:20.177][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2023-10-14 11:05:20.181][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2023-10-14 11:05:20.182][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:05:20.184][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:05:20.185][FUN] Functions in observer BiodbConfig: [21]: ".__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 11:05:20.186][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2023-10-14 11:05:20.188][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2023-10-14 11:05:20.189][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2023-10-14 11:05:20.190][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:05:20.191][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:05:20.193][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:05:20.197][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2023-10-14 11:05:20.240][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-10-14 11:05:20.254][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2023-10-14 11:05:20.255][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-10-14 11:05:20.256][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-10-14 11:05:20.258][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-10-14 11:05:20.259][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-10-14 11:05:20.260][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-10-14 11:05:20.261][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-10-14 11:05:20.262][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2023-10-14 11:05:20.263][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-10-14 11:05:20.265][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-10-14 11:05:20.266][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2023-10-14 11:05:20.267][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-10-14 11:05:20.268][self$setPropertyValue]
biodb.DEBUG[2023-10-14 11:05:20.269][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-10-14 11:05:20.271][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2023-10-14 11:05:20.271][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2023-10-14 11:05:20.271][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2023-10-14 11:05:20.271][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2023-10-14 11:05:20.271][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2023-10-14 11:05:20.272][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-10-14 11:05:20.273][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-10-14 11:05:20.274][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-10-14 11:05:20.275][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-10-14 11:05:20.277][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-10-14 11:05:20.278][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-10-14 11:05:20.279][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-10-14 11:05:20.280][self$setPropertyValue]
biodb.DEBUG[2023-10-14 11:05:20.281][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-10-14 11:05:20.282][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-10-14 11:05:20.283][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-10-14 11:05:20.285][self$setPropertyValue]
biodb.DEBUG[2023-10-14 11:05:20.286][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2023-10-14 11:05:20.289][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-10-14 11:05:20.290][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2023-10-14 11:05:20.292][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-10-14 11:05:20.294][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-10-14 11:05:20.295][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-10-14 11:05:20.297][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-10-14 11:05:20.298][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-10-14 11:05:20.300][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-10-14 11:05:20.301][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2023-10-14 11:05:20.303][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-10-14 11:05:20.304][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-10-14 11:05:20.306][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2023-10-14 11:05:20.308][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-10-14 11:05:20.309][self$setPropertyValue]
biodb.DEBUG[2023-10-14 11:05:20.311][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-10-14 11:05:20.312][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2023-10-14 11:05:20.312][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2023-10-14 11:05:20.312][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2023-10-14 11:05:20.312][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2023-10-14 11:05:20.312][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2023-10-14 11:05:20.314][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-10-14 11:05:20.315][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-10-14 11:05:20.317][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-10-14 11:05:20.318][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-10-14 11:05:20.320][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-10-14 11:05:20.321][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-10-14 11:05:20.323][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-10-14 11:05:20.324][self$setPropertyValue]
biodb.DEBUG[2023-10-14 11:05:20.326][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-10-14 11:05:20.327][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-10-14 11:05:20.329][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-10-14 11:05:20.331][self$setPropertyValue]
biodb.DEBUG[2023-10-14 11:05:20.332][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2023-10-14 11:05:20.335][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2023-10-14 11:05:20.337][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2023-10-14 11:05:20.338][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-10-14 11:05:20.340][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-10-14 11:05:20.341][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-10-14 11:05:20.343][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-10-14 11:05:20.344][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-10-14 11:05:20.346][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-10-14 11:05:20.348][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2023-10-14 11:05:20.349][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-10-14 11:05:20.351][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2023-10-14 11:05:20.352][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2023-10-14 11:05:20.354][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-10-14 11:05:20.355][self$setPropertyValue]
biodb.DEBUG[2023-10-14 11:05:20.357][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-10-14 11:05:20.359][self$setPropertyValue]
biodb.DEBUG[2023-10-14 11:05:20.360][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-10-14 11:05:20.362][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-10-14 11:05:20.363][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-10-14 11:05:20.365][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-10-14 11:05:20.366][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-10-14 11:05:20.368][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-10-14 11:05:20.369][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-10-14 11:05:20.371][self$setPropertyValue]
biodb.DEBUG[2023-10-14 11:05:20.372][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-10-14 11:05:20.374][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-10-14 11:05:20.375][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-10-14 11:05:20.377][self$setPropertyValue]
biodb.DEBUG[2023-10-14 11:05:20.379][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2023-10-14 11:05:20.381][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2023-10-14 11:05:20.383][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2023-10-14 11:05:20.384][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-10-14 11:05:20.386][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-10-14 11:05:20.387][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-10-14 11:05:20.389][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-10-14 11:05:20.391][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-10-14 11:05:20.392][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-10-14 11:05:20.394][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2023-10-14 11:05:20.395][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-10-14 11:05:20.397][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2023-10-14 11:05:20.398][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2023-10-14 11:05:20.400][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-10-14 11:05:20.402][self$setPropertyValue]
biodb.DEBUG[2023-10-14 11:05:20.403][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-10-14 11:05:20.405][self$setPropertyValue]
biodb.DEBUG[2023-10-14 11:05:20.406][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-10-14 11:05:20.408][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-10-14 11:05:20.409][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-10-14 11:05:20.411][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-10-14 11:05:20.412][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-10-14 11:05:20.414][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-10-14 11:05:20.415][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-10-14 11:05:20.417][self$setPropertyValue]
biodb.DEBUG[2023-10-14 11:05:20.418][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-10-14 11:05:20.420][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-10-14 11:05:20.421][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-10-14 11:05:20.423][self$setPropertyValue]
biodb.DEBUG[2023-10-14 11:05:20.427][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-10-14 11:05:20.429][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:05:20.430][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:05:20.432][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:05:20.433][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:05:20.434][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-14 11:05:20.436][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:05:20.437][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:05:20.439][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:05:20.440][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:05:20.442][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 11:05:20.443][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:05:20.445][FUN] Functions in observer BiodbConfig: [21]: ".__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 11:05:20.446][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:05:20.447][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:05:20.449][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 11:05:20.450][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:05:20.452][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:05:20.453][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:05:20.455][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:05:20.456][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-14 11:05:20.457][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:05:20.459][FUN] Functions in observer BiodbConfig: [21]: ".__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 11:05:20.460][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:05:20.462][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:05:20.463][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-14 11:05:20.465][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:05:20.466][FUN] Functions in observer BiodbConfig: [21]: ".__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 11:05:20.467][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:05:20.469][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:05:20.470][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-14 11:05:20.472][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:05:20.473][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:05:20.475][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:05:20.476][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:05:20.477][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-14 11:05:20.479][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:05:20.480][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:05:20.482][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:05:20.483][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:05:20.485][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 11:05:20.486][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:05:20.488][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:05:20.489][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:05:20.490][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:05:20.492][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 11:05:20.493][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:05:20.495][FUN] Functions in observer BiodbConfig: [21]: ".__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 11:05:20.496][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:05:20.498][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:05:20.499][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 11:05:20.501][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:05:20.502][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:05:20.504][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:05:20.505][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:05:20.506][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-14 11:05:20.508][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:05:20.509][FUN] Functions in observer BiodbConfig: [21]: ".__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 11:05:20.511][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:05:20.512][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:05:20.514][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-14 11:05:20.515][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:05:20.516][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:05:20.518][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:05:20.519][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:05:20.521][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-14 11:05:20.522][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:05:20.524][FUN] Functions in observer BiodbConfig: [21]: ".__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 11:05:20.525][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:05:20.526][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:05:20.528][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-14 11:05:20.529][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:05:20.531][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:05:20.532][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:05:20.534][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:05:20.535][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 11:05:20.537][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:05:20.538][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:05:20.540][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:05:20.541][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:05:20.542][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-14 11:05:20.544][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:05:20.545][FUN] Functions in observer BiodbConfig: [21]: ".__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 11:05:20.547][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:05:20.548][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:05:20.550][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-14 11:05:20.551][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:05:20.552][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:05:20.554][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2023-10-14 11:05:20.559][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2023-10-14 11:05:20.561][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2023-10-14 11:05:20.563][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2023-10-14 11:05:20.564][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2023-10-14 11:05:20.566][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2023-10-14 11:05:20.567][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2023-10-14 11:05:20.569][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2023-10-14 11:05:20.570][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2023-10-14 11:05:20.572][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2023-10-14 11:05:20.573][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2023-10-14 11:05:20.575][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2023-10-14 11:05:20.576][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2023-10-14 11:05:20.578][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2023-10-14 11:05:20.580][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2023-10-14 11:05:20.582][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2023-10-14 11:05:20.583][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2023-10-14 11:05:20.585][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2023-10-14 11:05:20.591][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2023-10-14 11:05:20.593][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2023-10-14 11:05:20.595][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2023-10-14 11:05:20.596][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2023-10-14 11:05:20.598][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2023-10-14 11:05:20.599][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2023-10-14 11:05:20.601][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2023-10-14 11:05:20.602][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2023-10-14 11:05:20.604][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2023-10-14 11:05:20.605][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2023-10-14 11:05:20.607][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2023-10-14 11:05:20.609][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2023-10-14 11:05:20.610][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2023-10-14 11:05:20.612][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2023-10-14 11:05:20.613][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2023-10-14 11:05:20.615][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2023-10-14 11:05:20.616][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2023-10-14 11:05:20.618][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2023-10-14 11:05:20.619][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2023-10-14 11:05:20.621][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2023-10-14 11:05:20.622][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2023-10-14 11:05:20.624][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2023-10-14 11:05:20.626][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2023-10-14 11:05:20.627][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2023-10-14 11:05:20.629][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2023-10-14 11:05:20.630][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2023-10-14 11:05:20.632][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2023-10-14 11:05:20.634][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2023-10-14 11:05:20.635][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2023-10-14 11:05:20.637][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2023-10-14 11:05:20.639][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2023-10-14 11:05:20.640][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2023-10-14 11:05:20.642][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2023-10-14 11:05:20.643][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2023-10-14 11:05:20.645][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2023-10-14 11:05:20.646][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2023-10-14 11:05:20.648][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2023-10-14 11:05:20.649][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2023-10-14 11:05:20.651][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2023-10-14 11:05:20.653][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2023-10-14 11:05:20.654][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2023-10-14 11:05:20.656][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2023-10-14 11:05:20.657][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2023-10-14 11:05:20.659][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2023-10-14 11:05:20.660][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2023-10-14 11:05:20.662][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2023-10-14 11:05:20.663][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2023-10-14 11:05:20.665][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2023-10-14 11:05:20.667][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2023-10-14 11:05:20.668][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2023-10-14 11:05:20.670][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2023-10-14 11:05:20.671][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2023-10-14 11:05:20.673][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2023-10-14 11:05:20.674][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2023-10-14 11:05:20.676][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2023-10-14 11:05:20.677][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2023-10-14 11:05:20.679][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2023-10-14 11:05:20.680][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2023-10-14 11:05:20.682][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2023-10-14 11:05:20.684][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2023-10-14 11:05:20.685][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2023-10-14 11:05:20.687][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2023-10-14 11:05:20.688][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2023-10-14 11:05:20.690][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2023-10-14 11:05:20.691][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2023-10-14 11:05:20.730][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2023-10-14 11:05:20.733][initialize] This is biodb version 1.8.1.
