Back to Long Tests report for BioC 3.19

This page was generated on 2024-05-11 23:55:02 -0400 (Sat, 11 May 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 (2024-04-24) -- "Puppy Cup" 4751
palomino3Windows Server 2022 Datacenterx644.4.0 (2024-04-24 ucrt) -- "Puppy Cup" 4485
lconwaymacOS 12.7.1 Montereyx86_644.4.0 (2024-04-24) -- "Puppy Cup" 4515
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 7/33HostnameOS / ArchCHECK
biodbExpasy 1.8.0  (landing page)
Pierrick Roger
Snapshot Date: 2024-05-11 09:55:01 -0400 (Sat, 11 May 2024)
git_url: https://git.bioconductor.org/packages/biodbExpasy
git_branch: RELEASE_3_19
git_last_commit: de004e8
git_last_commit_date: 2024-04-30 11:41:12 -0400 (Tue, 30 Apr 2024)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK  
palomino3Windows Server 2022 Datacenter / x64  OK  
lconwaymacOS 12.7.1 Monterey / x86_64  OK  

CHECK results for biodbExpasy on lconway


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: 1.8.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --test-dir=longtests --no-stop-on-test-error --no-codoc --no-examples --no-manual --ignore-vignettes --check-subdirs=no biodbExpasy_1.8.0.tar.gz
StartedAt: 2024-05-11 16:00:54 -0400 (Sat, 11 May 2024)
EndedAt: 2024-05-11 16:01:52 -0400 (Sat, 11 May 2024)
EllapsedTime: 57.6 seconds
RetCode: 0
Status:   OK  
CheckDir: biodbExpasy.Rcheck
Warnings: 0

Tests output

biodbExpasy.Rcheck/tests/testthat.Rout


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

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

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Type 'contributors()' for more information and
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Type 'demo()' for some demos, 'help()' for on-line help, or
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> # Script needed to run testthat automatically from ‘R CMD check’. See
> # testthat::test_dir documentation.
> library(testthat)
> library(biodbExpasy)
> Sys.setenv(TESTTHAT_REPORTER="summary")
> Sys.setenv(BIODB_LOG_DST="console")
> test_check("biodbExpasy")
biodb.INFO [2024-05-11 16:01:34.944][biodb::testContext]
biodb.INFO [2024-05-11 16:01:34.948][biodb::testContext] ********************************************************************************
biodb.INFO [2024-05-11 16:01:34.949][biodb::testContext] Test context - Generic long tests
biodb.INFO [2024-05-11 16:01:34.950][biodb::testContext] ********************************************************************************
biodb.INFO [2024-05-11 16:01:34.951][biodb::testContext]
biodb.INFO [2024-05-11 16:01:34.957][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.12.0.
biodb.DEBUG[2024-05-11 16:01:34.959][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2024-05-11 16:01:34.967][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-05-11 16:01:34.968][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-05-11 16:01:34.969][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-05-11 16:01:34.970][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:01:34.971][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:01:34.972][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:01:34.973][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-05-11 16:01:34.992][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-05-11 16:01:34.993][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:01:34.994][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:01:34.995][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:01:34.996][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-05-11 16:01:34.997][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-05-11 16:01:34.998][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:01:34.999][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:01:34.999][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:01:35.000][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-05-11 16:01:35.001][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-05-11 16:01:35.003][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-05-11 16:01:35.003][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:01:35.004][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:01:35.005][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:01:35.006][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-05-11 16:01:35.007][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-05-11 16:01:35.019][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-05-11 16:01:35.020][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:01:35.021][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:01:35.022][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:01:35.022][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-05-11 16:01:35.023][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-05-11 16:01:35.024][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:01:35.025][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:01:35.026][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:01:35.027][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-05-11 16:01:35.027][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-05-11 16:01:35.028][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-05-11 16:01:35.029][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:01:35.030][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:01:35.031][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:01:35.032][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-05-11 16:01:35.032][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-05-11 16:01:35.033][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:01:35.034][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:01:35.035][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:01:35.036][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-05-11 16:01:35.036][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-05-11 16:01:35.037][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-05-11 16:01:35.038][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:01:35.039][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:01:35.040][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:01:35.040][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-05-11 16:01:35.041][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-05-11 16:01:35.042][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-05-11 16:01:35.043][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-05-11 16:01:35.044][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-05-11 16:01:35.045][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-05-11 16:01:35.046][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:01:35.047][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:01:35.047][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[2024-05-11 16:01:35.048][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-05-11 16:01:35.049][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-05-11 16:01:35.050][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:01:35.051][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:01:35.052][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:01:35.052][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-05-11 16:01:35.053][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-05-11 16:01:35.054][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:01:35.055][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:01:35.056][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:01:35.057][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-05-11 16:01:35.058][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-05-11 16:01:35.058][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:01:35.059][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:01:35.060][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:01:35.061][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-05-11 16:01:35.062][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-05-11 16:01:35.063][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:01:35.063][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:01:35.064][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:01:35.065][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-05-11 16:01:35.066][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-05-11 