Back to Long Tests report for BioC 3.18

This page was generated on 2024-04-13 23:55:01 -0400 (Sat, 13 Apr 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.3.3 (2024-02-29) -- "Angel Food Cake" 4675
palomino4Windows Server 2022 Datacenterx644.3.3 (2024-02-29 ucrt) -- "Angel Food Cake" 4413
merida1macOS 12.7.1 Montereyx86_644.3.3 (2024-02-29) -- "Angel Food Cake" 4436
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 7/30HostnameOS / ArchCHECK
biodbExpasy 1.6.0  (landing page)
Pierrick Roger
Snapshot Date: 2024-04-13 09:55:01 -0400 (Sat, 13 Apr 2024)
git_url: https://git.bioconductor.org/packages/biodbExpasy
git_branch: RELEASE_3_18
git_last_commit: abe7f92
git_last_commit_date: 2023-10-24 11:40:32 -0400 (Tue, 24 Oct 2023)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  OK  
palomino4Windows Server 2022 Datacenter / x64  OK  
merida1macOS 12.7.1 Monterey / x86_64  OK  

CHECK results for biodbExpasy on nebbiolo2


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

raw results

Summary

Package: biodbExpasy
Version: 1.6.0
Command: /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD check --test-dir=longtests --no-stop-on-test-error --no-codoc --no-examples --no-manual --ignore-vignettes --check-subdirs=no biodbExpasy_1.6.0.tar.gz
StartedAt: 2024-04-13 16:04:43 -0400 (Sat, 13 Apr 2024)
EndedAt: 2024-04-13 16:05:29 -0400 (Sat, 13 Apr 2024)
EllapsedTime: 46.4 seconds
RetCode: 0
Status:   OK  
CheckDir: biodbExpasy.Rcheck
Warnings: 0

Tests output

biodbExpasy.Rcheck/tests/testthat.Rout


R version 4.3.3 (2024-02-29) -- "Angel Food Cake"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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 [2024-04-13 16:05:18.945][biodb::testContext]
biodb.INFO [2024-04-13 16:05:18.948][biodb::testContext] ********************************************************************************
biodb.INFO [2024-04-13 16:05:18.949][biodb::testContext] Test context - Generic long tests
biodb.INFO [2024-04-13 16:05:18.950][biodb::testContext] ********************************************************************************
biodb.INFO [2024-04-13 16:05:18.950][biodb::testContext]
biodb.INFO [2024-04-13 16:05:18.958][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.10.0.
biodb.DEBUG[2024-04-13 16:05:18.959][self$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.18-bioc/R/site-library/biodb/definitions.yml".
biodb.DEBUG[2024-04-13 16:05:18.967][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-04-13 16:05:18.968][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-04-13 16:05:18.969][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-04-13 16:05:18.970][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:05:18.971][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:05:18.972][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:05:18.973][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-04-13 16:05:18.993][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-04-13 16:05:18.994][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:05:18.995][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:05:18.996][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:05:18.997][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-04-13 16:05:18.998][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-04-13 16:05:18.999][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:05:19.000][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:05:19.000][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:05:19.001][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-04-13 16:05:19.002][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-04-13 16:05:19.004][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-04-13 16:05:19.004][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:05:19.005][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:05:19.006][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:05:19.007][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-04-13 16:05:19.008][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-04-13 16:05:19.009][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-04-13 16:05:19.010][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:05:19.011][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:05:19.012][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:05:19.013][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-04-13 16:05:19.014][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-04-13 16:05:19.015][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:05:19.016][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:05:19.017][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:05:19.018][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-04-13 16:05:19.019][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-04-13 16:05:19.020][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-04-13 16:05:19.021][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:05:19.022][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:05:19.023][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:05:19.024][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-04-13 16:05:19.025][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-04-13 16:05:19.026][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:05:19.027][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:05:19.027][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:05:19.028][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-04-13 16:05:19.029][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-04-13 16:05:19.031][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-04-13 16:05:19.031][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:05:19.032][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:05:19.033][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:05:19.034][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-04-13 16:05:19.035][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-04-13 16:05:19.036][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-04-13 16:05:19.037][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-04-13 16:05:19.038][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-04-13 16:05:19.039][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-04-13 16:05:19.040][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:05:19.041][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:05:19.042][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:05:19.043][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-04-13 16:05:19.044][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-04-13 16:05:19.045][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:05:19.046][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:05:19.047][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:05:19.048][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-04-13 16:05:19.049][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-04-13 16:05:19.050][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:05:19.051][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:05:19.052][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:05:19.053][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-04-13 16:05:19.054][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-04-13 16:05:19.055][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:05:19.056][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:05:19.057][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:05:19.058][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-04-13 16:05:19.059][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-04-13 16:05:19.060][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:05:19.060][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:05:19.061][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:05:19.062][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-04-13 16:05:19.063][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-04-13 16:05:19.064][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:05:19.065][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:05:19.066][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:05:19.067][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-04-13 16:05:19.068][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-04-13 16:05:19.072][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-04-13 16:05:19.073][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:05:19.074][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:05:19.075][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:05:19.076][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-04-13 16:05:19.077][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-04-13 16:05:19.078][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-04-13 16:05:19.079][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:05:19.080][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:05:19.081][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:05:19.085][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-04-13 16:05:19.121][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-04-13 16:05:19.143][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2024-04-13 16:05:19.144][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-04-13 16:05:19.145][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-04-13 16:05:19.146][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-04-13 16:05:19.147][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-04-13 16:05:19.148][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-04-13 16:05:19.149][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-04-13 16:05:19.150][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-04-13 16:05:19.151][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-04-13 16:05:19.151][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-04-13 16:05:19.152][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-04-13 16:05:19.153][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-04-13 16:05:19.154][self$setPropertyValue]
biodb.DEBUG[2024-04-13 16:05:19.155][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-04-13 16:05:19.156][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-04-13 16:05:19.156][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-04-13 16:05:19.156][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-04-13 16:05:19.156][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-04-13 16:05:19.156][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-04-13 16:05:19.157][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-04-13 16:05:19.158][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-04-13 16:05:19.158][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-04-13 16:05:19.159][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-04-13 16:05:19.160][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-04-13 16:05:19.161][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-04-13 16:05:19.162][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-04-13 16:05:19.163][self$setPropertyValue]
biodb.DEBUG[2024-04-13 16:05:19.164][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-04-13 16:05:19.164][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-04-13 16:05:19.165][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-04-13 16:05:19.166][self$setPropertyValue]
biodb.DEBUG[2024-04-13 16:05:19.167][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-04-13 16:05:19.169][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-04-13 16:05:19.170][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-04-13 16:05:19.171][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-04-13 16:05:19.171][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-04-13 16:05:19.172][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-04-13 16:05:19.173][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-04-13 16:05:19.174][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-04-13 16:05:19.175][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-04-13 16:05:19.176][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-04-13 16:05:19.177][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-04-13 16:05:19.178][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-04-13 16:05:19.179][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-04-13 16:05:19.180][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-04-13 16:05:19.180][self$setPropertyValue]
biodb.DEBUG[2024-04-13 16:05:19.181][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-04-13 16:05:19.182][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-04-13 16:05:19.182][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-04-13 16:05:19.182][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-04-13 16:05:19.182][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-04-13 16:05:19.182][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-04-13 16:05:19.183][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-04-13 16:05:19.184][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-04-13 16:05:19.185][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-04-13 16:05:19.186][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-04-13 16:05:19.187][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-04-13 16:05:19.187][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-04-13 16:05:19.188][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-04-13 16:05:19.189][self$setPropertyValue]
biodb.DEBUG[2024-04-13 16:05:19.190][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-04-13 16:05:19.191][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-04-13 16:05:19.192][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-04-13 16:05:19.193][self$setPropertyValue]
biodb.DEBUG[2024-04-13 16:05:19.194][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-04-13 16:05:19.195][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-04-13 16:05:19.196][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2024-04-13 16:05:19.197][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-04-13 16:05:19.198][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-04-13 16:05:19.199][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-04-13 16:05:19.200][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-04-13 16:05:19.201][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-04-13 16:05:19.201][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-04-13 16:05:19.202][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-04-13 16:05:19.203][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-04-13 16:05:19.204][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-04-13 16:05:19.205][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-04-13 16:05:19.206][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-04-13 16:05:19.207][self$setPropertyValue]
biodb.DEBUG[2024-04-13 16:05:19.208][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-04-13 16:05:19.209][self$setPropertyValue]
biodb.DEBUG[2024-04-13 16:05:19.210][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-04-13 16:05:19.210][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-04-13 16:05:19.211][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-04-13 16:05:19.212][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-04-13 16:05:19.213][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-04-13 16:05:19.214][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-04-13 16:05:19.215][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-04-13 16:05:19.215][self$setPropertyValue]
biodb.DEBUG[2024-04-13 16:05:19.216][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-04-13 16:05:19.217][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-04-13 16:05:19.218][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-04-13 16:05:19.219][self$setPropertyValue]
biodb.DEBUG[2024-04-13 16:05:19.220][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-04-13 16:05:19.222][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-04-13 16:05:19.222][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-04-13 16:05:19.223][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-04-13 16:05:19.224][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-04-13 16:05:19.225][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-04-13 16:05:19.226][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-04-13 16:05:19.227][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-04-13 16:05:19.228][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-04-13 16:05:19.229][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-04-13 16:05:19.230][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-04-13 16:05:19.231][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-04-13 16:05:19.231][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-04-13 16:05:19.232][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-04-13 16:05:19.233][self$setPropertyValue]
biodb.DEBUG[2024-04-13 16:05:19.234][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-04-13 16:05:19.235][self$setPropertyValue]
biodb.DEBUG[2024-04-13 16:05:19.236][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-04-13 16:05:19.237][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-04-13 16:05:19.238][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-04-13 16:05:19.238][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-04-13 16:05:19.239][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-04-13 16:05:19.240][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-04-13 16:05:19.241][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-04-13 16:05:19.242][self$setPropertyValue]
biodb.DEBUG[2024-04-13 16:05:19.243][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-04-13 16:05:19.244][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-04-13 16:05:19.244][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-04-13 16:05:19.245][self$setPropertyValue]