biodb.DEBUG[2023-10-14 11:05:20.736][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-10-14 11:05:20.737][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:05:20.738][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-14 11:05:20.740][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:05:20.741][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:05:20.746][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:05:20.747][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-14 11:05:20.748][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-14 11:05:20.749][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:05:20.750][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-14 11:05:20.752][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:05:20.753][FUN] Functions in observer BiodbConfig: [21]: ".__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 11:05:20.754][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:05:20.755][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-14 11:05:20.756][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-14 11:05:20.758][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:05:20.759][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 11:05:20.760][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:05:20.761][FUN] Functions in observer BiodbConfig: [21]: ".__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 11:05:20.762][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:05:20.763][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-14 11:05:20.765][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-14 11:05:20.766][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:05:20.767][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 11:05:20.768][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:05:20.769][FUN] Functions in observer BiodbConfig: [21]: ".__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 11:05:20.770][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:05:20.771][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-14 11:05:20.773][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-14 11:05:20.774][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:05:20.775][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 11:05:20.776][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:05:20.777][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:05:20.778][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:05:20.780][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-14 11:05:20.782][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-14 11:05:20.783][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:05:20.784][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 11:05:20.785][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:05:20.786][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:05:20.788][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:05:20.789][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-14 11:05:20.790][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-14 11:05:20.791][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:05:20.792][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 11:05:20.793][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:05:20.795][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:05:20.796][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:05:20.797][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-14 11:05:20.798][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-14 11:05:20.799][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:05:20.801][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-14 11:05:20.802][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:05:20.803][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:05:20.804][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:05:20.806][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-14 11:05:20.807][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-14 11:05:20.808][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:05:20.809][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 11:05:20.810][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:05:20.812][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:05:20.813][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:05:20.814][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-14 11:05:20.815][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-14 11:05:20.816][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:05:20.817][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 11:05:20.818][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:05:20.819][FUN] Functions in observer BiodbConfig: [21]: ".__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 11:05:20.821][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:05:20.822][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-14 11:05:20.823][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-14 11:05:20.824][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:05:20.825][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 11:05:20.826][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:05:20.827][FUN] Functions in observer BiodbConfig: [21]: ".__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 11:05:20.829][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:05:20.830][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-14 11:05:20.831][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-14 11:05:20.832][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:05:20.833][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 11:05:20.834][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:05:20.836][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:05:20.837][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:05:20.838][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-14 11:05:20.839][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-14 11:05:20.840][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:05:20.841][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 11:05:20.842][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:05:20.844][FUN] Functions in observer BiodbConfig: [21]: ".__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 11:05:20.845][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:05:20.846][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-14 11:05:20.847][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-14 11:05:20.848][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:05:20.849][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 11:05:20.850][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:05:20.851][FUN] Functions in observer BiodbConfig: [21]: ".__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 11:05:20.853][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:05:20.854][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-14 11:05:20.855][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-14 11:05:20.856][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:05:20.857][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 11:05:20.858][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:05:20.859][FUN] Functions in observer BiodbConfig: [21]: ".__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 11:05:20.860][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:05:20.862][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-14 11:05:20.863][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-14 11:05:20.864][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:05:20.865][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 11:05:20.866][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:05:20.867][FUN] Functions in observer BiodbConfig: [21]: ".__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 11:05:20.868][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:05:20.870][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-14 11:05:20.871][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-14 11:05:20.872][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:05:20.873][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 11:05:20.874][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:05:20.875][FUN] Functions in observer BiodbConfig: [21]: ".__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 11:05:20.876][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:05:20.877][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-14 11:05:20.878][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-14 11:05:20.880][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:05:20.881][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 11:05:20.882][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:05:20.883][FUN] Functions in observer BiodbConfig: [21]: ".__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 11:05:20.886][biodb$loadDefinitions] Load definitions from file "F:/biocbuild/bbs-3.17-bioc-longtests/meat/biodbExpasy.Rcheck/biodbExpasy/definitions.yml".
biodb.DEBUG[2023-10-14 11:05:20.895][self$getDbsInfo()$define] Define connector expasy.enzyme.
biodb.DEBUG[2023-10-14 11:05:20.897][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-10-14 11:05:20.899][self$setPropertyValue] Setting property "description" to "Write here the description of this database.".
biodb.DEBUG[2023-10-14 11:05:20.901][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-10-14 11:05:20.902][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-10-14 11:05:20.903][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-10-14 11:05:20.904][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-10-14 11:05:20.911][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2023-10-14 11:05:20.912][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-10-14 11:05:20.913][self$setPropertyValue] Setting property "entry.content.type" to "txt".
biodb.DEBUG[2023-10-14 11:05:20.915][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-10-14 11:05:20.916][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-10-14 11:05:20.917][self$setPropertyValue] Setting property "name" to "Expasy ENZYME database.".
biodb.DEBUG[2023-10-14 11:05:20.918][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-10-14 11:05:20.920][self$setPropertyValue] Setting property "parsing.expr" to "^ID\s+([0-9.]+)$".
biodb.DEBUG[2023-10-14 11:05:20.920][self$setPropertyValue] Setting property "parsing.expr" to "^CA\s+(.+?)\.?$".
biodb.DEBUG[2023-10-14 11:05:20.920][self$setPropertyValue] Setting property "parsing.expr" to "^CF\s+(.+?)\.?$".
biodb.DEBUG[2023-10-14 11:05:20.920][self$setPropertyValue] Setting property "parsing.expr" to "^DE\s+(.+?)\.?$".
biodb.DEBUG[2023-10-14 11:05:20.921][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2023-10-14 11:05:20.922][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2023-10-14 11:05:20.923][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2023-10-14 11:05:20.925][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-10-14 11:05:20.926][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-10-14 11:05:20.927][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-10-14 11:05:20.928][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-10-14 11:05:20.929][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-10-14 11:05:20.930][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-10-14 11:05:20.932][self$setPropertyValue] Setting property "urls" to "https://enzyme.expasy.org/".
biodb.DEBUG[2023-10-14 11:05:20.933][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-10-14 11:05:20.934][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-10-14 11:05:20.935][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2023-10-14 11:05:20.936][self$setPropertyValue]
biodb.DEBUG[2023-10-14 11:05:20.942][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2023-10-14 11:05:20.965][super$initialize] Initialize connector expasy.enzyme.
biodb.DEBUG[2023-10-14 11:05:20.967][super$initialize] Register connector expasy.enzyme with the request scheduler
biodb.DEBUG[2023-10-14 11:05:20.971][private$bdb$getRequestScheduler()$re ...] Register connector expasy.enzyme.
biodb.DEBUG[2023-10-14 11:05:20.975][private$addConnectorRules] Create new rule for URL "enzyme.expasy.org" of connector "expasy.enzyme".
biodb.DEBUG[2023-10-14 11:05:20.979][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2023-10-14 11:05:20.981][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2023-10-14 11:05:20.982][biodb$getFactory()$createConn] Creating new connector expasy.enzyme for database class expasy.enzyme .