16:01:35.067][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:01:35.068][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:01:35.069][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:01:35.069][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-05-11 16:01:35.070][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-05-11 16:01:35.094][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-05-11 16:01:35.095][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:01:35.096][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:01:35.096][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:01:35.097][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-05-11 16:01:35.098][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-05-11 16:01:35.099][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-05-11 16:01:35.100][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:01:35.101][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:01:35.102][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:01:35.105][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-05-11 16:01:35.134][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-05-11 16:01:35.148][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2024-05-11 16:01:35.149][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-11 16:01:35.150][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-11 16:01:35.151][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-11 16:01:35.152][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-11 16:01:35.153][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-05-11 16:01:35.154][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-11 16:01:35.155][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-05-11 16:01:35.156][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-11 16:01:35.157][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-05-11 16:01:35.157][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-05-11 16:01:35.158][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-11 16:01:35.159][self$setPropertyValue]
biodb.DEBUG[2024-05-11 16:01:35.160][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-05-11 16:01:35.161][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-05-11 16:01:35.161][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-05-11 16:01:35.161][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-05-11 16:01:35.161][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-05-11 16:01:35.161][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-05-11 16:01:35.162][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-05-11 16:01:35.163][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-11 16:01:35.164][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-11 16:01:35.165][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-11 16:01:35.166][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-11 16:01:35.166][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-11 16:01:35.167][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-11 16:01:35.168][self$setPropertyValue]
biodb.DEBUG[2024-05-11 16:01:35.169][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-11 16:01:35.170][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-11 16:01:35.171][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-05-11 16:01:35.171][self$setPropertyValue]
biodb.DEBUG[2024-05-11 16:01:35.173][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-05-11 16:01:35.174][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-05-11 16:01:35.175][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-05-11 16:01:35.176][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-11 16:01:35.177][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-11 16:01:35.178][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-11 16:01:35.178][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-11 16:01:35.179][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-05-11 16:01:35.180][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-11 16:01:35.181][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-05-11 16:01:35.182][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-11 16:01:35.183][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-05-11 16:01:35.184][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-05-11 16:01:35.185][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-11 16:01:35.186][self$setPropertyValue]
biodb.DEBUG[2024-05-11 16:01:35.186][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-05-11 16:01:35.187][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-05-11 16:01:35.187][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-05-11 16:01:35.187][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-05-11 16:01:35.187][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-05-11 16:01:35.187][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-05-11 16:01:35.188][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-05-11 16:01:35.189][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-11 16:01:35.190][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-11 16:01:35.191][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-11 16:01:35.192][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-11 16:01:35.192][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-11 16:01:35.193][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-11 16:01:35.194][self$setPropertyValue]
biodb.DEBUG[2024-05-11 16:01:35.195][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-11 16:01:35.196][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-11 16:01:35.196][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-05-11 16:01:35.197][self$setPropertyValue]
biodb.DEBUG[2024-05-11 16:01:35.198][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-05-11 16:01:35.200][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-05-11 16:01:35.201][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2024-05-11 16:01:35.202][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-11 16:01:35.203][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-11 16:01:35.203][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-11 16:01:35.204][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-11 16:01:35.205][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-05-11 16:01:35.206][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-11 16:01:35.207][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-05-11 16:01:35.208][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-11 16:01:35.209][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-05-11 16:01:35.210][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-05-11 16:01:35.211][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-11 16:01:35.212][self$setPropertyValue]
biodb.DEBUG[2024-05-11 16:01:35.213][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-05-11 16:01:35.218][self$setPropertyValue]
biodb.DEBUG[2024-05-11 16:01:35.219][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-05-11 16:01:35.220][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-11 16:01:35.221][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-11 16:01:35.222][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-11 16:01:35.222][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-11 16:01:35.223][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-11 16:01:35.224][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-11 16:01:35.225][self$setPropertyValue]
biodb.DEBUG[2024-05-11 16:01:35.226][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-11 16:01:35.227][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-11 16:01:35.227][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-05-11 16:01:35.228][self$setPropertyValue]
biodb.DEBUG[2024-05-11 16:01:35.229][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-05-11 16:01:35.231][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-05-11 16:01:35.232][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-05-11 16:01:35.233][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-11 16:01:35.233][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-11 16:01:35.234][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-11 16:01:35.235][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-11 16:01:35.236][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-05-11 16:01:35.237][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-11 16:01:35.238][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-05-11 16:01:35.238][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-11 16:01:35.239][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-05-11 16:01:35.240][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-05-11 16:01:35.241][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-11 16:01:35.242][self$setPropertyValue]