biodb.DEBUG[2024-04-13 16:05:19.249][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-04-13 16:05:19.250][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:05:19.251][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:05:19.252][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:05:19.252][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-13 16:05:19.253][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-13 16:05:19.254][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:05:19.255][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:05:19.256][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:05:19.256][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-13 16:05:19.257][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-13 16:05:19.258][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:05:19.259][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:05:19.260][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:05:19.260][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-13 16:05:19.261][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-13 16:05:19.262][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:05:19.263][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:05:19.264][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:05:19.264][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-13 16:05:19.265][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-13 16:05:19.266][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:05:19.267][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:05:19.268][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:05:19.268][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-13 16:05:19.269][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-13 16:05:19.270][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:05:19.271][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:05:19.272][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:05:19.272][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-13 16:05:19.273][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-13 16:05:19.274][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:05:19.275][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:05:19.276][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:05:19.276][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-13 16:05:19.277][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-13 16:05:19.278][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:05:19.279][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:05:19.280][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:05:19.280][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-13 16:05:19.281][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-13 16:05:19.282][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:05:19.283][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:05:19.284][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:05:19.284][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-13 16:05:19.285][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-13 16:05:19.286][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:05:19.287][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:05:19.288][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:05:19.288][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-13 16:05:19.289][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-13 16:05:19.290][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:05:19.291][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:05:19.292][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:05:19.292][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-13 16:05:19.293][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-13 16:05:19.294][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:05:19.295][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:05:19.296][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:05:19.296][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-13 16:05:19.297][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-13 16:05:19.298][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:05:19.299][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:05:19.300][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:05:19.300][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-13 16:05:19.301][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-13 16:05:19.302][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:05:19.303][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:05:19.304][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:05:19.305][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-13 16:05:19.305][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-13 16:05:19.306][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:05:19.307][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:05:19.308][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:05:19.309][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-13 16:05:19.309][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-13 16:05:19.310][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:05:19.311][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:05:19.312][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:05:19.313][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-13 16:05:19.313][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-13 16:05:19.318][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:05:19.320][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:05:19.321][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:05:19.322][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-13 16:05:19.322][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-13 16:05:19.323][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:05:19.324][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:05:19.325][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-04-13 16:05:19.331][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-04-13 16:05:19.333][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-04-13 16:05:19.334][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-04-13 16:05:19.336][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-04-13 16:05:19.337][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-04-13 16:05:19.338][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-04-13 16:05:19.340][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-04-13 16:05:19.341][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-04-13 16:05:19.343][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-04-13 16:05:19.344][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-04-13 16:05:19.345][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-04-13 16:05:19.347][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-04-13 16:05:19.348][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-04-13 16:05:19.350][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-04-13 16:05:19.351][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-04-13 16:05:19.352][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-04-13 16:05:19.354][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-04-13 16:05:19.355][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-04-13 16:05:19.356][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-04-13 16:05:19.358][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-04-13 16:05:19.359][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-04-13 16:05:19.361][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-04-13 16:05:19.362][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-04-13 16:05:19.363][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-04-13 16:05:19.365][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-04-13 16:05:19.366][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-04-13 16:05:19.367][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-04-13 16:05:19.369][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-04-13 16:05:19.370][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-04-13 16:05:19.372][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-04-13 16:05:19.373][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-04-13 16:05:19.374][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-04-13 16:05:19.376][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-04-13 16:05:19.377][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-04-13 16:05:19.378][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-04-13 16:05:19.393][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-04-13 16:05:19.394][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-04-13 16:05:19.396][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-04-13 16:05:19.397][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-04-13 16:05:19.398][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-04-13 16:05:19.400][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-04-13 16:05:19.401][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-04-13 16:05:19.402][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-04-13 16:05:19.404][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-04-13 16:05:19.405][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-04-13 16:05:19.407][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-04-13 16:05:19.408][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-04-13 16:05:19.409][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-04-13 16:05:19.411][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-04-13 16:05:19.412][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-04-13 16:05:19.413][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-04-13 16:05:19.415][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-04-13 16:05:19.416][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-04-13 16:05:19.417][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-04-13 16:05:19.419][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-04-13 16:05:19.420][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-04-13 16:05:19.421][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-04-13 16:05:19.423][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-04-13 16:05:19.424][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-04-13 16:05:19.426][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-04-13 16:05:19.427][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-04-13 16:05:19.428][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-04-13 16:05:19.430][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-04-13 16:05:19.431][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-04-13 16:05:19.433][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-04-13 16:05:19.434][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-04-13 16:05:19.435][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-04-13 16:05:19.437][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-04-13 16:05:19.438][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-04-13 16:05:19.439][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-04-13 16:05:19.441][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-04-13 16:05:19.442][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-04-13 16:05:19.444][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-04-13 16:05:19.445][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-04-13 16:05:19.446][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-04-13 16:05:19.448][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-04-13 16:05:19.449][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-04-13 16:05:19.450][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-04-13 16:05:19.452][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-04-13 16:05:19.453][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-04-13 16:05:19.455][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-04-13 16:05:19.456][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-04-13 16:05:19.462][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-04-13 16:05:19.463][initialize] This is biodb version 1.10.0.
biodb.DEBUG[2024-04-13 16:05:19.467][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-04-13 16:05:19.468][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-04-13 16:05:19.469][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-13 16:05:19.470][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:05:19.470][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:05:19.475][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:05:19.476][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-13 16:05:19.477][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-13 16:05:19.478][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-13 16:05:19.478][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-13 16:05:19.479][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:05:19.480][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:05:19.481][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:05:19.482][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-13 16:05:19.483][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-13 16:05:19.484][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-13 16:05:19.485][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-13 16:05:19.485][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:05:19.486][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:05:19.487][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:05:19.488][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-13 16:05:19.489][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-13 16:05:19.490][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-13 16:05:19.491][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-13 16:05:19.492][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:05:19.492][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:05:19.493][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:05:19.494][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-13 16:05:19.495][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-13 16:05:19.496][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-13 16:05:19.497][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-13 16:05:19.498][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:05:19.499][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:05:19.499][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:05:19.500][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-13 16:05:19.501][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-13 16:05:19.502][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-13 16:05:19.503][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-13 16:05:19.504][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:05:19.505][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:05:19.506][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:05:19.506][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-13 16:05:19.507][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-13 16:05:19.508][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-13 16:05:19.509][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-13 16:05:19.510][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:05:19.511][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:05:19.512][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:05:19.512][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-13 16:05:19.513][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-13 16:05:19.514][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-13 16:05:19.515][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-13 16:05:19.516][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:05:19.517][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:05:19.518][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:05:19.519][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-13 16:05:19.519][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-13 16:05:19.520][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-13 16:05:19.521][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-13 16:05:19.522][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:05:19.523][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:05:19.524][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:05:19.525][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-13 16:05:19.525][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-13 16:05:19.526][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-13 16:05:19.527][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-13 16:05:19.528][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:05:19.529][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:05:19.530][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:05:19.531][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-13 16:05:19.532][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-13 16:05:19.532][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-13 16:05:19.533][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-13 16:05:19.534][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:05:19.535][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:05:19.536][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:05:19.537][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-13 16:05:19.538][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-13 16:05:19.538][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-13 16:05:19.539][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-13 16:05:19.540][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:05:19.541][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:05:19.542][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:05:19.543][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-13 16:05:19.544][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-13 16:05:19.544][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-13 16:05:19.545][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-13 16:05:19.546][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:05:19.547][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:05:19.548][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:05:19.549][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-13 16:05:19.550][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-13 16:05:19.551][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-13 16:05:19.551][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-13 16:05:19.552][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:05:19.553][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:05:19.554][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:05:19.555][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-13 16:05:19.556][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-13 16:05:19.557][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-13 16:05:19.557][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-13 16:05:19.558][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:05:19.559][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:05:19.560][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:05:19.561][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-13 16:05:19.562][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-13 16:05:19.563][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-13 16:05:19.563][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-13 16:05:19.564][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:05:19.565][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:05:19.566][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:05:19.567][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-13 16:05:19.568][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-13 16:05:19.569][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-13 16:05:19.569][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-13 16:05:19.570][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:05:19.571][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:05:19.572][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:05:19.573][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-13 16:05:19.574][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-13 16:05:19.575][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-13 16:05:19.576][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-13 16:05:19.576][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:05:19.577][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:05:19.579][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.18-bioc-longtests/meat/biodbExpasy.Rcheck/biodbExpasy/definitions.yml".