biodb.INFO [2023-10-14 11:05:20.996][biodb::testThat]
biodb.INFO [2023-10-14 11:05:20.998][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2023-10-14 11:05:20.999][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-10-14 11:05:21.001][biodb::testThat]
biodb.TRACE[2023-10-14 11:05:21.007][loadFileContents] Loaded 1 files from cache: [1]: "F:/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 11:05:21.010][biodb$getFactory()$createEntryFromCo ...] Creating Expasy ENZYME database. entries from 1 content(s).
biodb.DEBUG[2023-10-14 11:05:21.013][biodb$getFactory()$createEntryFromCo ...] Parsing 1 Expasy ENZYME database. entries.
biodb.DEBUG[2023-10-14 11:05:21.032][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-10-14 11:05:21.033][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-14 11:05:21.034][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-14 11:05:21.081][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:05:21.083][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 11:05:21.084][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:05:21.085][FUN] Functions in observer BiodbConfig: [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 11:05:21.096][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-14 11:05:21.097][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-14 11:05:21.098][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:05:21.100][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:05:21.123][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2023-10-14 11:05:21.139][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2023-10-14 11:05:21.140][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:05:21.142][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:05:21.144][self$getBiodb()$getEntryFields()$get] Asked field names are: cofactor.
biodb.TRACE[2023-10-14 11:05:21.146][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2023-10-14 11:05:21.147][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:05:21.149][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:05:21.151][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-10-14 11:05:21.153][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-14 11:05:21.155][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:05:21.156][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:05:21.158][self$getBiodb()$getEntryFields()$get] Asked field names are: COFACTOR.
biodb.TRACE[2023-10-14 11:05:21.160][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2023-10-14 11:05:21.162][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:05:21.163][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:05:21.165][self$getBiodb()$getEntryFields()$get] Asked field names are: cofactor.
biodb.TRACE[2023-10-14 11:05:21.167][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2023-10-14 11:05:21.169][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:05:21.170][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:05:21.172][self$getBiodb()$getEntryFields()$get] Asked field names are: cofactor.
biodb.TRACE[2023-10-14 11:05:21.174][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2023-10-14 11:05:21.175][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:05:21.177][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:05:21.178][self$getBiodb()$getEntryFields()$get] Asked field names are: cofactor.
biodb.TRACE[2023-10-14 11:05:21.180][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2023-10-14 11:05:21.182][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:05:21.183][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:05:21.185][self$getBiodb()$getEntryFields()$get] Asked field names are: COFACTOR.
biodb.TRACE[2023-10-14 11:05:21.187][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2023-10-14 11:05:21.188][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:05:21.190][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:05:21.209][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-10-14 11:05:21.210][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-14 11:05:21.212][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:05:21.213][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:05:21.214][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-10-14 11:05:21.216][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-14 11:05:21.217][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:05:21.218][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:05:21.259][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-10-14 11:05:21.261][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-14 11:05:21.262][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:05:21.263][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:05:21.265][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-10-14 11:05:21.266][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-14 11:05:21.267][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:05:21.268][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:05:21.269][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-10-14 11:05:21.271][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-14 11:05:21.272][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:05:21.273][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:05:21.275][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2023-10-14 11:05:21.276][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2023-10-14 11:05:21.277][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:05:21.278][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:05:21.280][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2023-10-14 11:05:21.281][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2023-10-14 11:05:21.282][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:05:21.283][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:05:21.284][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-14 11:05:21.286][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-14 11:05:21.287][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:05:21.288][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:05:21.289][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2023-10-14 11:05:21.291][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2023-10-14 11:05:21.292][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:05:21.293][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:05:21.294][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-14 11:05:21.296][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-14 11:05:21.297][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:05:21.298][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:05:21.299][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-14 11:05:21.301][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-14 11:05:21.302][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:05:21.303][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:05:21.304][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-14 11:05:21.306][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-14 11:05:21.307][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:05:21.308][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:05:21.310][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-14 11:05:21.311][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-14 11:05:21.312][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:05:21.313][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:05:21.314][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-14 11:05:21.316][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-14 11:05:21.317][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:05:21.318][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:05:21.319][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-14 11:05:21.321][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-14 11:05:21.322][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:05:21.323][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-10-14 11:05:21.324][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 1.1.1.1.
biodb.TRACE[2023-10-14 11:05:21.328][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2023-10-14 11:05:21.329][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2023-10-14 11:05:21.331][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:05:21.332][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:05:21.333][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2023-10-14 11:05:21.334][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2023-10-14 11:05:21.335][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:05:21.337][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:05:21.338][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2023-10-14 11:05:21.339][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2023-10-14 11:05:21.340][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:05:21.342][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:05:21.343][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2023-10-14 11:05:21.344][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2023-10-14 11:05:21.345][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:05:21.347][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:05:21.371][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-14 11:05:21.372][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-14 11:05:21.373][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:05:21.375][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:05:21.391][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2023-10-14 11:05:21.392][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2023-10-14 11:05:21.393][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:05:21.394][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:05:21.402][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-14 11:05:21.404][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-14 11:05:21.405][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:05:21.406][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:05:21.408][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-14 11:05:21.409][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-14 11:05:21.410][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:05:21.411][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:05:21.412][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-14 11:05:21.414][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-14 11:05:21.417][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:05:21.419][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:05:21.422][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-14 11:05:21.423][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-14 11:05:21.424][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:05:21.425][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:05:21.427][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-14 11:05:21.428][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-14 11:05:21.429][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:05:21.430][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:05:21.432][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-14 11:05:21.433][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-14 11:05:21.434][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:05:21.435][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:05:21.437][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2023-10-14 11:05:21.438][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2023-10-14 11:05:21.439][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:05:21.441][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:05:21.442][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2023-10-14 11:05:21.443][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2023-10-14 11:05:21.444][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:05:21.445][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:05:21.447][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2023-10-14 11:05:21.448][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2023-10-14 11:05:21.449][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:05:21.450][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:05:21.463][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-14 11:05:21.464][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-14 11:05:21.466][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:05:21.467][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:05:21.468][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-14 11:05:21.469][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-14 11:05:21.471][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:05:21.472][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:05:21.473][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-14 11:05:21.474][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-14 11:05:21.475][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:05:21.477][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:05:21.478][ef$get] Asked field names are: accession.
biodb.TRACE[2023-10-14 11:05:21.479][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-14 11:05:21.480][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:05:21.481][ef$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:05:21.483][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-14 11:05:21.484][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-14 11:05:21.485][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:05:21.486][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:05:21.498][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-10-14 11:05:21.500][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-14 11:05:21.501][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:05:21.502][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:05:21.504][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-10-14 11:05:21.505][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-14 11:05:21.506][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:05:21.507][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:05:21.509][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-10-14 11:05:21.516][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-14 11:05:21.517][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:05:21.518][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:05:21.519][ef$get] Asked field names are: name.
biodb.TRACE[2023-10-14 11:05:21.521][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-10-14 11:05:21.522][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:05:21.523][ef$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:05:21.524][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-10-14 11:05:21.526][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-14 11:05:21.527][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:05:21.528][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:05:21.540][self$getBiodb()$getEntryFields()$get] Asked field names are: cofactor.
biodb.TRACE[2023-10-14 11:05:21.541][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2023-10-14 11:05:21.542][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:05:21.544][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:05:21.545][self$getBiodb()$getEntryFields()$get] Asked field names are: cofactor.
biodb.TRACE[2023-10-14 11:05:21.546][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2023-10-14 11:05:21.547][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:05:21.549][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:05:21.550][self$getBiodb()$getEntryFields()$get] Asked field names are: cofactor.
biodb.TRACE[2023-10-14 11:05:21.551][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2023-10-14 11:05:21.552][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:05:21.553][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:05:21.555][ef$get] Asked field names are: cofactor.
biodb.TRACE[2023-10-14 11:05:21.556][ef$get] Realnames of fields are: cofactor.
biodb.TRACE[2023-10-14 11:05:21.557][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:05:21.558][ef$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:05:21.560][self$getBiodb()$getEntryFields()$get] Asked field names are: cofactor.
biodb.TRACE[2023-10-14 11:05:21.561][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2023-10-14 11:05:21.562][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:05:21.563][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:05:21.575][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2023-10-14 11:05:21.576][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2023-10-14 11:05:21.578][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:05:21.579][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:05:21.580][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2023-10-14 11:05:21.581][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2023-10-14 11:05:21.583][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:05:21.584][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:05:21.585][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2023-10-14 11:05:21.586][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2023-10-14 11:05:21.588][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:05:21.589][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:05:21.590][ef$get] Asked field names are: catalytic.activity.
biodb.TRACE[2023-10-14 11:05:21.591][ef$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2023-10-14 11:05:21.593][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:05:21.594][ef$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:05:21.595][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2023-10-14 11:05:21.596][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2023-10-14 11:05:21.598][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:05:21.599][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:05:21.614][ef$get] Asked field names are: accession.
biodb.TRACE[2023-10-14 11:05:21.616][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-14 11:05:21.618][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:05:21.619][ef$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:05:21.629][ef$get] Asked field names are: catalytic.activity.
biodb.TRACE[2023-10-14 11:05:21.631][ef$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2023-10-14 11:05:21.633][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:05:21.634][ef$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:05:21.644][ef$get] Asked field names are: cofactor.
biodb.TRACE[2023-10-14 11:05:21.646][ef$get] Realnames of fields are: cofactor.