biodb.DEBUG[2024-05-11 16:01:35.243][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-05-11 16:01:35.244][self$setPropertyValue]
biodb.DEBUG[2024-05-11 16:01:35.244][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-05-11 16:01:35.245][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-11 16:01:35.246][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-11 16:01:35.247][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-11 16:01:35.248][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-11 16:01:35.248][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-11 16:01:35.249][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-11 16:01:35.250][self$setPropertyValue]
biodb.DEBUG[2024-05-11 16:01:35.251][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-11 16:01:35.252][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-11 16:01:35.253][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-05-11 16:01:35.254][self$setPropertyValue]
biodb.DEBUG[2024-05-11 16:01:35.257][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-05-11 16:01:35.258][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:01:35.259][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:01:35.260][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:01:35.261][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-11 16:01:35.261][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-11 16:01:35.262][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:01:35.263][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:01:35.264][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:01:35.264][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-11 16:01:35.265][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-11 16:01:35.266][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:01:35.267][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:01:35.268][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:01:35.268][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-11 16:01:35.269][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-11 16:01:35.270][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:01:35.271][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:01:35.272][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:01:35.273][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-11 16:01:35.274][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-11 16:01:35.274][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:01:35.275][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:01:35.276][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:01:35.277][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-11 16:01:35.278][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-11 16:01:35.279][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:01:35.279][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:01:35.280][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:01:35.281][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-11 16:01:35.282][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-11 16:01:35.283][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:01:35.283][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[2024-05-11 16:01:35.284][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:01:35.285][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-11 16:01:35.286][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-11 16:01:35.287][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:01:35.287][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[2024-05-11 16:01:35.288][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:01:35.289][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-11 16:01:35.290][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-11 16:01:35.291][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:01:35.291][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[2024-05-11 16:01:35.292][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:01:35.293][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-11 16:01:35.294][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-11 16:01:35.294][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:01:35.295][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[2024-05-11 16:01:35.296][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:01:35.297][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-11 16:01:35.298][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-11 16:01:35.299][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:01:35.299][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[2024-05-11 16:01:35.300][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:01:35.301][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-11 16:01:35.302][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-11 16:01:35.302][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:01:35.303][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[2024-05-11 16:01:35.304][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:01:35.305][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-11 16:01:35.306][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-11 16:01:35.306][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:01:35.307][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[2024-05-11 16:01:35.308][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:01:35.309][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-11 16:01:35.310][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-11 16:01:35.310][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:01:35.311][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[2024-05-11 16:01:35.312][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:01:35.313][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-11 16:01:35.314][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-11 16:01:35.314][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:01:35.315][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:01:35.316][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:01:35.317][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-11 16:01:35.318][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-11 16:01:35.318][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:01:35.319][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:01:35.320][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:01:35.321][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-11 16:01:35.321][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-11 16:01:35.322][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:01:35.323][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:01:35.324][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:01:35.325][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-11 16:01:35.325][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-11 16:01:35.326][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:01:35.327][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:01:35.328][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-05-11 16:01:35.332][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-05-11 16:01:35.333][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-05-11 16:01:35.335][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-05-11 16:01:35.336][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-05-11 16:01:35.337][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-05-11 16:01:35.338][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-05-11 16:01:35.339][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-05-11 16:01:35.341][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-05-11 16:01:35.342][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-05-11 16:01:35.343][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-05-11 16:01:35.344][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-05-11 16:01:35.345][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-05-11 16:01:35.347][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-05-11 