biodb.DEBUG[2024-04-13 16:05:19.587][self$getDbsInfo()$define] Define connector expasy.enzyme.
biodb.DEBUG[2024-04-13 16:05:19.589][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-04-13 16:05:19.590][self$setPropertyValue] Setting property "description" to "Write here the description of this database.".
biodb.DEBUG[2024-04-13 16:05:19.591][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-04-13 16:05:19.592][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-04-13 16:05:19.593][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-04-13 16:05:19.594][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-04-13 16:05:19.594][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-04-13 16:05:19.595][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-04-13 16:05:19.596][self$setPropertyValue] Setting property "entry.content.type" to "txt".
biodb.DEBUG[2024-04-13 16:05:19.597][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-04-13 16:05:19.598][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-04-13 16:05:19.599][self$setPropertyValue] Setting property "name" to "Expasy ENZYME database.".
biodb.DEBUG[2024-04-13 16:05:19.600][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-04-13 16:05:19.601][self$setPropertyValue] Setting property "parsing.expr" to "^ID\s+([0-9.]+)$".
biodb.DEBUG[2024-04-13 16:05:19.601][self$setPropertyValue] Setting property "parsing.expr" to "^CA\s+(.+?)\.?$".
biodb.DEBUG[2024-04-13 16:05:19.601][self$setPropertyValue] Setting property "parsing.expr" to "^CF\s+(.+?)\.?$".
biodb.DEBUG[2024-04-13 16:05:19.601][self$setPropertyValue] Setting property "parsing.expr" to "^DE\s+(.+?)\.?$".
biodb.DEBUG[2024-04-13 16:05:19.602][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-04-13 16:05:19.603][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-04-13 16:05:19.603][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2024-04-13 16:05:19.604][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-04-13 16:05:19.605][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-04-13 16:05:19.606][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-04-13 16:05:19.607][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-04-13 16:05:19.608][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-04-13 16:05:19.609][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-04-13 16:05:19.609][self$setPropertyValue] Setting property "urls" to "https://enzyme.expasy.org/".
biodb.DEBUG[2024-04-13 16:05:19.610][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-04-13 16:05:19.611][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-04-13 16:05:19.612][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-04-13 16:05:19.613][self$setPropertyValue]
biodb.DEBUG[2024-04-13 16:05:19.618][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-04-13 16:05:19.645][super$initialize] Initialize connector expasy.enzyme.
biodb.DEBUG[2024-04-13 16:05:19.646][super$initialize] Register connector expasy.enzyme with the request scheduler
biodb.DEBUG[2024-04-13 16:05:19.650][private$bdb$getRequestScheduler()$re ...] Register connector expasy.enzyme.
biodb.DEBUG[2024-04-13 16:05:19.654][private$addConnectorRules] Create new rule for URL "enzyme.expasy.org" of connector "expasy.enzyme".
biodb.DEBUG[2024-04-13 16:05:19.658][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-04-13 16:05:19.659][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-04-13 16:05:19.660][biodb$getFactory()$createConn] Creating new connector expasy.enzyme for database class expasy.enzyme .
biodb.INFO [2024-04-13 16:05:19.669][biodb::testThat]
biodb.INFO [2024-04-13 16:05:19.670][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2024-04-13 16:05:19.671][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-04-13 16:05:19.671][biodb::testThat]
biodb.TRACE[2024-04-13 16:05:19.674][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/bbs-3.18-bioc-longtests/meat/biodbExpasy.Rcheck/biodbExpasy/testref/entry-expasy.enzyme-1.1.1.1-content.txt".
biodb.DEBUG[2024-04-13 16:05:19.676][biodb$getFactory()$createEntryFromCo ...] Creating Expasy ENZYME database. entries from 1 content(s).
biodb.DEBUG[2024-04-13 16:05:19.680][biodb$getFactory()$createEntryFromCo ...] Parsing 1 Expasy ENZYME database. entries.
biodb.DEBUG[2024-04-13 16:05:19.688][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-13 16:05:19.689][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-13 16:05:19.690][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-13 16:05:19.701][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-13 16:05:19.702][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-13 16:05:19.703][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:05:19.704][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-04-13 16:05:19.715][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-13 16:05:19.716][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-13 16:05:19.716][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:19.717][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:19.741][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-04-13 16:05:19.752][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-04-13 16:05:19.753][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:19.754][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:19.755][self$getBiodb()$getEntryFields()$get] Asked field names are: cofactor.
biodb.TRACE[2024-04-13 16:05:19.756][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-04-13 16:05:19.757][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:19.758][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:19.759][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-04-13 16:05:19.760][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-13 16:05:19.761][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:19.762][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:19.763][self$getBiodb()$getEntryFields()$get] Asked field names are: COFACTOR.
biodb.TRACE[2024-04-13 16:05:19.764][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-04-13 16:05:19.764][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:19.765][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:19.766][self$getBiodb()$getEntryFields()$get] Asked field names are: cofactor.
biodb.TRACE[2024-04-13 16:05:19.767][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-04-13 16:05:19.768][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:19.769][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:19.770][self$getBiodb()$getEntryFields()$get] Asked field names are: cofactor.
biodb.TRACE[2024-04-13 16:05:19.771][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-04-13 16:05:19.772][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:19.773][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:19.774][self$getBiodb()$getEntryFields()$get] Asked field names are: cofactor.
biodb.TRACE[2024-04-13 16:05:19.774][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-04-13 16:05:19.775][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:19.776][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:19.777][self$getBiodb()$getEntryFields()$get] Asked field names are: COFACTOR.
biodb.TRACE[2024-04-13 16:05:19.778][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-04-13 16:05:19.779][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:19.780][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:19.796][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-04-13 16:05:19.797][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-13 16:05:19.798][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:19.799][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:19.799][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-04-13 16:05:19.800][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-13 16:05:19.801][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:19.802][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:19.832][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-04-13 16:05:19.833][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-13 16:05:19.834][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:19.835][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:19.836][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-04-13 16:05:19.837][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-13 16:05:19.838][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:19.839][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:19.840][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-04-13 16:05:19.841][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-13 16:05:19.841][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:19.842][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:19.843][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-04-13 16:05:19.844][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-04-13 16:05:19.845][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:19.846][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:19.847][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-04-13 16:05:19.848][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-04-13 16:05:19.849][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:19.850][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:19.851][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-13 16:05:19.852][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-13 16:05:19.853][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:19.853][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:19.854][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-04-13 16:05:19.855][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-04-13 16:05:19.856][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:19.857][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:19.858][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-13 16:05:19.867][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-13 16:05:19.867][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:19.868][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:19.869][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-13 16:05:19.870][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-13 16:05:19.871][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:19.872][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:19.873][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-13 16:05:19.874][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-13 16:05:19.875][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:19.875][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:19.876][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-13 16:05:19.877][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-13 16:05:19.878][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:19.879][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:19.880][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-13 16:05:19.881][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-13 16:05:19.882][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:19.883][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:19.884][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-13 16:05:19.884][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-13 16:05:19.885][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:19.886][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-04-13 16:05:19.887][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 1.1.1.1.
biodb.TRACE[2024-04-13 16:05:19.889][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-04-13 16:05:19.890][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-04-13 16:05:19.891][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:19.892][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:19.893][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-04-13 16:05:19.894][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-04-13 16:05:19.895][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:19.896][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:19.897][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-04-13 16:05:19.898][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-04-13 16:05:19.898][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:19.899][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:19.900][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-04-13 16:05:19.901][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-04-13 16:05:19.902][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:19.903][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:19.917][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-13 16:05:19.918][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-13 16:05:19.919][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:19.920][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:19.932][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-04-13 16:05:19.933][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-04-13 16:05:19.933][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:19.934][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:19.938][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-13 16:05:19.939][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-13 16:05:19.940][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:19.941][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:19.942][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-13 16:05:19.943][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-13 16:05:19.944][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:19.945][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:19.946][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-13 16:05:19.947][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-13 16:05:19.947][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:19.948][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:19.951][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-13 16:05:19.952][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-13 16:05:19.953][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:19.953][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:19.954][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-13 16:05:19.955][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-13 16:05:19.956][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:19.957][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:19.958][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-13 16:05:19.959][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-13 16:05:19.960][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:19.961][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:19.962][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-04-13 16:05:19.963][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-04-13 16:05:19.963][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:19.964][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:19.965][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-04-13 16:05:19.966][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-04-13 16:05:19.967][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:19.968][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:19.969][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-04-13 16:05:19.970][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-04-13 16:05:19.971][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:19.972][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:19.978][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-13 16:05:19.979][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-13 16:05:19.980][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:19.981][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:19.982][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-13 16:05:19.983][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-13 16:05:19.984][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:19.985][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:19.985][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-13 16:05:19.986][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-13 16:05:19.987][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:19.988][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:19.989][ef$get] Asked field names are: accession.