biodb.TRACE[2023-10-14 11:05:21.647][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:05:21.649][ef$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:05:21.659][ef$get] Asked field names are: name.
biodb.TRACE[2023-10-14 11:05:21.661][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-10-14 11:05:21.662][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:05:21.664][ef$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:05:21.690][loadFileContents] Loaded 1 files from cache: [1]: "F:/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 11:05:21.731][biodb$getFactory()$createEntryFromCo ...] Creating Expasy ENZYME database. entries from 1 content(s).
biodb.DEBUG[2023-10-14 11:05:21.733][biodb$getFactory()$createEntryFromCo ...] Parsing 1 Expasy ENZYME database. entries.
biodb.DEBUG[2023-10-14 11:05:21.736][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-10-14 11:05:21.737][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-14 11:05:21.739][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-14 11:05:21.747][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:05:21.749][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 11:05:21.750][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:05:21.751][FUN] Functions in observer BiodbConfig: [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 11:05:21.753][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-14 11:05:21.755][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-14 11:05:21.756][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:05:21.757][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:05:21.759][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2023-10-14 11:05:21.760][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2023-10-14 11:05:21.761][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:05:21.763][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:05:21.764][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-10-14 11:05:21.765][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-14 11:05:21.767][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:05:21.768][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:05:21.769][self$getBiodb()$getEntryFields()$get] Asked field names are: COFACTOR.
biodb.TRACE[2023-10-14 11:05:21.770][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2023-10-14 11:05:21.772][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:05:21.773][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:05:21.774][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2023-10-14 11:05:21.802][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2023-10-14 11:05:21.804][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:05:21.805][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:05:21.806][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2023-10-14 11:05:21.808][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2023-10-14 11:05:21.809][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:05:21.810][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:05:21.811][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-14 11:05:21.813][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-14 11:05:21.814][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:05:21.815][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:05:21.816][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2023-10-14 11:05:21.818][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2023-10-14 11:05:21.819][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:05:21.820][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:05:21.821][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-14 11:05:21.822][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-14 11:05:21.824][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:05:21.825][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:05:21.826][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-14 11:05:21.827][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-14 11:05:21.829][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:05:21.830][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:05:21.831][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-14 11:05:21.832][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-14 11:05:21.833][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:05:21.834][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:05:21.836][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-14 11:05:21.837][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-14 11:05:21.838][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:05:21.840][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:05:21.841][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-14 11:05:21.842][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-14 11:05:21.843][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:05:21.844][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:05:21.846][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-14 11:05:21.847][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-14 11:05:21.848][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:05:21.849][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-10-14 11:05:21.851][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 1.1.1.54.
biodb.TRACE[2023-10-14 11:05:21.872][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2023-10-14 11:05:21.873][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2023-10-14 11:05:21.874][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:05:21.876][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:05:21.877][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2023-10-14 11:05:21.878][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2023-10-14 11:05:21.879][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:05:21.881][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:05:21.882][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2023-10-14 11:05:21.883][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2023-10-14 11:05:21.884][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:05:21.885][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:05:21.887][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2023-10-14 11:05:21.888][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2023-10-14 11:05:21.889][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:05:21.890][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:05:21.893][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-14 11:05:21.894][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-14 11:05:21.895][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:05:21.896][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:05:21.904][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2023-10-14 11:05:21.905][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2023-10-14 11:05:21.907][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:05:21.908][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:05:21.915][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-14 11:05:21.917][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-14 11:05:21.918][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:05:21.919][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:05:21.921][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-14 11:05:21.922][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-14 11:05:21.923][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:05:21.924][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:05:21.925][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-14 11:05:21.927][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-14 11:05:21.928][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:05:21.929][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:05:21.932][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-14 11:05:21.933][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-14 11:05:21.934][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:05:21.935][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:05:21.937][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-14 11:05:21.938][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-14 11:05:21.939][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:05:21.940][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:05:21.942][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-14 11:05:21.943][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-14 11:05:21.944][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:05:21.945][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:05:21.947][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2023-10-14 11:05:21.948][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2023-10-14 11:05:21.949][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:05:21.950][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:05:21.951][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2023-10-14 11:05:21.953][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2023-10-14 11:05:21.954][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:05:21.955][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:05:21.956][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2023-10-14 11:05:21.957][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2023-10-14 11:05:21.959][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:05:21.960][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:05:21.980][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-14 11:05:21.981][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-14 11:05:21.982][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:05:21.984][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:05:21.985][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-14 11:05:21.986][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-14 11:05:21.987][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:05:21.988][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:05:21.990][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-14 11:05:21.991][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-14 11:05:21.992][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:05:21.994][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:05:21.995][ef$get] Asked field names are: accession.
biodb.TRACE[2023-10-14 11:05:21.997][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-14 11:05:21.998][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:05:21.999][ef$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:05:22.000][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-14 11:05:22.002][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-14 11:05:22.003][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:05:22.004][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:05:22.016][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-10-14 11:05:22.017][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-14 11:05:22.018][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:05:22.020][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:05:22.021][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-10-14 11:05:22.022][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-14 11:05:22.023][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:05:22.024][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:05:22.026][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-10-14 11:05:22.027][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-14 11:05:22.028][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:05:22.029][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:05:22.031][ef$get] Asked field names are: name.
biodb.TRACE[2023-10-14 11:05:22.032][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-10-14 11:05:22.033][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:05:22.034][ef$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:05:22.035][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-10-14 11:05:22.037][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-14 11:05:22.038][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:05:22.039][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:05:22.056][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2023-10-14 11:05:22.058][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2023-10-14 11:05:22.059][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:05:22.060][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:05:22.061][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2023-10-14 11:05:22.063][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2023-10-14 11:05:22.064][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:05:22.065][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:05:22.066][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2023-10-14 11:05:22.067][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2023-10-14 11:05:22.069][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:05:22.070][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:05:22.071][ef$get] Asked field names are: catalytic.activity.
biodb.TRACE[2023-10-14 11:05:22.072][ef$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2023-10-14 11:05:22.073][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:05:22.074][ef$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:05:22.076][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2023-10-14 11:05:22.077][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2023-10-14 11:05:22.078][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:05:22.079][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:05:22.091][ef$get] Asked field names are: accession.
biodb.TRACE[2023-10-14 11:05:22.092][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-14 11:05:22.094][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:05:22.095][ef$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:05:22.102][ef$get] Asked field names are: catalytic.activity.
biodb.TRACE[2023-10-14 11:05:22.103][ef$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2023-10-14 11:05:22.105][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:05:22.106][ef$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:05:22.113][ef$get] Asked field names are: name.
biodb.TRACE[2023-10-14 11:05:22.115][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-10-14 11:05:22.116][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:05:22.117][ef$get] fields variable is a list.
biodb.INFO [2023-10-14 11:05:22.130][biodb::testThat]
biodb.INFO [2023-10-14 11:05:22.131][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2023-10-14 11:05:22.133][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-10-14 11:05:22.134][biodb::testThat]
biodb.DEBUG[2023-10-14 11:05:22.137][private$loadEntries] Creating entries from ids [2]: "1.1.1.1, 1.1.1.54".
biodb.DEBUG[2023-10-14 11:05:22.143][conn$getEntryContent] Get Expasy ENZYME database. entry content(s) for 2 id(s)...
biodb.TRACE[2023-10-14 11:05:22.161][cch$loadFileContent] Trying to load 2 files from cache: [2]: "1.1.1.1, 1.1.1.54".
biodb.INFO [2023-10-14 11:05:22.163][self$getFolderPath] Create cache folder "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280" for "expasy.enzyme-b59b84d962b6741050ba8f70ff4db280".
biodb.TRACE[2023-10-14 11:05:22.165][cch$loadFileContent] file.exist = [2]: "FALSE, FALSE".
biodb.TRACE[2023-10-14 11:05:22.167][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2023-10-14 11:05:22.168][conn$getEntryContent] 0 Expasy ENZYME database. entry content(s) loaded from cache.
biodb.DEBUG[2023-10-14 11:05:22.169][conn$getEntryContent] 2 entry content(s) need to be fetched from Expasy ENZYME database. database "https://enzyme.expasy.org/".
biodb.DEBUG[2023-10-14 11:05:22.171][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2023-10-14 11:05:22.172][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2023-10-14 11:05:22.177][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-10-14 11:05:22.178][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-14 11:05:22.179][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-14 11:05:22.187][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:05:22.188][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-14 11:05:22.189][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:05:22.190][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:05:22.192][scheduler$sendRequest] Getting content of get URL request "https://enzyme.expasy.org/EC/1.1.1.1.txt".
biodb.DEBUG[2023-10-14 11:05:22.210][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-10-14 11:05:22.211][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-10-14 11:05:22.213][private$doSendRequestOnce] Sent URL is "https://enzyme.expasy.org/EC/1.1.1.1.txt".
biodb.TRACE[2023-10-14 11:05:22.891][doesRCurlRequestUrlExist] According to RCurl, URL https://enzyme.expasy.org/EC/1.1.1.1.txt does not exist.
biodb.TRACE[2023-10-14 11:05:22.893][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2023-10-14 11:05:22.894][getUrlRequestResult] URL "https://enzyme.expasy.org/EC/1.1.1.1.txt" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2023-10-14 11:05:22.896][getBaseUrlRequestResult] Using base::url() for sending request (https://enzyme.expasy.org/EC/1.1.1.1.txt).