16:01:35.348][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-05-11 16:01:35.349][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-05-11 16:01:35.351][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-05-11 16:01:35.352][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-05-11 16:01:35.353][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-05-11 16:01:35.354][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-05-11 16:01:35.356][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-05-11 16:01:35.357][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-05-11 16:01:35.358][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-05-11 16:01:35.359][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-05-11 16:01:35.360][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-05-11 16:01:35.362][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-05-11 16:01:35.363][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-05-11 16:01:35.364][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-05-11 16:01:35.365][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-05-11 16:01:35.367][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-05-11 16:01:35.368][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-05-11 16:01:35.369][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-05-11 16:01:35.370][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-05-11 16:01:35.372][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-05-11 16:01:35.373][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-05-11 16:01:35.374][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-05-11 16:01:35.375][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-05-11 16:01:35.376][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-05-11 16:01:35.378][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-05-11 16:01:35.379][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-05-11 16:01:35.380][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-05-11 16:01:35.381][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-05-11 16:01:35.383][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-05-11 16:01:35.384][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-05-11 16:01:35.385][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-05-11 16:01:35.386][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-05-11 16:01:35.387][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-05-11 16:01:35.389][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-05-11 16:01:35.390][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-05-11 16:01:35.396][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-05-11 16:01:35.397][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-05-11 16:01:35.399][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-05-11 16:01:35.400][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-05-11 16:01:35.401][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-05-11 16:01:35.402][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-05-11 16:01:35.403][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-05-11 16:01:35.405][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-05-11 16:01:35.406][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-05-11 16:01:35.407][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-05-11 16:01:35.408][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-05-11 16:01:35.409][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-05-11 16:01:35.411][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-05-11 16:01:35.412][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-05-11 16:01:35.413][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-05-11 16:01:35.414][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-05-11 16:01:35.416][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-05-11 16:01:35.417][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-05-11 16:01:35.418][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-05-11 16:01:35.419][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-05-11 16:01:35.420][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-05-11 16:01:35.422][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-05-11 16:01:35.423][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-05-11 16:01:35.424][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-05-11 16:01:35.425][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-05-11 16:01:35.426][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-05-11 16:01:35.428][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-05-11 16:01:35.429][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-05-11 16:01:35.430][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-05-11 16:01:35.431][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-05-11 16:01:35.432][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-05-11 16:01:35.433][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-05-11 16:01:35.435][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-05-11 16:01:35.436][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-05-11 16:01:35.441][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-05-11 16:01:35.442][initialize] This is biodb version 1.12.0.
biodb.DEBUG[2024-05-11 16:01:35.445][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-05-11 16:01:35.446][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-05-11 16:01:35.447][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-11 16:01:35.447][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:01:35.448][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:01:35.452][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:01:35.453][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-11 16:01:35.454][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-11 16:01:35.455][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-11 16:01:35.456][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-11 16:01:35.456][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:01:35.457][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:01:35.458][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:01:35.459][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-11 16:01:35.460][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-11 16:01:35.460][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-11 16:01:35.461][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-11 16:01:35.462][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:01:35.463][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:01:35.463][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:01:35.464][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-11 16:01:35.465][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-11 16:01:35.466][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-11 16:01:35.466][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-11 16:01:35.467][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:01:35.468][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:01:35.469][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:01:35.470][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-11 16:01:35.470][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-11 16:01:35.471][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-11 16:01:35.472][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-11 16:01:35.473][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:01:35.473][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:01:35.474][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:01:35.475][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-11 16:01:35.476][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-11 16:01:35.477][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-11 16:01:35.477][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-11 16:01:35.478][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:01:35.479][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[2024-05-11 16:01:35.480][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:01:35.481][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-11 16:01:35.481][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-11 16:01:35.482][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-11 16:01:35.483][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-11 