biodb.TRACE[2024-04-13 16:05:19.990][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-13 16:05:19.991][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:19.992][ef$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:19.993][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-13 16:05:19.994][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-13 16:05:19.994][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:19.995][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:20.003][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-04-13 16:05:20.004][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-13 16:05:20.005][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:20.006][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:20.007][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-04-13 16:05:20.008][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-13 16:05:20.009][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:20.009][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:20.010][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-04-13 16:05:20.011][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-13 16:05:20.012][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:20.013][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:20.014][ef$get] Asked field names are: name.
biodb.TRACE[2024-04-13 16:05:20.015][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-04-13 16:05:20.016][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:20.017][ef$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:20.017][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-04-13 16:05:20.018][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-13 16:05:20.019][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:20.020][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:20.028][self$getBiodb()$getEntryFields()$get] Asked field names are: cofactor.
biodb.TRACE[2024-04-13 16:05:20.029][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-04-13 16:05:20.030][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:20.030][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:20.031][self$getBiodb()$getEntryFields()$get] Asked field names are: cofactor.
biodb.TRACE[2024-04-13 16:05:20.032][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-04-13 16:05:20.033][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:20.034][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:20.035][self$getBiodb()$getEntryFields()$get] Asked field names are: cofactor.
biodb.TRACE[2024-04-13 16:05:20.036][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-04-13 16:05:20.037][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:20.038][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:20.039][ef$get] Asked field names are: cofactor.
biodb.TRACE[2024-04-13 16:05:20.040][ef$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-04-13 16:05:20.040][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:20.041][ef$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:20.042][self$getBiodb()$getEntryFields()$get] Asked field names are: cofactor.
biodb.TRACE[2024-04-13 16:05:20.043][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-04-13 16:05:20.044][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:20.045][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:20.052][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-04-13 16:05:20.053][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-04-13 16:05:20.054][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:20.055][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:20.056][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-04-13 16:05:20.057][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-04-13 16:05:20.058][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:20.059][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:20.059][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-04-13 16:05:20.060][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-04-13 16:05:20.061][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:20.062][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:20.063][ef$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-04-13 16:05:20.064][ef$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-04-13 16:05:20.065][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:20.066][ef$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:20.067][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-04-13 16:05:20.068][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-04-13 16:05:20.073][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:20.074][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:20.081][ef$get] Asked field names are: accession.
biodb.TRACE[2024-04-13 16:05:20.082][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-13 16:05:20.083][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:20.084][ef$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:20.087][ef$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-04-13 16:05:20.088][ef$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-04-13 16:05:20.089][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:20.090][ef$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:20.094][ef$get] Asked field names are: cofactor.
biodb.TRACE[2024-04-13 16:05:20.095][ef$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-04-13 16:05:20.096][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:20.096][ef$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:20.100][ef$get] Asked field names are: name.
biodb.TRACE[2024-04-13 16:05:20.101][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-04-13 16:05:20.102][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:20.103][ef$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:20.118][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/bbs-3.18-bioc-longtests/meat/biodbExpasy.Rcheck/biodbExpasy/testref/entry-expasy.enzyme-1.1.1.54-content.txt".
biodb.DEBUG[2024-04-13 16:05:20.149][biodb$getFactory()$createEntryFromCo ...] Creating Expasy ENZYME database. entries from 1 content(s).
biodb.DEBUG[2024-04-13 16:05:20.150][biodb$getFactory()$createEntryFromCo ...] Parsing 1 Expasy ENZYME database. entries.
biodb.DEBUG[2024-04-13 16:05:20.151][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-13 16:05:20.152][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-13 16:05:20.153][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-13 16:05:20.157][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-13 16:05:20.158][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-13 16:05:20.159][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:05:20.160][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-04-13 16:05:20.161][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-13 16:05:20.162][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-13 16:05:20.163][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:20.164][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:20.165][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-04-13 16:05:20.166][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-04-13 16:05:20.167][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:20.168][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:20.169][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-04-13 16:05:20.170][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-13 16:05:20.171][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:20.172][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:20.173][self$getBiodb()$getEntryFields()$get] Asked field names are: COFACTOR.
biodb.TRACE[2024-04-13 16:05:20.174][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-04-13 16:05:20.175][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:20.176][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:20.177][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-04-13 16:05:20.178][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-04-13 16:05:20.178][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:20.179][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:20.180][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-04-13 16:05:20.181][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-04-13 16:05:20.182][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:20.183][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:20.184][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-13 16:05:20.185][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-13 16:05:20.186][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:20.186][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:20.187][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-04-13 16:05:20.188][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-04-13 16:05:20.189][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:20.190][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:20.191][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-13 16:05:20.192][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-13 16:05:20.193][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:20.194][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:20.195][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-13 16:05:20.196][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-13 16:05:20.196][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:20.197][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:20.198][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-13 16:05:20.199][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-13 16:05:20.200][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:20.201][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:20.202][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-13 16:05:20.203][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-13 16:05:20.204][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:20.205][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:20.205][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-13 16:05:20.206][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-13 16:05:20.207][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:20.208][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:20.209][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-13 16:05:20.210][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-13 16:05:20.211][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:20.212][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-04-13 16:05:20.213][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 1.1.1.54.
biodb.TRACE[2024-04-13 16:05:20.231][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-04-13 16:05:20.232][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-04-13 16:05:20.233][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:20.234][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:20.235][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-04-13 16:05:20.236][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-04-13 16:05:20.236][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:20.237][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:20.238][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-04-13 16:05:20.239][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-04-13 16:05:20.240][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:20.241][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:20.242][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-04-13 16:05:20.243][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-04-13 16:05:20.244][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:20.244][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:20.246][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-13 16:05:20.247][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-13 16:05:20.248][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:20.248][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:20.274][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-04-13 16:05:20.275][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-04-13 16:05:20.276][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:20.277][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:20.281][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-13 16:05:20.282][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-13 16:05:20.283][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:20.283][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:20.284][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-13 16:05:20.285][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-13 16:05:20.286][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:20.287][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:20.288][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-13 16:05:20.289][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-13 16:05:20.290][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:20.290][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:20.293][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-13 16:05:20.294][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-13 16:05:20.294][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:20.295][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:20.296][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-13 16:05:20.297][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-13 16:05:20.298][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:20.299][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:20.300][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-13 16:05:20.301][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-13 16:05:20.302][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:20.303][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:20.304][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-04-13 16:05:20.305][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-04-13 16:05:20.306][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:20.306][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:20.307][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-04-13 16:05:20.308][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-04-13 16:05:20.309][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:20.310][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:20.311][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-04-13 16:05:20.312][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-04-13 16:05:20.313][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:20.314][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:20.329][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-13 16:05:20.330][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-13 16:05:20.330][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:20.331][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:20.332][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-13 16:05:20.333][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-13 16:05:20.334][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:20.335][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:20.336][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-13 16:05:20.337][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-13 16:05:20.338][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:20.338][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:20.339][ef$get] Asked field names are: accession.
biodb.TRACE[2024-04-13 16:05:20.340][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-13 16:05:20.341][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:20.343][ef$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:20.344][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-13 16:05:20.344][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-13 16:05:20.345][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:20.346][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:20.354][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-04-13 16:05:20.355][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-13 16:05:20.355][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:20.356][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:20.357][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-04-13 16:05:20.358][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-13 16:05:20.359][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:20.360][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:20.361][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-04-13 16:05:20.362][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-13 16:05:20.363][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:20.363][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:20.364][ef$get] Asked field names are: name.
biodb.TRACE[2024-04-13 16:05:20.365][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-04-13 16:05:20.366][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:20.367][ef$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:20.368][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-04-13 16:05:20.369][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-13 16:05:20.370][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:20.371][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:20.378][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-04-13 16:05:20.379][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-04-13 16:05:20.380][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:20.381][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:20.381][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-04-13 16:05:20.382][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-04-13 16:05:20.383][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:20.384][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:20.385][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-04-13 16:05:20.386][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-04-13 16:05:20.387][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:20.388][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:20.389][ef$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-04-13 16:05:20.390][ef$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-04-13 16:05:20.390][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:20.391][ef$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:20.392][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-04-13 16:05:20.393][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-04-13 16:05:20.394][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:20.395][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:20.402][ef$get] Asked field names are: accession.