biodb.DEBUG[2023-10-14 11:05:23.534][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2023-10-14 11:05:23.538][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280/a52675cfd2f0c2b41556caa64d9341e3.content"
biodb.TRACE[2023-10-14 11:05:23.553][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280/a52675cfd2f0c2b41556caa64d9341e3.request"
biodb.DEBUG[2023-10-14 11:05:23.556][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-10-14 11:05:23.558][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-14 11:05:23.559][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-14 11:05:23.567][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:05:23.568][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 11:05:23.569][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:05:23.570][FUN] Functions in observer BiodbConfig: [21]: ".__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 11:05:23.588][scheduler$sendRequest] Getting content of get URL request "https://enzyme.expasy.org/EC/1.1.1.54.txt".
biodb.DEBUG[2023-10-14 11:05:23.606][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-10-14 11:05:23.608][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-10-14 11:05:23.626][private$doSendRequestOnce] Sent URL is "https://enzyme.expasy.org/EC/1.1.1.54.txt".
biodb.TRACE[2023-10-14 11:05:23.953][doesRCurlRequestUrlExist] According to RCurl, URL https://enzyme.expasy.org/EC/1.1.1.54.txt does not exist.
biodb.TRACE[2023-10-14 11:05:23.954][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2023-10-14 11:05:23.956][getUrlRequestResult] URL "https://enzyme.expasy.org/EC/1.1.1.54.txt" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2023-10-14 11:05:23.957][getBaseUrlRequestResult] Using base::url() for sending request (https://enzyme.expasy.org/EC/1.1.1.54.txt).
biodb.DEBUG[2023-10-14 11:05:24.676][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2023-10-14 11:05:24.679][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280/a9b93566a091cbe35a06e4b3871f95c9.content"
biodb.TRACE[2023-10-14 11:05:24.684][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280/a9b93566a091cbe35a06e4b3871f95c9.request"
biodb.TRACE[2023-10-14 11:05:24.687][private$doSaveContentToFile] Saving to cache [2]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280/1.1.1.1.txt, C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280/1.1.1.54.txt"
biodb.DEBUG[2023-10-14 11:05:24.691][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2023-10-14 11:05:24.692][self$createEntryFromContent] Creating Expasy ENZYME database. entries from 2 content(s).
biodb.DEBUG[2023-10-14 11:05:24.694][self$createEntryFromContent] Parsing 2 Expasy ENZYME database. entries.
biodb.DEBUG[2023-10-14 11:05:24.696][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-10-14 11:05:24.697][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-14 11:05:24.699][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-14 11:05:24.706][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:05:24.707][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-14 11:05:24.709][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:05:24.710][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-10-14 11:05:24.712][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-14 11:05:24.714][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-14 11:05:24.715][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:05:24.716][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:05:24.718][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2023-10-14 11:05:24.719][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2023-10-14 11:05:24.720][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:05:24.722][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:05:24.723][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-10-14 11:05:24.730][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-14 11:05:24.732][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:05:24.733][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:05:24.734][self$getBiodb()$getEntryFields()$get] Asked field names are: COFACTOR.
biodb.TRACE[2023-10-14 11:05:24.736][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2023-10-14 11:05:24.737][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:05:24.738][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:05:24.739][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-10-14 11:05:24.741][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-14 11:05:24.742][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:05:24.743][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:05:24.744][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-10-14 11:05:24.746][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-14 11:05:24.747][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:05:24.748][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:05:24.749][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-10-14 11:05:24.751][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-14 11:05:24.752][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:05:24.753][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:05:24.754][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-10-14 11:05:24.755][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-14 11:05:24.757][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:05:24.758][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:05:24.759][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-10-14 11:05:24.760][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-14 11:05:24.762][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:05:24.763][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:05:24.764][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2023-10-14 11:05:24.766][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2023-10-14 11:05:24.767][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:05:24.768][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:05:24.769][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2023-10-14 11:05:24.771][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2023-10-14 11:05:24.772][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:05:24.773][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:05:24.774][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-14 11:05:24.776][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-14 11:05:24.777][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:05:24.779][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:05:24.781][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2023-10-14 11:05:24.782][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2023-10-14 11:05:24.784][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:05:24.785][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:05:24.787][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-14 11:05:24.789][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-14 11:05:24.790][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:05:24.792][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:05:24.794][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-14 11:05:24.795][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-14 11:05:24.797][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:05:24.799][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:05:24.800][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-14 11:05:24.802][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-14 11:05:24.803][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:05:24.805][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-10-14 11:05:24.807][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-10-14 11:05:24.808][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-14 11:05:24.810][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-14 11:05:24.820][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:05:24.821][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-14 11:05:24.823][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:05:24.824][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-10-14 11:05:24.827][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-14 11:05:24.829][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-14 11:05:24.831][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:05:24.832][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:05:24.834][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2023-10-14 11:05:24.835][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2023-10-14 11:05:24.836][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:05:24.837][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:05:24.839][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-10-14 11:05:24.840][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-14 11:05:24.842][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:05:24.843][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:05:24.844][self$getBiodb()$getEntryFields()$get] Asked field names are: COFACTOR.
biodb.TRACE[2023-10-14 11:05:24.845][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2023-10-14 11:05:24.847][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:05:24.848][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:05:24.849][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2023-10-14 11:05:24.851][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2023-10-14 11:05:24.852][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:05:24.853][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:05:24.854][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2023-10-14 11:05:24.855][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2023-10-14 11:05:24.857][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:05:24.858][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:05:24.859][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-14 11:05:24.860][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-14 11:05:24.862][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:05:24.863][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:05:24.864][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2023-10-14 11:05:24.865][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2023-10-14 11:05:24.866][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:05:24.868][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:05:24.869][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-14 11:05:24.870][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-14 11:05:24.871][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:05:24.873][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:05:24.874][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-14 11:05:24.875][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-14 11:05:24.876][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:05:24.877][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:05:24.879][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-14 11:05:24.880][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-14 11:05:24.881][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:05:24.882][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:05:24.884][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-14 11:05:24.885][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-14 11:05:24.886][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:05:24.887][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:05:24.889][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-14 11:05:24.890][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-14 11:05:24.891][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:05:24.892][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:05:24.894][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-14 11:05:24.895][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-14 11:05:24.896][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:05:24.897][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:05:24.899][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-14 11:05:24.900][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-14 11:05:24.901][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:05:24.902][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:05:24.904][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-14 11:05:24.905][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-14 11:05:24.906][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:05:24.907][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:05:24.908][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-14 11:05:24.910][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-14 11:05:24.911][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:05:24.912][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-10-14 11:05:24.914][self$createEntryFromContent] Accession numbers: 1.1.1.1, 1.1.1.54.
biodb.TRACE[2023-10-14 11:05:24.915][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2023-10-14 11:05:24.916][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2023-10-14 11:05:24.917][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:05:24.919][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:05:24.920][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2023-10-14 11:05:24.921][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2023-10-14 11:05:24.922][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:05:24.924][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:05:24.925][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2023-10-14 11:05:24.926][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2023-10-14 11:05:24.927][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:05:24.929][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:05:24.936][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2023-10-14 11:05:24.938][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2023-10-14 11:05:24.939][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:05:24.940][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:05:24.942][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2023-10-14 11:05:24.943][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2023-10-14 11:05:24.944][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:05:24.945][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:05:24.947][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2023-10-14 11:05:24.948][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2023-10-14 11:05:24.949][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:05:24.950][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2023-10-14 11:05:24.968][biodb::testThat]
biodb.INFO [2023-10-14 11:05:24.970][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2023-10-14 11:05:24.971][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-10-14 11:05:24.972][biodb::testThat]
biodb.TRACE[2023-10-14 11:05:24.976][ef$get] Asked field names are: name.
biodb.TRACE[2023-10-14 11:05:24.977][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-10-14 11:05:24.978][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:05:24.979][ef$get] fields variable is a list.
biodb.DEBUG[2023-10-14 11:05:24.981][function(conn, opt)] Testing searchForEntries() with entry "1.1.1.1" and field "name".
biodb.TRACE[2023-10-14 11:05:25.012][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-10-14 11:05:25.014][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-14 11:05:25.015][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:05:25.016][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:05:25.018][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-10-14 11:05:25.019][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-14 11:05:25.020][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:05:25.021][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:05:25.023][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-10-14 11:05:25.024][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-14 11:05:25.025][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:05:25.026][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-10-14 11:05:25.030][function(conn, opt)] With value "alcohol dehydrogenase".
biodb.DEBUG[2023-10-14 11:05:25.033][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://enzyme.expasy.org/enzyme-byname.html?alcohol dehydrogenase".
biodb.DEBUG[2023-10-14 11:05:25.036][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-10-14 11:05:25.037][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-10-14 11:05:25.039][private$doSendRequestOnce] Sent URL is "https://enzyme.expasy.org/enzyme-byname.html?alcohol%20dehydrogenase".
biodb.TRACE[2023-10-14 11:05:25.377][doesRCurlRequestUrlExist] According to RCurl, URL https://enzyme.expasy.org/enzyme-byname.html?alcohol%20dehydrogenase does not exist.