16:01:35.484][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:01:35.484][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:01:35.485][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:01:35.486][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-11 16:01:35.487][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-11 16:01:35.487][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-11 16:01:35.488][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-11 16:01:35.489][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:01:35.490][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:01:35.490][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:01:35.491][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-11 16:01:35.492][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-11 16:01:35.493][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-11 16:01:35.494][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-11 16:01:35.494][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:01:35.495][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:01:35.496][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:01:35.497][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-11 16:01:35.497][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-11 16:01:35.498][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-11 16:01:35.499][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-11 16:01:35.500][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:01:35.501][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:01:35.501][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:01:35.502][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-11 16:01:35.503][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-11 16:01:35.504][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-11 16:01:35.504][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-11 16:01:35.505][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:01:35.506][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:01:35.507][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:01:35.508][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-11 16:01:35.508][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-11 16:01:35.509][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-11 16:01:35.510][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-11 16:01:35.511][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:01:35.511][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[2024-05-11 16:01:35.512][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:01:35.513][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-11 16:01:35.514][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-11 16:01:35.515][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-11 16:01:35.515][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-11 16:01:35.516][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:01:35.517][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[2024-05-11 16:01:35.518][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:01:35.518][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-11 16:01:35.519][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-11 16:01:35.520][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-11 16:01:35.521][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-11 16:01:35.522][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:01:35.522][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:01:35.523][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:01:35.524][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-11 16:01:35.525][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-11 16:01:35.525][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-11 16:01:35.526][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-11 16:01:35.527][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:01:35.528][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[2024-05-11 16:01:35.529][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:01:35.529][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-11 16:01:35.530][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-11 16:01:35.531][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-11 16:01:35.532][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-11 16:01:35.532][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:01:35.533][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:01:35.534][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:01:35.535][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-11 16:01:35.536][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-11 16:01:35.536][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-11 16:01:35.537][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-11 16:01:35.538][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:01:35.539][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:01:35.540][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:01:35.540][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-11 16:01:35.541][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-11 16:01:35.542][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-11 16:01:35.543][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-11 16:01:35.543][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:01:35.544][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:01:35.546][biodb$loadDefinitions] Load definitions from file "/Users/biocbuild/bbs-3.19-bioc-longtests/meat/biodbExpasy.Rcheck/biodbExpasy/definitions.yml".
biodb.DEBUG[2024-05-11 16:01:35.555][self$getDbsInfo()$define] Define connector expasy.enzyme.
biodb.DEBUG[2024-05-11 16:01:35.557][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-05-11 16:01:35.558][self$setPropertyValue] Setting property "description" to "Write here the description of this database.".
biodb.DEBUG[2024-05-11 16:01:35.559][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-11 16:01:35.559][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-11 16:01:35.565][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-11 16:01:35.566][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-11 16:01:35.567][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-05-11 16:01:35.567][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-11 16:01:35.568][self$setPropertyValue] Setting property "entry.content.type" to "txt".
biodb.DEBUG[2024-05-11 16:01:35.569][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-11 16:01:35.570][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-05-11 16:01:35.571][self$setPropertyValue] Setting property "name" to "Expasy ENZYME database.".
biodb.DEBUG[2024-05-11 16:01:35.572][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-11 16:01:35.573][self$setPropertyValue] Setting property "parsing.expr" to "^ID\s+([0-9.]+)$".
biodb.DEBUG[2024-05-11 16:01:35.573][self$setPropertyValue] Setting property "parsing.expr" to "^CA\s+(.+?)\.?$".
biodb.DEBUG[2024-05-11 16:01:35.573][self$setPropertyValue] Setting property "parsing.expr" to "^CF\s+(.+?)\.?$".
biodb.DEBUG[2024-05-11 16:01:35.573][self$setPropertyValue] Setting property "parsing.expr" to "^DE\s+(.+?)\.?$".
biodb.DEBUG[2024-05-11 16:01:35.574][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-05-11 16:01:35.574][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-05-11 16:01:35.575][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2024-05-11 16:01:35.576][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-11 16:01:35.577][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-11 16:01:35.578][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-11 16:01:35.579][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-11 16:01:35.579][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-11 16:01:35.580][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-11 16:01:35.581][self$setPropertyValue] Setting property "urls" to "https://enzyme.expasy.org/".
biodb.DEBUG[2024-05-11 16:01:35.582][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-11 16:01:35.583][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-11 16:01:35.584][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-05-11 16:01:35.584][self$setPropertyValue]
biodb.DEBUG[2024-05-11 16:01:35.590][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-05-11 16:01:35.612][super$initialize] Initialize connector expasy.enzyme.