biodb.TRACE[2024-04-13 16:05:20.403][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-13 16:05:20.404][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:20.405][ef$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:20.408][ef$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-04-13 16:05:20.409][ef$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-04-13 16:05:20.410][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:20.411][ef$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:20.415][ef$get] Asked field names are: name.
biodb.TRACE[2024-04-13 16:05:20.416][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-04-13 16:05:20.417][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:20.418][ef$get] fields variable is a list.
biodb.INFO [2024-04-13 16:05:20.424][biodb::testThat]
biodb.INFO [2024-04-13 16:05:20.425][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2024-04-13 16:05:20.426][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-04-13 16:05:20.426][biodb::testThat]
biodb.DEBUG[2024-04-13 16:05:20.428][private$loadEntries] Creating entries from ids [2]: "1.1.1.1, 1.1.1.54".
biodb.DEBUG[2024-04-13 16:05:20.435][conn$getEntryContent] Get Expasy ENZYME database. entry content(s) for 2 id(s)...
biodb.TRACE[2024-04-13 16:05:20.439][cch$loadFileContent] Trying to load 2 files from cache: [2]: "1.1.1.1, 1.1.1.54".
biodb.TRACE[2024-04-13 16:05:20.441][cch$loadFileContent] file.exist = [2]: "TRUE, FALSE".
biodb.TRACE[2024-04-13 16:05:20.442][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280/1.1.1.1.txt".
biodb.DEBUG[2024-04-13 16:05:20.443][conn$getEntryContent] 1 Expasy ENZYME database. entry content(s) loaded from cache.
biodb.DEBUG[2024-04-13 16:05:20.444][conn$getEntryContent] 1 entry content(s) need to be fetched from Expasy ENZYME database. database "https://enzyme.expasy.org/".
biodb.DEBUG[2024-04-13 16:05:20.445][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-04-13 16:05:20.446][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-04-13 16:05:20.450][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-13 16:05:20.451][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-13 16:05:20.452][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-13 16:05:20.456][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-13 16:05:20.457][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-13 16:05:20.458][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:05:20.458][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:05:20.459][scheduler$sendRequest] Getting content of get URL request "https://enzyme.expasy.org/EC/1.1.1.54.txt".
biodb.DEBUG[2024-04-13 16:05:20.482][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-04-13 16:05:20.483][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-04-13 16:05:20.484][private$doSendRequestOnce] Sent URL is "https://enzyme.expasy.org/EC/1.1.1.54.txt".
biodb.TRACE[2024-04-13 16:05:21.569][getRCurlRequestResult] Using RCurl package for sending request (https://enzyme.expasy.org/EC/1.1.1.54.txt).
biodb.DEBUG[2024-04-13 16:05:22.280][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-04-13 16:05:22.283][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280/a9b93566a091cbe35a06e4b3871f95c9.content"
biodb.TRACE[2024-04-13 16:05:22.296][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280/a9b93566a091cbe35a06e4b3871f95c9.request"
biodb.TRACE[2024-04-13 16:05:22.299][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280/1.1.1.54.txt"
biodb.DEBUG[2024-04-13 16:05:22.300][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-04-13 16:05:22.301][self$createEntryFromContent] Creating Expasy ENZYME database. entries from 2 content(s).
biodb.DEBUG[2024-04-13 16:05:22.303][self$createEntryFromContent] Parsing 2 Expasy ENZYME database. entries.
biodb.DEBUG[2024-04-13 16:05:22.304][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-13 16:05:22.305][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-13 16:05:22.306][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-13 16:05:22.310][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-13 16:05:22.311][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-13 16:05:22.312][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:05:22.313][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-04-13 16:05:22.316][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-13 16:05:22.317][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-13 16:05:22.318][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:22.319][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:22.320][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-04-13 16:05:22.321][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-04-13 16:05:22.322][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:22.323][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:22.324][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-04-13 16:05:22.325][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-13 16:05:22.326][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:22.327][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:22.328][self$getBiodb()$getEntryFields()$get] Asked field names are: COFACTOR.
biodb.TRACE[2024-04-13 16:05:22.329][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-04-13 16:05:22.330][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:22.331][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:22.332][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-04-13 16:05:22.333][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-13 16:05:22.334][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:22.335][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:22.336][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-04-13 16:05:22.337][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-13 16:05:22.338][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:22.339][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:22.340][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-04-13 16:05:22.341][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-13 16:05:22.342][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:22.343][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:22.343][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-04-13 16:05:22.344][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-13 16:05:22.345][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:22.346][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:22.347][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-04-13 16:05:22.348][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-13 16:05:22.349][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:22.350][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:22.351][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-04-13 16:05:22.352][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-04-13 16:05:22.353][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:22.354][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:22.355][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-04-13 16:05:22.356][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-04-13 16:05:22.357][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:22.357][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:22.358][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-13 16:05:22.359][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-13 16:05:22.360][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:22.361][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:22.362][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-04-13 16:05:22.374][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-04-13 16:05:22.374][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:22.375][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:22.376][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-13 16:05:22.377][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-13 16:05:22.378][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:22.379][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:22.380][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-13 16:05:22.381][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-13 16:05:22.382][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:22.383][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:22.384][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-13 16:05:22.385][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-13 16:05:22.385][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:22.386][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-04-13 16:05:22.387][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-13 16:05:22.388][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-13 16:05:22.389][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-13 16:05:22.393][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-13 16:05:22.394][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-13 16:05:22.395][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:05:22.396][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-04-13 16:05:22.398][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-13 16:05:22.399][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-13 16:05:22.400][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:22.400][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:22.402][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-04-13 16:05:22.403][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-04-13 16:05:22.404][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:22.404][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:22.406][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-04-13 16:05:22.407][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-13 16:05:22.407][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:22.408][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:22.409][self$getBiodb()$getEntryFields()$get] Asked field names are: COFACTOR.
biodb.TRACE[2024-04-13 16:05:22.410][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-04-13 16:05:22.411][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:22.412][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:22.413][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-04-13 16:05:22.414][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-04-13 16:05:22.415][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:22.416][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:22.417][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-04-13 16:05:22.418][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-04-13 16:05:22.418][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:22.419][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:22.420][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-13 16:05:22.421][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-13 16:05:22.422][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:22.423][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:22.424][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-04-13 16:05:22.425][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-04-13 16:05:22.426][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:22.427][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:22.428][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-13 16:05:22.428][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-13 16:05:22.429][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:22.430][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:22.431][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-13 16:05:22.432][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-13 16:05:22.433][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:22.434][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:22.435][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-13 16:05:22.436][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-13 16:05:22.436][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:22.437][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:22.438][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-13 16:05:22.439][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-13 16:05:22.440][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:22.441][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:22.442][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-13 16:05:22.443][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-13 16:05:22.444][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:22.445][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:22.446][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-13 16:05:22.447][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-13 16:05:22.447][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:22.448][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:22.449][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-13 16:05:22.450][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-13 16:05:22.451][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:22.452][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:22.453][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-13 16:05:22.454][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-13 16:05:22.455][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:22.455][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:22.456][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-13 16:05:22.457][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-13 16:05:22.458][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:22.459][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-04-13 16:05:22.460][self$createEntryFromContent] Accession numbers: 1.1.1.1, 1.1.1.54.
biodb.TRACE[2024-04-13 16:05:22.461][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2024-04-13 16:05:22.462][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2024-04-13 16:05:22.463][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:22.464][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:22.465][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2024-04-13 16:05:22.466][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2024-04-13 16:05:22.466][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:22.467][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:22.468][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2024-04-13 16:05:22.469][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2024-04-13 16:05:22.470][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:22.471][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:22.475][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2024-04-13 16:05:22.476][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2024-04-13 16:05:22.477][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:22.478][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:22.479][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2024-04-13 16:05:22.480][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2024-04-13 16:05:22.481][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:22.482][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:22.483][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2024-04-13 16:05:22.484][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2024-04-13 16:05:22.484][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:22.485][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-04-13 16:05:22.492][biodb::testThat]
biodb.INFO [2024-04-13 16:05:22.493][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2024-04-13 16:05:22.494][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-04-13 16:05:22.495][biodb::testThat]
biodb.TRACE[2024-04-13 16:05:22.498][ef$get] Asked field names are: name.
biodb.TRACE[2024-04-13 16:05:22.498][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-04-13 16:05:22.499][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:22.500][ef$get] fields variable is a list.
biodb.DEBUG[2024-04-13 16:05:22.501][function(conn, opt)] Testing searchForEntries() with entry "1.1.1.1" and field "name".
biodb.TRACE[2024-04-13 16:05:22.523][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-04-13 16:05:22.524][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-13 16:05:22.525][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:22.526][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:22.527][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-04-13 16:05:22.528][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-13 16:05:22.529][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:22.530][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:22.531][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-04-13 16:05:22.532][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-13 16:05:22.533][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:22.533][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-04-13 16:05:22.537][function(conn, opt)] With value "alcohol dehydrogenase".
biodb.DEBUG[2024-04-13 16:05:22.560][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://enzyme.expasy.org/enzyme-byname.html?alcohol dehydrogenase".