biodb.TRACE[2023-10-14 11:05:25.378][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2023-10-14 11:05:25.379][getUrlRequestResult] URL "https://enzyme.expasy.org/enzyme-byname.html?alcohol%20dehydrogenase" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2023-10-14 11:05:25.381][getBaseUrlRequestResult] Using base::url() for sending request (https://enzyme.expasy.org/enzyme-byname.html?alcohol%20dehydrogenase).
biodb.DEBUG[2023-10-14 11:05:26.215][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2023-10-14 11:05:26.218][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280/f603fa2a57aec59588edc37541c6f6d5.content"
biodb.TRACE[2023-10-14 11:05:26.223][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280/f603fa2a57aec59588edc37541c6f6d5.request"
biodb.DEBUG[2023-10-14 11:05:26.230][function(conn, opt)] With found IDs [1]: "1.1.1.1".
biodb.INFO [2023-10-14 11:05:26.256][biodb::testThat]
biodb.INFO [2023-10-14 11:05:26.257][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2023-10-14 11:05:26.258][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-10-14 11:05:26.260][biodb::testThat]
biodb.TRACE[2023-10-14 11:05:26.289][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-10-14 11:05:26.290][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-14 11:05:26.291][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:05:26.293][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:05:26.294][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-10-14 11:05:26.295][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-14 11:05:26.296][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:05:26.297][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:05:26.299][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-10-14 11:05:26.300][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-14 11:05:26.301][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:05:26.302][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-10-14 11:05:26.342][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://enzyme.expasy.org/enzyme-byname.html?alcohol dehydrogenase".
biodb.DEBUG[2023-10-14 11:05:26.346][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-10-14 11:05:26.364][cch$loadFileContent] Trying to load 1 files from cache: [1]: "f603fa2a57aec59588edc37541c6f6d5".
biodb.TRACE[2023-10-14 11:05:26.366][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-10-14 11:05:26.372][loadFileContents] Loaded 1 files from cache: [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280/f603fa2a57aec59588edc37541c6f6d5.content".
biodb.INFO [2023-10-14 11:05:26.399][biodb::testThat]
biodb.INFO [2023-10-14 11:05:26.400][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2023-10-14 11:05:26.401][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-10-14 11:05:26.403][biodb::testThat]
biodb.TRACE[2023-10-14 11:05:26.416][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2023-10-14 11:05:26.418][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2023-10-14 11:05:26.419][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:05:26.420][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:05:26.421][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2023-10-14 11:05:26.423][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2023-10-14 11:05:26.424][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:05:26.425][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:05:26.426][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2023-10-14 11:05:26.428][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2023-10-14 11:05:26.429][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:05:26.430][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:05:26.431][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2023-10-14 11:05:26.433][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2023-10-14 11:05:26.434][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:05:26.435][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:05:26.463][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2023-10-14 11:05:26.465][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2023-10-14 11:05:26.466][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:05:26.467][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:05:26.469][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2023-10-14 11:05:26.470][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2023-10-14 11:05:26.471][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:05:26.472][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:05:26.474][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2023-10-14 11:05:26.475][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2023-10-14 11:05:26.476][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:05:26.477][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:05:26.479][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2023-10-14 11:05:26.480][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2023-10-14 11:05:26.481][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:05:26.482][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2023-10-14 11:05:26.492][biodb::testThat]
biodb.INFO [2023-10-14 11:05:26.494][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2023-10-14 11:05:26.495][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-10-14 11:05:26.496][biodb::testThat]
biodb.INFO [2023-10-14 11:05:26.509][biodb::testThat]
biodb.INFO [2023-10-14 11:05:26.511][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2023-10-14 11:05:26.512][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-10-14 11:05:26.513][biodb::testThat]
biodb.INFO [2023-10-14 11:05:26.525][biodb::testThat]
biodb.INFO [2023-10-14 11:05:26.527][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2023-10-14 11:05:26.528][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-10-14 11:05:26.529][biodb::testThat]
biodb.DEBUG[2023-10-14 11:05:26.548][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 11:05:26.862][getUrlContent] Use base::url() 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 11:05:27.704][biodb::testThat]
biodb.INFO [2023-10-14 11:05:27.705][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2023-10-14 11:05:27.706][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-10-14 11:05:27.708][biodb::testThat]
biodb.DEBUG[2023-10-14 11:05:28.028][getUrlContent] Use base::url() for downloading content of URL https://enzyme.expasy.org/images/1.1.1.1/image.png.
biodb.TRACE[2023-10-14 11:05:29.925][ef$get] Asked field names are: name.
biodb.TRACE[2023-10-14 11:05:29.927][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-10-14 11:05:29.928][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:05:29.929][ef$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:05:29.931][ef$get] Asked field names are: name.
biodb.TRACE[2023-10-14 11:05:29.932][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-10-14 11:05:29.933][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:05:29.935][ef$get] fields variable is a list.
biodb.INFO [2023-10-14 11:05:29.936][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2023-10-14 11:05:29.937][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector expasy.enzyme from the request scheduler
biodb.INFO [2023-10-14 11:05:29.939][self$deleteConn] Connector "expasy.enzyme" deleted.
biodb.DEBUG[2023-10-14 11:05:29.940][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2023-10-14 11:05:29.941][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-14 11:05:29.942][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-14 11:05:29.943][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:05:29.944][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-14 11:05:29.945][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:05:29.946][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2023-10-14 11:05:29.957][biodb::testContext]
biodb.INFO [2023-10-14 11:05:29.958][biodb::testContext] ********************************************************************************
biodb.INFO [2023-10-14 11:05:29.959][biodb::testContext] Test context - Example long tests
biodb.INFO [2023-10-14 11:05:29.961][biodb::testContext] ********************************************************************************
biodb.INFO [2023-10-14 11:05:29.962][biodb::testContext]
biodb.INFO [2023-10-14 11:05:29.964][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.8.1.
biodb.DEBUG[2023-10-14 11:05:29.967][self$loadDefinitions] Load definitions from file "F:/biocbuild/bbs-3.17-bioc/R/library/biodb/definitions.yml".
biodb.DEBUG[2023-10-14 11:05:29.972][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-10-14 11:05:29.973][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2023-10-14 11:05:29.975][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2023-10-14 11:05:29.976][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:05:29.977][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:05:29.978][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:05:29.979][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2023-10-14 11:05:29.980][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2023-10-14 11:05:29.982][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:05:29.983][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:05:29.984][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:05:29.985][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2023-10-14 11:05:29.986][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2023-10-14 11:05:29.987][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:05:29.988][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:05:29.990][FUN] Functions in observer BiodbConfig: [21]: ".__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 11:05:29.991][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2023-10-14 11:05:29.992][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2023-10-14 11:05:29.993][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2023-10-14 11:05:29.994][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:05:29.995][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:05:29.997][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:05:29.998][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2023-10-14 11:05:29.999][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2023-10-14 11:05:30.000][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2023-10-14 11:05:30.001][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:05:30.002][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:05:30.004][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 11:05:30.006][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2023-10-14 11:05:30.007][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2023-10-14 11:05:30.009][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:05:30.010][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:05:30.012][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:05:30.013][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2023-10-14 11:05:30.015][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2023-10-14 11:05:30.016][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2023-10-14 11:05:30.018][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:05:30.019][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:05:30.020][FUN] Functions in observer BiodbConfig: [21]: ".__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 11:05:30.021][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2023-10-14 11:05:30.022][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2023-10-14 11:05:30.023][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:05:30.025][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:05:30.026][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:05:30.027][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2023-10-14 11:05:30.028][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2023-10-14 11:05:30.029][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2023-10-14 11:05:30.030][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:05:30.032][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:05:30.033][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:05:30.034][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2023-10-14 11:05:30.035][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2023-10-14 11:05:30.036][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2023-10-14 11:05:30.038][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2023-10-14 11:05:30.039][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2023-10-14 11:05:30.040][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2023-10-14 11:05:30.041][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:05:30.042][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:05:30.044][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:05:30.047][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2023-10-14 11:05:30.049][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2023-10-14 11:05:30.050][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:05:30.051][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:05:30.052][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:05:30.053][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2023-10-14 11:05:30.055][self$set] Set key entries.sep to "|".
biodb.DEBUG[2023-10-14 11:05:30.056][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:05:30.057][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:05:30.058][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:05:30.059][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2023-10-14 11:05:30.061][self$set] Set key offline to FALSE.