biodb.DEBUG[2024-05-11 16:01:35.613][super$initialize] Register connector expasy.enzyme with the request scheduler
biodb.DEBUG[2024-05-11 16:01:35.617][private$bdb$getRequestScheduler()$re ...] Register connector expasy.enzyme.
biodb.DEBUG[2024-05-11 16:01:35.620][private$addConnectorRules] Create new rule for URL "enzyme.expasy.org" of connector "expasy.enzyme".
biodb.DEBUG[2024-05-11 16:01:35.624][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-05-11 16:01:35.625][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-05-11 16:01:35.626][biodb$getFactory()$createConn] Creating new connector expasy.enzyme for database class expasy.enzyme .
biodb.INFO [2024-05-11 16:01:35.635][biodb::testThat]
biodb.INFO [2024-05-11 16:01:35.636][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2024-05-11 16:01:35.637][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-11 16:01:35.638][biodb::testThat]
biodb.TRACE[2024-05-11 16:01:35.641][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/bbs-3.19-bioc-longtests/meat/biodbExpasy.Rcheck/biodbExpasy/testref/entry-expasy.enzyme-1.1.1.1-content.txt".
biodb.DEBUG[2024-05-11 16:01:35.643][biodb$getFactory()$createEntryFromCo ...] Creating Expasy ENZYME database. entries from 1 content(s).
biodb.DEBUG[2024-05-11 16:01:35.646][biodb$getFactory()$createEntryFromCo ...] Parsing 1 Expasy ENZYME database. entries.
biodb.DEBUG[2024-05-11 16:01:35.653][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-11 16:01:35.654][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-11 16:01:35.655][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-11 16:01:35.668][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-11 16:01:35.669][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-11 16:01:35.670][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:01:35.671][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-11 16:01:35.680][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-11 16:01:35.682][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-11 16:01:35.682][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:35.683][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:01:35.706][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-05-11 16:01:35.718][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-05-11 16:01:35.719][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:35.720][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:01:35.721][self$getBiodb()$getEntryFields()$get] Asked field names are: cofactor.
biodb.TRACE[2024-05-11 16:01:35.722][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-05-11 16:01:35.723][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:35.723][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:01:35.725][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-11 16:01:35.726][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-11 16:01:35.726][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:35.727][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:01:35.728][self$getBiodb()$getEntryFields()$get] Asked field names are: COFACTOR.
biodb.TRACE[2024-05-11 16:01:35.729][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-05-11 16:01:35.730][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:35.731][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:01:35.732][self$getBiodb()$getEntryFields()$get] Asked field names are: cofactor.
biodb.TRACE[2024-05-11 16:01:35.733][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-05-11 16:01:35.734][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:35.735][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:01:35.735][self$getBiodb()$getEntryFields()$get] Asked field names are: cofactor.
biodb.TRACE[2024-05-11 16:01:35.736][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-05-11 16:01:35.737][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:35.738][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:01:35.739][self$getBiodb()$getEntryFields()$get] Asked field names are: cofactor.
biodb.TRACE[2024-05-11 16:01:35.740][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-05-11 16:01:35.741][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:35.742][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:01:35.743][self$getBiodb()$getEntryFields()$get] Asked field names are: COFACTOR.
biodb.TRACE[2024-05-11 16:01:35.744][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-05-11 16:01:35.744][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:35.745][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:01:35.770][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-11 16:01:35.771][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-11 16:01:35.772][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:35.773][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:01:35.774][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-11 16:01:35.775][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-11 16:01:35.776][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:35.776][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:01:35.806][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-11 16:01:35.807][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-11 16:01:35.808][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:35.809][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:01:35.810][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-11 16:01:35.810][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-11 16:01:35.811][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:35.812][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:01:35.813][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-11 16:01:35.814][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-11 16:01:35.815][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:35.816][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:01:35.817][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-05-11 16:01:35.818][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-05-11 16:01:35.819][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:35.819][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:01:35.820][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-05-11 16:01:35.821][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-05-11 16:01:35.822][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:35.823][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:01:35.824][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-11 16:01:35.825][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-11 16:01:35.826][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:35.826][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:01:35.827][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-05-11 16:01:35.829][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-05-11 16:01:35.829][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:35.830][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:01:35.831][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-11 16:01:35.832][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-11 16:01:35.833][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:35.834][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:01:35.835][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-11 16:01:35.836][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-11 16:01:35.837][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:35.837][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:01:35.838][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-11 16:01:35.839][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-11 16:01:35.840][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:35.841][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:01:35.842][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-11 16:01:35.843][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-11 16:01:35.844][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:35.844][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:01:35.845][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-11 16:01:35.846][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-11 16:01:35.847][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:35.848][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:01:35.849][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-11 16:01:35.850][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-11 16:01:35.850][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:35.851][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-11 16:01:35.852][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 1.1.1.1.