biodb.DEBUG[2024-04-13 16:05:22.574][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-04-13 16:05:22.575][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-04-13 16:05:22.589][private$doSendRequestOnce] Sent URL is "https://enzyme.expasy.org/enzyme-byname.html?alcohol%20dehydrogenase".
biodb.TRACE[2024-04-13 16:05:23.485][getRCurlRequestResult] Using RCurl package for sending request (https://enzyme.expasy.org/enzyme-byname.html?alcohol%20dehydrogenase).
biodb.DEBUG[2024-04-13 16:05:24.239][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-04-13 16:05:24.243][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280/f603fa2a57aec59588edc37541c6f6d5.content"
biodb.TRACE[2024-04-13 16:05:24.250][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280/f603fa2a57aec59588edc37541c6f6d5.request"
biodb.DEBUG[2024-04-13 16:05:24.263][function(conn, opt)] With found IDs [1]: "1.1.1.1".
biodb.INFO [2024-04-13 16:05:24.290][biodb::testThat]
biodb.INFO [2024-04-13 16:05:24.291][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2024-04-13 16:05:24.293][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-04-13 16:05:24.294][biodb::testThat]
biodb.TRACE[2024-04-13 16:05:24.322][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-04-13 16:05:24.323][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-13 16:05:24.324][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:24.325][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:24.326][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-04-13 16:05:24.327][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-13 16:05:24.328][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:24.329][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:24.330][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-04-13 16:05:24.331][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-13 16:05:24.332][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:24.333][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-04-13 16:05:24.357][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://enzyme.expasy.org/enzyme-byname.html?alcohol dehydrogenase".
biodb.DEBUG[2024-04-13 16:05:24.360][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-04-13 16:05:24.379][cch$loadFileContent] Trying to load 1 files from cache: [1]: "f603fa2a57aec59588edc37541c6f6d5".
biodb.TRACE[2024-04-13 16:05:24.402][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-04-13 16:05:24.403][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280/f603fa2a57aec59588edc37541c6f6d5.content".
biodb.INFO [2024-04-13 16:05:24.419][biodb::testThat]
biodb.INFO [2024-04-13 16:05:24.420][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2024-04-13 16:05:24.421][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-04-13 16:05:24.422][biodb::testThat]
biodb.TRACE[2024-04-13 16:05:24.432][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-04-13 16:05:24.433][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-04-13 16:05:24.434][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:24.435][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:24.436][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-04-13 16:05:24.437][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-04-13 16:05:24.438][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:24.439][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:24.440][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-04-13 16:05:24.441][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-04-13 16:05:24.442][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:24.443][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:24.444][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-04-13 16:05:24.445][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-04-13 16:05:24.446][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:24.447][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:24.480][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-04-13 16:05:24.481][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-04-13 16:05:24.482][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:24.483][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:24.484][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-04-13 16:05:24.485][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-04-13 16:05:24.486][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:24.487][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:24.488][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-04-13 16:05:24.489][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-04-13 16:05:24.490][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:24.491][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:24.492][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-04-13 16:05:24.493][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-04-13 16:05:24.494][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:24.495][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-04-13 16:05:24.501][biodb::testThat]
biodb.INFO [2024-04-13 16:05:24.502][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2024-04-13 16:05:24.503][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-04-13 16:05:24.504][biodb::testThat]
biodb.INFO [2024-04-13 16:05:24.512][biodb::testThat]
biodb.INFO [2024-04-13 16:05:24.513][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2024-04-13 16:05:24.514][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-04-13 16:05:24.515][biodb::testThat]
biodb.INFO [2024-04-13 16:05:24.522][biodb::testThat]
biodb.INFO [2024-04-13 16:05:24.523][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2024-04-13 16:05:24.524][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-04-13 16:05:24.525][biodb::testThat]
biodb.DEBUG[2024-04-13 16:05:24.538][function(conn, opt)] Trying to download "https://enzyme.expasy.org/cgi-bin/enzyme/enzyme-search-ec?field1=1&field2=1&field3=1&field4=1".
biodb.DEBUG[2024-04-13 16:05:25.214][getUrlContent] Use RCurl for downloading content of URL https://enzyme.expasy.org/cgi-bin/enzyme/enzyme-search-ec?field1=1&field2=1&field3=1&field4=1.
biodb.INFO [2024-04-13 16:05:26.184][biodb::testThat]
biodb.INFO [2024-04-13 16:05:26.186][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2024-04-13 16:05:26.189][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-04-13 16:05:26.191][biodb::testThat]
biodb.DEBUG[2024-04-13 16:05:27.982][getUrlContent] Use RCurl for downloading content of URL https://enzyme.expasy.org/images/1.1.1.1/image.png.
biodb.TRACE[2024-04-13 16:05:28.383][ef$get] Asked field names are: name.
biodb.TRACE[2024-04-13 16:05:28.385][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-04-13 16:05:28.388][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:28.390][ef$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:28.392][ef$get] Asked field names are: name.
biodb.TRACE[2024-04-13 16:05:28.394][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-04-13 16:05:28.396][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:28.399][ef$get] fields variable is a list.
biodb.INFO [2024-04-13 16:05:28.401][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-04-13 16:05:28.403][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector expasy.enzyme from the request scheduler
biodb.INFO [2024-04-13 16:05:28.406][self$deleteConn] Connector "expasy.enzyme" deleted.
biodb.DEBUG[2024-04-13 16:05:28.408][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-04-13 16:05:28.426][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-13 16:05:28.428][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-13 16:05:28.430][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-13 16:05:28.431][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-13 16:05:28.433][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:05:28.434][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2024-04-13 16:05:28.447][biodb::testContext]
biodb.INFO [2024-04-13 16:05:28.448][biodb::testContext] ********************************************************************************
biodb.INFO [2024-04-13 16:05:28.449][biodb::testContext] Test context - Example long tests
biodb.INFO [2024-04-13 16:05:28.450][biodb::testContext] ********************************************************************************
biodb.INFO [2024-04-13 16:05:28.451][biodb::testContext]
biodb.INFO [2024-04-13 16:05:28.454][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.10.0.
biodb.DEBUG[2024-04-13 16:05:28.456][self$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.18-bioc/R/site-library/biodb/definitions.yml".
biodb.DEBUG[2024-04-13 16:05:28.460][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-04-13 16:05:28.461][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-04-13 16:05:28.462][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-04-13 16:05:28.463][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:05:28.464][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:05:28.465][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:05:28.466][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-04-13 16:05:28.467][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-04-13 16:05:28.468][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:05:28.469][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:05:28.469][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:05:28.470][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-04-13 16:05:28.471][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-04-13 16:05:28.472][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:05:28.473][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:05:28.474][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:05:28.475][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-04-13 16:05:28.476][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-04-13 16:05:28.477][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-04-13 16:05:28.477][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:05:28.478][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:05:28.479][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:05:28.480][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-04-13 16:05:28.481][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-04-13 16:05:28.482][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-04-13 16:05:28.483][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:05:28.483][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:05:28.484][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:05:28.485][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-04-13 16:05:28.486][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-04-13 16:05:28.487][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:05:28.488][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:05:28.488][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:05:28.489][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-04-13 16:05:28.490][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-04-13 16:05:28.491][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-04-13 16:05:28.492][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:05:28.493][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:05:28.494][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:05:28.494][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-04-13 16:05:28.495][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-04-13 16:05:28.496][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:05:28.497][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:05:28.498][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:05:28.499][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-04-13 16:05:28.500][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-04-13 16:05:28.501][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-04-13 16:05:28.501][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:05:28.502][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:05:28.503][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[2024-04-13 16:05:28.504][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-04-13 16:05:28.505][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-04-13 16:05:28.506][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-04-13 16:05:28.507][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-04-13 16:05:28.507][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-04-13 16:05:28.508][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-04-13 16:05:28.509][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:05:28.510][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:05:28.511][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:05:28.512][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-04-13 16:05:28.513][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-04-13 16:05:28.514][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:05:28.514][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:05:28.515][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:05:28.516][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-04-13 16:05:28.517][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-04-13 16:05:28.518][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:05:28.519][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:05:28.519][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:05:28.520][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-04-13 16:05:28.521][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-04-13 16:05:28.522][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:05:28.523][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:05:28.524][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[2024-04-13 16:05:28.524][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-04-13 16:05:28.525][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-04-13 16:05:28.526][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:05:28.527][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:05:28.528][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:05:28.529][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-04-13 16:05:28.530][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-04-13 16:05:28.531][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:05:28.531][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:05:28.532][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:05:28.533][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-04-13 16:05:28.534][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-04-13 16:05:28.538][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-04-13 16:05:28.539][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:05:28.540][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:05:28.541][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:05:28.542][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-04-13 16:05:28.543][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-04-13 16:05:28.544][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-04-13 16:05:28.544][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:05:28.545][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:05:28.546][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:05:28.547][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-04-13 16:05:28.549][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-04-13 16:05:28.550][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2024-04-13 16:05:28.551][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-04-13 16:05:28.552][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-04-13 16:05:28.552][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-04-13 16:05:28.553][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-04-13 16:05:28.554][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-04-13 16:05:28.555][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-04-13 16:05:28.556][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-04-13 16:05:28.557][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-04-13 16:05:28.558][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-04-13 16:05:28.559][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-04-13 16:05:28.560][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-04-13 16:05:28.561][self$setPropertyValue]
biodb.DEBUG[2024-04-13 16:05:28.562][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-04-13 16:05:28.563][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-04-13 16:05:28.563][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-04-13 16:05:28.563][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-04-13 16:05:28.563][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-04-13 16:05:28.563][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-04-13 16:05:28.563][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-04-13 16:05:28.564][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-04-13 16:05:28.565][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-04-13 16:05:28.566][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-04-13 16:05:28.567][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-04-13 16:05:28.568][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-04-13 16:05:28.569][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-04-13 16:05:28.569][self$setPropertyValue]
biodb.DEBUG[2024-04-13 16:05:28.570][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-04-13 16:05:28.571][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-04-13 16:05:28.572][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-04-13 16:05:28.573][self$setPropertyValue]
biodb.DEBUG[2024-04-13 16:05:28.574][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-04-13 16:05:28.576][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-04-13 16:05:28.577][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-04-13 16:05:28.578][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-04-13 16:05:28.578][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-04-13 16:05:28.579][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-04-13 16:05:28.580][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-04-13 16:05:28.581][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-04-13 16:05:28.582][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-04-13 16:05:28.583][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-04-13 16:05:28.584][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-04-13 16:05:28.585][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-04-13 16:05:28.586][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-04-13 16:05:28.587][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-04-13 16:05:28.588][self$setPropertyValue]