biodb.DEBUG[2023-10-14 11:05:30.062][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:05:30.063][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:05:30.064][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:05:30.065][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2023-10-14 11:05:30.066][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2023-10-14 11:05:30.067][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:05:30.069][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:05:30.070][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:05:30.071][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2023-10-14 11:05:30.072][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2023-10-14 11:05:30.073][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:05:30.074][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:05:30.075][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:05:30.077][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2023-10-14 11:05:30.078][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2023-10-14 11:05:30.082][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2023-10-14 11:05:30.083][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:05:30.084][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:05:30.085][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:05:30.086][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2023-10-14 11:05:30.093][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2023-10-14 11:05:30.095][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2023-10-14 11:05:30.096][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:05:30.097][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:05:30.098][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:05:30.099][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2023-10-14 11:05:30.101][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-10-14 11:05:30.102][self$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 11:05:30.104][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-10-14 11:05:30.105][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-10-14 11:05:30.106][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-10-14 11:05:30.107][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-10-14 11:05:30.108][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-10-14 11:05:30.110][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-10-14 11:05:30.111][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2023-10-14 11:05:30.112][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-10-14 11:05:30.113][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-10-14 11:05:30.115][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2023-10-14 11:05:30.116][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-10-14 11:05:30.118][self$setPropertyValue]
biodb.DEBUG[2023-10-14 11:05:30.119][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-10-14 11:05:30.120][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2023-10-14 11:05:30.120][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2023-10-14 11:05:30.120][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2023-10-14 11:05:30.120][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2023-10-14 11:05:30.120][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2023-10-14 11:05:30.121][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-10-14 11:05:30.122][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-10-14 11:05:30.123][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-10-14 11:05:30.125][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-10-14 11:05:30.126][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-10-14 11:05:30.127][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-10-14 11:05:30.128][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-10-14 11:05:30.129][self$setPropertyValue]
biodb.DEBUG[2023-10-14 11:05:30.131][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-10-14 11:05:30.132][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-10-14 11:05:30.133][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-10-14 11:05:30.134][self$setPropertyValue]
biodb.DEBUG[2023-10-14 11:05:30.135][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2023-10-14 11:05:30.138][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-10-14 11:05:30.139][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2023-10-14 11:05:30.140][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-10-14 11:05:30.141][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-10-14 11:05:30.142][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-10-14 11:05:30.144][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-10-14 11:05:30.145][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-10-14 11:05:30.146][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-10-14 11:05:30.147][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2023-10-14 11:05:30.149][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-10-14 11:05:30.150][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-10-14 11:05:30.151][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2023-10-14 11:05:30.152][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-10-14 11:05:30.153][self$setPropertyValue]
biodb.DEBUG[2023-10-14 11:05:30.155][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-10-14 11:05:30.156][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2023-10-14 11:05:30.156][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2023-10-14 11:05:30.156][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2023-10-14 11:05:30.156][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2023-10-14 11:05:30.156][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2023-10-14 11:05:30.157][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-10-14 11:05:30.158][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-10-14 11:05:30.159][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-10-14 11:05:30.161][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-10-14 11:05:30.162][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-10-14 11:05:30.163][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-10-14 11:05:30.164][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-10-14 11:05:30.165][self$setPropertyValue]
biodb.DEBUG[2023-10-14 11:05:30.166][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-10-14 11:05:30.168][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-10-14 11:05:30.169][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-10-14 11:05:30.170][self$setPropertyValue]
biodb.DEBUG[2023-10-14 11:05:30.171][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2023-10-14 11:05:30.173][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2023-10-14 11:05:30.175][self$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 11:05:30.176][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-10-14 11:05:30.177][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-10-14 11:05:30.178][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-10-14 11:05:30.179][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-10-14 11:05:30.181][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-10-14 11:05:30.182][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-10-14 11:05:30.183][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2023-10-14 11:05:30.184][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-10-14 11:05:30.185][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2023-10-14 11:05:30.187][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2023-10-14 11:05:30.188][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-10-14 11:05:30.189][self$setPropertyValue]
biodb.DEBUG[2023-10-14 11:05:30.190][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-10-14 11:05:30.191][self$setPropertyValue]
biodb.DEBUG[2023-10-14 11:05:30.193][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-10-14 11:05:30.194][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-10-14 11:05:30.195][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-10-14 11:05:30.196][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-10-14 11:05:30.197][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-10-14 11:05:30.198][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-10-14 11:05:30.200][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-10-14 11:05:30.201][self$setPropertyValue]
biodb.DEBUG[2023-10-14 11:05:30.202][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-10-14 11:05:30.203][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-10-14 11:05:30.204][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-10-14 11:05:30.205][self$setPropertyValue]
biodb.DEBUG[2023-10-14 11:05:30.207][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2023-10-14 11:05:30.209][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2023-10-14 11:05:30.210][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2023-10-14 11:05:30.211][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-10-14 11:05:30.212][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-10-14 11:05:30.214][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-10-14 11:05:30.215][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-10-14 11:05:30.216][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-10-14 11:05:30.217][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-10-14 11:05:30.218][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2023-10-14 11:05:30.220][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-10-14 11:05:30.221][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2023-10-14 11:05:30.222][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2023-10-14 11:05:30.223][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-10-14 11:05:30.224][self$setPropertyValue]
biodb.DEBUG[2023-10-14 11:05:30.226][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-10-14 11:05:30.227][self$setPropertyValue]
biodb.DEBUG[2023-10-14 11:05:30.228][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-10-14 11:05:30.229][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-10-14 11:05:30.230][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-10-14 11:05:30.231][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-10-14 11:05:30.233][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-10-14 11:05:30.234][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-10-14 11:05:30.235][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-10-14 11:05:30.236][self$setPropertyValue]
biodb.DEBUG[2023-10-14 11:05:30.237][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-10-14 11:05:30.238][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-10-14 11:05:30.239][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-10-14 11:05:30.241][self$setPropertyValue]
biodb.DEBUG[2023-10-14 11:05:30.242][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-10-14 11:05:30.243][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:05:30.244][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:05:30.245][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:05:30.247][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:05:30.248][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-14 11:05:30.249][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:05:30.250][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:05:30.251][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:05:30.252][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:05:30.253][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-14 11:05:30.254][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:05:30.255][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:05:30.256][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:05:30.258][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:05:30.259][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-14 11:05:30.260][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:05:30.261][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:05:30.262][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:05:30.263][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:05:30.264][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-14 11:05:30.265][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:05:30.266][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:05:30.267][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:05:30.269][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:05:30.270][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-14 11:05:30.271][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:05:30.272][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:05:30.273][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:05:30.274][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:05:30.275][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-14 11:05:30.276][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:05:30.277][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 11:05:30.279][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:05:30.280][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:05:30.281][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-14 11:05:30.282][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:05:30.283][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:05:30.284][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:05:30.285][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:05:30.286][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 11:05:30.287][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:05:30.288][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 11:05:30.289][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:05:30.290][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:05:30.292][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 11:05:30.293][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:05:30.294][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 11:05:30.300][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:05:30.301][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:05:30.302][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-14 11:05:30.303][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:05:30.304][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:05:30.305][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:05:30.306][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:05:30.307][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 11:05:30.308][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:05:30.309][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 11:05:30.310][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:05:30.311][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:05:30.313][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-14 11:05:30.314][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:05:30.315][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:05:30.316][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:05:30.317][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:05:30.318][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-14 11:05:30.319][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:05:30.320][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:05:30.321][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:05:30.322][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:05:30.323][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 11:05:30.325][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:05:30.326][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:05:30.327][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:05:30.328][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:05:30.329][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 11:05:30.330][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:05:30.331][FUN] Functions in observer BiodbConfig: [21]: ".__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 11:05:30.332][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:05:30.333][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:05:30.334][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 11:05:30.335][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:05:30.336][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:05:30.338][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:05:30.339][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:05:30.340][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-14 11:05:30.341][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:05:30.342][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:05:30.343][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2023-10-14 11:05:30.345][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2023-10-14 11:05:30.346][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2023-10-14 11:05:30.348][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2023-10-14 11:05:30.350][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2023-10-14 11:05:30.351][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2023-10-14 11:05:30.353][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2023-10-14 11:05:30.354][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2023-10-14 11:05:30.356][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2023-10-14 11:05:30.358][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2023-10-14 11:05:30.359][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2023-10-14 11:05:30.361][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2023-10-14 11:05:30.362][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2023-10-14 11:05:30.364][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2023-10-14 11:05:30.365][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2023-10-14 11:05:30.367][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2023-10-14 11:05:30.369][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2023-10-14 11:05:30.370][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2023-10-14 11:05:30.372][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2023-10-14 11:05:30.373][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2023-10-14 11:05:30.375][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2023-10-14 11:05:30.376][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2023-10-14 11:05:30.378][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2023-10-14 11:05:30.380][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2023-10-14 11:05:30.381][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2023-10-14 11:05:30.383][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2023-10-14 11:05:30.384][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2023-10-14 11:05:30.386][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2023-10-14 11:05:30.387][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2023-10-14 11:05:30.389][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2023-10-14 11:05:30.391][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2023-10-14 11:05:30.392][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2023-10-14 11:05:30.394][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2023-10-14 11:05:30.395][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2023-10-14 11:05:30.397][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2023-10-14 11:05:30.398][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2023-10-14 11:05:30.400][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2023-10-14 11:05:30.401][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2023-10-14 11:05:30.403][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2023-10-14 11:05:30.405][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2023-10-14 11:05:30.406][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2023-10-14 11:05:30.408][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2023-10-14 11:05:30.409][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2023-10-14 11:05:30.411][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2023-10-14 11:05:30.412][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2023-10-14 11:05:30.414][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2023-10-14 11:05:30.416][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2023-10-14 11:05:30.417][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2023-10-14 11:05:30.419][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2023-10-14 11:05:30.420][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2023-10-14 11:05:30.422][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2023-10-14 11:05:30.423][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2023-10-14 11:05:30.425][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2023-10-14 11:05:30.427][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2023-10-14 11:05:30.428][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2023-10-14 11:05:30.430][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2023-10-14 11:05:30.431][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2023-10-14 11:05:30.433][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2023-10-14 11:05:30.434][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2023-10-14 11:05:30.436][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2023-10-14 11:05:30.438][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2023-10-14 11:05:30.439][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2023-10-14 11:05:30.441][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2023-10-14 11:05:30.442][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2023-10-14 11:05:30.444][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2023-10-14 11:05:30.445][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2023-10-14 11:05:30.447][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2023-10-14 11:05:30.448][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2023-10-14 11:05:30.450][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2023-10-14 11:05:30.452][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2023-10-14 11:05:30.453][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2023-10-14 11:05:30.455][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2023-10-14 11:05:30.456][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2023-10-14 11:05:30.458][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2023-10-14 11:05:30.460][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2023-10-14 11:05:30.461][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2023-10-14 11:05:30.463][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2023-10-14 11:05:30.464][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2023-10-14 11:05:30.466][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2023-10-14 11:05:30.467][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2023-10-14 11:05:30.469][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2023-10-14 11:05:30.471][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2023-10-14 11:05:30.472][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2023-10-14 11:05:30.474][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2023-10-14 11:05:30.476][initialize] This is biodb version 1.8.1.