biodb.DEBUG[2024-04-13 16:05:28.589][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-04-13 16:05:28.589][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-04-13 16:05:28.589][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-04-13 16:05:28.589][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-04-13 16:05:28.589][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-04-13 16:05:28.589][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-04-13 16:05:28.590][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-04-13 16:05:28.591][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-04-13 16:05:28.592][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-04-13 16:05:28.593][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-04-13 16:05:28.594][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-04-13 16:05:28.595][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-04-13 16:05:28.596][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-04-13 16:05:28.596][self$setPropertyValue]
biodb.DEBUG[2024-04-13 16:05:28.597][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-04-13 16:05:28.598][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-04-13 16:05:28.599][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-04-13 16:05:28.600][self$setPropertyValue]
biodb.DEBUG[2024-04-13 16:05:28.601][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-04-13 16:05:28.603][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-04-13 16:05:28.604][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2024-04-13 16:05:28.605][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-04-13 16:05:28.610][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-04-13 16:05:28.611][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-04-13 16:05:28.612][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-04-13 16:05:28.613][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-04-13 16:05:28.614][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-04-13 16:05:28.615][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-04-13 16:05:28.616][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-04-13 16:05:28.617][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-04-13 16:05:28.617][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-04-13 16:05:28.618][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-04-13 16:05:28.619][self$setPropertyValue]
biodb.DEBUG[2024-04-13 16:05:28.620][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-04-13 16:05:28.621][self$setPropertyValue]
biodb.DEBUG[2024-04-13 16:05:28.622][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-04-13 16:05:28.623][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-04-13 16:05:28.624][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-04-13 16:05:28.625][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-04-13 16:05:28.625][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-04-13 16:05:28.626][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-04-13 16:05:28.627][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-04-13 16:05:28.628][self$setPropertyValue]
biodb.DEBUG[2024-04-13 16:05:28.629][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-04-13 16:05:28.630][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-04-13 16:05:28.631][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-04-13 16:05:28.631][self$setPropertyValue]
biodb.DEBUG[2024-04-13 16:05:28.633][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-04-13 16:05:28.634][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-04-13 16:05:28.635][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-04-13 16:05:28.636][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-04-13 16:05:28.637][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-04-13 16:05:28.638][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-04-13 16:05:28.639][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-04-13 16:05:28.640][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-04-13 16:05:28.641][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-04-13 16:05:28.641][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-04-13 16:05:28.642][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-04-13 16:05:28.643][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-04-13 16:05:28.644][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-04-13 16:05:28.645][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-04-13 16:05:28.646][self$setPropertyValue]
biodb.DEBUG[2024-04-13 16:05:28.647][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-04-13 16:05:28.648][self$setPropertyValue]
biodb.DEBUG[2024-04-13 16:05:28.649][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-04-13 16:05:28.650][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-04-13 16:05:28.650][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-04-13 16:05:28.651][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-04-13 16:05:28.652][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-04-13 16:05:28.653][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-04-13 16:05:28.654][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-04-13 16:05:28.655][self$setPropertyValue]
biodb.DEBUG[2024-04-13 16:05:28.656][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-04-13 16:05:28.656][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-04-13 16:05:28.657][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-04-13 16:05:28.658][self$setPropertyValue]
biodb.DEBUG[2024-04-13 16:05:28.659][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-04-13 16:05:28.660][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:05:28.661][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:05:28.662][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:05:28.663][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-13 16:05:28.663][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-13 16:05:28.664][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:05:28.665][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:05:28.666][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:05:28.667][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-13 16:05:28.668][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-13 16:05:28.668][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:05:28.669][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:05:28.670][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:05:28.671][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-13 16:05:28.672][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-13 16:05:28.672][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:05:28.673][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:05:28.674][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:05:28.675][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-13 16:05:28.676][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-13 16:05:28.676][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:05:28.677][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:05:28.678][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:05:28.679][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-13 16:05:28.680][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-13 16:05:28.680][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:05:28.681][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:05:28.682][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:05:28.683][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-13 16:05:28.684][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-13 16:05:28.684][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:05:28.685][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:05:28.686][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:05:28.687][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-13 16:05:28.688][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-13 16:05:28.688][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:05:28.689][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:05:28.690][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:05:28.691][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-13 16:05:28.692][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-13 16:05:28.692][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:05:28.693][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:05:28.694][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:05:28.695][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-13 16:05:28.696][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-13 16:05:28.697][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:05:28.697][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:05:28.698][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:05:28.699][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-13 16:05:28.700][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-13 16:05:28.701][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:05:28.701][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:05:28.702][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:05:28.703][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-13 16:05:28.704][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-13 16:05:28.705][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:05:28.705][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:05:28.706][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:05:28.707][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-13 16:05:28.708][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-13 16:05:28.709][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:05:28.710][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:05:28.710][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:05:28.711][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-13 16:05:28.712][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-13 16:05:28.713][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:05:28.714][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:05:28.714][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:05:28.715][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-13 16:05:28.716][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-13 16:05:28.717][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:05:28.718][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:05:28.718][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:05:28.719][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-13 16:05:28.720][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-13 16:05:28.721][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:05:28.722][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:05:28.722][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:05:28.723][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-13 16:05:28.724][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-13 16:05:28.725][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:05:28.726][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:05:28.727][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:05:28.727][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-13 16:05:28.728][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-13 16:05:28.729][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:05:28.730][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:05:28.731][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-04-13 16:05:28.732][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-04-13 16:05:28.733][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-04-13 16:05:28.735][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-04-13 16:05:28.736][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-04-13 16:05:28.737][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-04-13 16:05:28.739][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-04-13 16:05:28.740][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-04-13 16:05:28.741][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-04-13 16:05:28.742][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-04-13 16:05:28.744][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-04-13 16:05:28.745][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-04-13 16:05:28.746][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-04-13 16:05:28.748][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-04-13 16:05:28.749][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-04-13 16:05:28.750][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-04-13 16:05:28.751][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-04-13 16:05:28.753][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-04-13 16:05:28.754][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-04-13 16:05:28.755][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-04-13 16:05:28.757][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-04-13 16:05:28.758][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-04-13 16:05:28.759][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-04-13 16:05:28.760][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-04-13 16:05:28.762][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-04-13 16:05:28.763][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-04-13 16:05:28.764][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-04-13 16:05:28.765][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-04-13 16:05:28.767][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-04-13 16:05:28.768][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-04-13 16:05:28.769][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-04-13 16:05:28.775][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-04-13 16:05:28.776][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-04-13 16:05:28.777][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-04-13 16:05:28.778][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-04-13 16:05:28.780][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-04-13 16:05:28.781][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-04-13 16:05:28.782][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-04-13 16:05:28.783][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-04-13 16:05:28.785][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-04-13 16:05:28.786][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-04-13 16:05:28.787][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-04-13 16:05:28.788][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-04-13 16:05:28.790][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-04-13 16:05:28.791][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-04-13 16:05:28.792][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-04-13 16:05:28.794][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-04-13 16:05:28.795][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-04-13 16:05:28.796][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-04-13 16:05:28.797][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-04-13 16:05:28.799][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-04-13 16:05:28.800][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-04-13 16:05:28.801][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-04-13 16:05:28.802][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-04-13 16:05:28.804][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-04-13 16:05:28.805][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-04-13 16:05:28.806][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-04-13 16:05:28.807][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-04-13 16:05:28.809][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-04-13 16:05:28.810][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-04-13 16:05:28.811][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-04-13 16:05:28.812][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-04-13 16:05:28.814][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-04-13 16:05:28.815][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-04-13 16:05:28.816][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-04-13 16:05:28.818][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-04-13 16:05:28.819][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-04-13 16:05:28.820][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-04-13 16:05:28.821][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-04-13 16:05:28.823][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-04-13 16:05:28.824][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-04-13 16:05:28.825][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-04-13 16:05:28.826][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-04-13 16:05:28.828][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-04-13 16:05:28.829][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-04-13 16:05:28.830][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-04-13 16:05:28.831][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-04-13 16:05:28.833][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-04-13 16:05:28.834][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-04-13 16:05:28.835][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-04-13 16:05:28.836][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-04-13 16:05:28.838][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-04-13 16:05:28.839][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-04-13 16:05:28.840][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-04-13 16:05:28.842][initialize] This is biodb version 1.10.0.
biodb.DEBUG[2024-04-13 16:05:28.843][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-04-13 16:05:28.843][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-04-13 16:05:28.844][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-13 16:05:28.845][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:05:28.846][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:05:28.847][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:05:28.847][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-13 16:05:28.848][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-13 16:05:28.849][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-13 16:05:28.850][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-13 16:05:28.851][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:05:28.851][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[2024-04-13 16:05:28.852][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:05:28.853][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-13 16:05:28.854][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-13 16:05:28.855][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-13 16:05:28.855][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-13 16:05:28.856][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:05:28.857][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:05:28.858][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:05:28.859][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-13 16:05:28.859][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-13 16:05:28.860][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-13 16:05:28.861][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-13 16:05:28.862][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:05:28.863][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:05:28.863][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:05:28.864][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-13 16:05:28.865][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-13 16:05:28.866][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-13 16:05:28.867][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-13 16:05:28.867][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:05:28.868][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:05:28.869][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:05:28.870][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-13 16:05:28.871][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-13 16:05:28.871][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-13 16:05:28.872][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-13 16:05:28.873][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:05:28.874][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:05:28.875][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:05:28.875][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-13 16:05:28.876][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-13 16:05:28.877][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-13 16:05:28.878][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-13 16:05:28.879][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:05:28.879][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:05:28.880][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:05:28.881][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-13 16:05:28.882][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-13 16:05:28.883][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-13 16:05:28.883][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-13 16:05:28.884][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:05:28.885][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:05:28.886][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:05:28.887][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-13 16:05:28.888][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-13 16:05:28.888][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-13 16:05:28.889][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-13 16:05:28.890][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:05:28.891][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:05:28.892][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:05:28.892][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-13 16:05:28.893][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-13 16:05:28.894][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-13 16:05:28.895][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-13 16:05:28.896][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:05:28.896][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:05:28.897][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:05:28.898][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-13 16:05:28.899][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-13 16:05:28.900][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-13 16:05:28.900][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-13 16:05:28.901][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:05:28.902][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:05:28.903][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:05:28.904][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-13 16:05:28.904][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-13 16:05:28.905][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-13 16:05:28.906][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-13 16:05:28.907][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:05:28.908][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:05:28.908][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:05:28.909][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-13 16:05:28.910][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-13 16:05:28.911][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-13 16:05:28.912][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-13 16:05:28.912][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:05:28.913][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:05:28.914][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:05:28.915][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-13 16:05:28.916][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-13 16:05:28.916][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-13 16:05:28.917][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-13 16:05:28.918][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:05:28.919][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:05:28.920][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:05:28.920][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-13 16:05:28.921][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-13 16:05:28.922][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-13 16:05:28.923][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-13 16:05:28.924][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:05:28.924][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:05:28.925][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:05:28.926][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-13 16:05:28.927][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-13 16:05:28.928][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-13 16:05:28.928][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-13 16:05:28.929][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:05:28.930][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:05:28.935][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:05:28.936][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-13 16:05:28.937][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-13 16:05:28.938][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-13 16:05:28.938][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-13 16:05:28.939][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:05:28.940][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:05:28.941][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:05:28.942][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-13 16:05:28.942][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-13 16:05:28.943][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-13 16:05:28.944][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-13 16:05:28.945][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:05:28.946][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.DEBUG[2024-04-13 16:05:28.947][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.18-bioc-longtests/meat/biodbExpasy.Rcheck/biodbExpasy/definitions.yml".
biodb.DEBUG[2024-04-13 16:05:28.948][self$getDbsInfo()$define] Define connector expasy.enzyme.
biodb.DEBUG[2024-04-13 16:05:28.950][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-04-13 16:05:28.951][self$setPropertyValue] Setting property "description" to "Write here the description of this database.".
biodb.DEBUG[2024-04-13 16:05:28.952][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-04-13 16:05:28.953][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-04-13 16:05:28.954][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-04-13 16:05:28.955][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-04-13 16:05:28.955][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-04-13 16:05:28.956][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-04-13 16:05:28.957][self$setPropertyValue] Setting property "entry.content.type" to "txt".
biodb.DEBUG[2024-04-13 16:05:28.958][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-04-13 16:05:28.959][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-04-13 16:05:28.960][self$setPropertyValue] Setting property "name" to "Expasy ENZYME database.".
biodb.DEBUG[2024-04-13 16:05:28.961][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-04-13 16:05:28.962][self$setPropertyValue] Setting property "parsing.expr" to "^ID\s+([0-9.]+)$".
biodb.DEBUG[2024-04-13 16:05:28.962][self$setPropertyValue] Setting property "parsing.expr" to "^CA\s+(.+?)\.?$".
biodb.DEBUG[2024-04-13 16:05:28.962][self$setPropertyValue] Setting property "parsing.expr" to "^CF\s+(.+?)\.?$".
biodb.DEBUG[2024-04-13 16:05:28.962][self$setPropertyValue] Setting property "parsing.expr" to "^DE\s+(.+?)\.?$".
biodb.DEBUG[2024-04-13 16:05:28.963][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-04-13 16:05:28.964][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-04-13 16:05:28.965][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2024-04-13 16:05:28.965][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-04-13 16:05:28.966][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-04-13 16:05:28.967][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-04-13 16:05:28.968][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-04-13 16:05:28.969][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-04-13 16:05:28.970][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-04-13 16:05:28.971][self$setPropertyValue] Setting property "urls" to "https://enzyme.expasy.org/".
biodb.DEBUG[2024-04-13 16:05:28.972][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-04-13 16:05:28.972][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-04-13 16:05:28.973][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-04-13 16:05:28.974][self$setPropertyValue]
biodb.DEBUG[2024-04-13 16:05:28.975][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-04-13 16:05:28.978][super$initialize] Initialize connector expasy.enzyme.
biodb.DEBUG[2024-04-13 16:05:28.979][super$initialize] Register connector expasy.enzyme with the request scheduler
biodb.DEBUG[2024-04-13 16:05:28.980][private$bdb$getRequestScheduler()$re ...] Register connector expasy.enzyme.
biodb.DEBUG[2024-04-13 16:05:28.982][private$addConnectorRules] Create new rule for URL "enzyme.expasy.org" of connector "expasy.enzyme".
biodb.DEBUG[2024-04-13 16:05:28.983][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-04-13 16:05:28.984][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-04-13 16:05:28.985][biodb$getFactory()$createConn] Creating new connector expasy.enzyme for database class expasy.enzyme .
biodb.INFO [2024-04-13 16:05:28.986][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-04-13 16:05:28.987][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector expasy.enzyme from the request scheduler
biodb.INFO [2024-04-13 16:05:28.988][self$deleteConn] Connector "expasy.enzyme" deleted.
biodb.DEBUG[2024-04-13 16:05:28.988][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-04-13 16:05:28.989][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-13 16:05:28.990][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-13 16:05:28.991][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-13 16:05:28.992][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-13 16:05:28.992][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:05:28.993][FUN] Functions in observer 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 85 ]
> 
> proc.time()
   user  system elapsed 
  5.179   0.181  11.713

'R CMD check' output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD check --test-dir=longtests --no-stop-on-test-error --no-codoc --no-examples --no-manual --ignore-vignettes --check-subdirs=no biodbExpasy_1.6.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.18-bioc-longtests/meat/biodbExpasy.Rcheck’
* using R version 4.3.3 (2024-02-29)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
    GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* using options ‘--no-codoc --no-examples --no-manual --ignore-vignettes --no-stop-on-test-error’
* checking for file ‘biodbExpasy/DESCRIPTION’ ... OK
* this is package ‘biodbExpasy’ version ‘1.6.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘biodbExpasy’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Title field: should not end in a period.
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... SKIPPED
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... SKIPPED
* checking examples ... SKIPPED
* checking for unstated dependencies in ‘longtests’ ... OK
* checking tests in ‘longtests’ ...
  Running ‘testthat.R’
 OK
* DONE

Status: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.18-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)