biodb.DEBUG[2023-10-14 11:05:30.477][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-10-14 11:05:30.478][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:05:30.479][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 11:05:30.481][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:05:30.482][FUN] Functions in observer BiodbConfig: [21]: ".__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 11:05:30.483][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:05:30.484][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-14 11:05:30.485][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-14 11:05:30.486][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:05:30.493][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-14 11:05:30.494][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:05:30.495][FUN] Functions in observer BiodbConfig: [21]: ".__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 11:05:30.496][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:05:30.497][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-14 11:05:30.498][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-14 11:05:30.499][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:05:30.501][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-14 11:05:30.502][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:05:30.503][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:05:30.504][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:05:30.505][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-14 11:05:30.506][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-14 11:05:30.507][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:05:30.508][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-14 11:05:30.509][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:05:30.510][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:05:30.511][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:05:30.512][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-14 11:05:30.514][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-14 11:05:30.515][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:05:30.516][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 11:05:30.517][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:05:30.518][FUN] Functions in observer BiodbConfig: [21]: ".__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 11:05:30.519][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:05:30.520][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-14 11:05:30.521][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-14 11:05:30.522][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:05:30.523][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 11:05:30.524][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:05:30.525][FUN] Functions in observer BiodbConfig: [21]: ".__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 11:05:30.527][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:05:30.528][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-14 11:05:30.529][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-14 11:05:30.530][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:05:30.531][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 11:05:30.532][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:05:30.533][FUN] Functions in observer BiodbConfig: [21]: ".__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 11:05:30.534][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:05:30.535][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-14 11:05:30.536][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-14 11:05:30.538][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:05:30.539][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-14 11:05:30.540][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:05:30.542][FUN] Functions in observer BiodbConfig: [21]: ".__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 11:05:30.543][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:05:30.545][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-14 11:05:30.546][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-14 11:05:30.548][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:05:30.549][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 11:05:30.550][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:05:30.552][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:05:30.553][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:05:30.555][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-14 11:05:30.556][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-14 11:05:30.557][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:05:30.558][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 11:05:30.559][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:05:30.560][FUN] Functions in observer BiodbConfig: [21]: ".__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 11:05:30.561][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:05:30.562][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-14 11:05:30.563][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-14 11:05:30.564][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:05:30.566][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 11:05:30.567][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:05:30.568][FUN] Functions in observer BiodbConfig: [21]: ".__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 11:05:30.569][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:05:30.570][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-14 11:05:30.571][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-14 11:05:30.572][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:05:30.573][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-14 11:05:30.574][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:05:30.575][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:05:30.577][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:05:30.578][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-14 11:05:30.579][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-14 11:05:30.580][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:05:30.581][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 11:05:30.582][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:05:30.583][FUN] Functions in observer BiodbConfig: [21]: ".__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 11:05:30.584][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:05:30.585][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-14 11:05:30.586][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-14 11:05:30.587][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:05:30.589][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-14 11:05:30.590][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:05:30.591][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:05:30.592][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:05:30.593][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-14 11:05:30.594][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-14 11:05:30.595][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:05:30.596][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 11:05:30.597][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:05:30.598][FUN] Functions in observer BiodbConfig: [21]: ".__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 11:05:30.599][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:05:30.601][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-14 11:05:30.602][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-14 11:05:30.603][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:05:30.604][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 11:05:30.605][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:05:30.606][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 11:05:30.607][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:05:30.608][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-14 11:05:30.609][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-14 11:05:30.610][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:05:30.611][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 11:05:30.612][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:05:30.614][FUN] Functions in observer BiodbConfig: [21]: ".__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 11:05:30.615][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:05:30.616][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-14 11:05:30.617][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-14 11:05:30.618][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:05:30.619][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 11:05:30.620][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:05:30.621][FUN] Functions in observer BiodbConfig: [21]: ".__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 11:05:30.624][biodb$loadDefinitions] Load definitions from file "F:/biocbuild/bbs-3.17-bioc-longtests/meat/biodbExpasy.Rcheck/biodbExpasy/definitions.yml".
biodb.DEBUG[2023-10-14 11:05:30.626][self$getDbsInfo()$define] Define connector expasy.enzyme.
biodb.DEBUG[2023-10-14 11:05:30.628][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-10-14 11:05:30.629][self$setPropertyValue] Setting property "description" to "Write here the description of this database.".
biodb.DEBUG[2023-10-14 11:05:30.631][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-10-14 11:05:30.632][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-10-14 11:05:30.633][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-10-14 11:05:30.634][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-10-14 11:05:30.635][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2023-10-14 11:05:30.637][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-10-14 11:05:30.638][self$setPropertyValue] Setting property "entry.content.type" to "txt".
biodb.DEBUG[2023-10-14 11:05:30.639][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-10-14 11:05:30.640][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-10-14 11:05:30.641][self$setPropertyValue] Setting property "name" to "Expasy ENZYME database.".
biodb.DEBUG[2023-10-14 11:05:30.643][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-10-14 11:05:30.644][self$setPropertyValue] Setting property "parsing.expr" to "^ID\s+([0-9.]+)$".
biodb.DEBUG[2023-10-14 11:05:30.644][self$setPropertyValue] Setting property "parsing.expr" to "^CA\s+(.+?)\.?$".
biodb.DEBUG[2023-10-14 11:05:30.644][self$setPropertyValue] Setting property "parsing.expr" to "^CF\s+(.+?)\.?$".
biodb.DEBUG[2023-10-14 11:05:30.644][self$setPropertyValue] Setting property "parsing.expr" to "^DE\s+(.+?)\.?$".
biodb.DEBUG[2023-10-14 11:05:30.645][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2023-10-14 11:05:30.646][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2023-10-14 11:05:30.647][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2023-10-14 11:05:30.649][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-10-14 11:05:30.650][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-10-14 11:05:30.651][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-10-14 11:05:30.652][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-10-14 11:05:30.653][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-10-14 11:05:30.654][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-10-14 11:05:30.655][self$setPropertyValue] Setting property "urls" to "https://enzyme.expasy.org/".
biodb.DEBUG[2023-10-14 11:05:30.657][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-10-14 11:05:30.658][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-10-14 11:05:30.659][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2023-10-14 11:05:30.660][self$setPropertyValue]
biodb.DEBUG[2023-10-14 11:05:30.662][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2023-10-14 11:05:30.665][super$initialize] Initialize connector expasy.enzyme.
biodb.DEBUG[2023-10-14 11:05:30.666][super$initialize] Register connector expasy.enzyme with the request scheduler
biodb.DEBUG[2023-10-14 11:05:30.668][private$bdb$getRequestScheduler()$re ...] Register connector expasy.enzyme.
biodb.DEBUG[2023-10-14 11:05:30.670][private$addConnectorRules] Create new rule for URL "enzyme.expasy.org" of connector "expasy.enzyme".
biodb.DEBUG[2023-10-14 11:05:30.671][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2023-10-14 11:05:30.672][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2023-10-14 11:05:30.674][biodb$getFactory()$createConn] Creating new connector expasy.enzyme for database class expasy.enzyme .
biodb.INFO [2023-10-14 11:05:30.675][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2023-10-14 11:05:30.676][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector expasy.enzyme from the request scheduler
biodb.INFO [2023-10-14 11:05:30.677][self$deleteConn] Connector "expasy.enzyme" deleted.
biodb.DEBUG[2023-10-14 11:05:30.678][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2023-10-14 11:05:30.680][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-14 11:05:30.681][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-14 11:05:30.682][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:05:30.683][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 11:05:30.684][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:05:30.685][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 86 ]
> 
> proc.time()
   user  system elapsed 
   5.39    0.60   12.84

'R CMD check' output

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --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 'F:/biocbuild/bbs-3.17-bioc-longtests/meat/biodbExpasy.Rcheck'
* using R version 4.3.1 (2023-06-16 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* R was compiled by
    gcc.exe (GCC) 12.2.0
    GNU Fortran (GCC) 12.2.0
* running under: Windows Server 2022 x64 (build 20348)
* 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 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
  'F:/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)