biodb.TRACE[2024-05-11 16:01:35.855][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-05-11 16:01:35.856][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-05-11 16:01:35.856][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:35.857][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:01:35.858][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-05-11 16:01:35.859][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-05-11 16:01:35.860][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:35.861][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:01:35.862][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-05-11 16:01:35.863][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-05-11 16:01:35.863][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:35.864][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:01:35.865][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-05-11 16:01:35.866][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-05-11 16:01:35.867][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:35.868][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:01:35.883][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-11 16:01:35.884][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-11 16:01:35.885][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:35.886][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:01:35.929][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-05-11 16:01:35.930][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-05-11 16:01:35.931][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:35.932][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:01:35.937][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-11 16:01:35.938][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-11 16:01:35.939][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:35.940][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:01:35.941][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-11 16:01:35.942][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-11 16:01:35.942][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:35.943][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:01:35.944][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-11 16:01:35.945][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-11 16:01:35.946][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:35.947][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:01:35.949][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-11 16:01:35.950][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-11 16:01:35.951][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:35.952][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:01:35.952][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-11 16:01:35.953][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-11 16:01:35.954][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:35.955][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:01:35.956][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-11 16:01:35.957][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-11 16:01:35.958][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:35.958][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:01:35.960][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-05-11 16:01:35.961][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-05-11 16:01:35.961][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:35.962][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:01:35.963][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-05-11 16:01:35.964][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-05-11 16:01:35.965][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:35.966][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:01:35.967][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-05-11 16:01:35.968][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-05-11 16:01:35.968][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:35.969][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:01:35.977][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-11 16:01:35.979][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-11 16:01:35.979][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:35.980][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:01:35.981][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-11 16:01:35.982][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-11 16:01:35.983][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:35.984][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:01:35.985][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-11 16:01:35.986][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-11 16:01:35.987][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:35.987][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:01:35.988][ef$get] Asked field names are: accession.
biodb.TRACE[2024-05-11 16:01:35.989][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-11 16:01:35.990][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:35.991][ef$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:01:35.992][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-11 16:01:35.993][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-11 16:01:35.994][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:35.995][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:01:36.004][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-11 16:01:36.005][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-11 16:01:36.006][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:36.007][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:01:36.008][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-11 16:01:36.009][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-11 16:01:36.010][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:36.010][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:01:36.011][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-11 16:01:36.012][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-11 16:01:36.013][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:36.014][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:01:36.015][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-11 16:01:36.016][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-11 16:01:36.017][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:36.017][ef$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:01:36.018][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-11 16:01:36.019][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-11 16:01:36.020][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:36.021][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:01:36.030][self$getBiodb()$getEntryFields()$get] Asked field names are: cofactor.
biodb.TRACE[2024-05-11 16:01:36.031][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-05-11 16:01:36.032][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:36.033][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:01:36.034][self$getBiodb()$getEntryFields()$get] Asked field names are: cofactor.
biodb.TRACE[2024-05-11 16:01:36.035][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-05-11 16:01:36.036][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:36.037][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:01:36.037][self$getBiodb()$getEntryFields()$get] Asked field names are: cofactor.
biodb.TRACE[2024-05-11 16:01:36.038][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-05-11 16:01:36.039][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:36.040][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:01:36.041][ef$get] Asked field names are: cofactor.
biodb.TRACE[2024-05-11 16:01:36.042][ef$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-05-11 16:01:36.043][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:36.044][ef$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:01:36.045][self$getBiodb()$getEntryFields()$get] Asked field names are: cofactor.
biodb.TRACE[2024-05-11 16:01:36.046][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-05-11 16:01:36.046][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:36.047][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:01:36.056][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-05-11 16:01:36.057][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-05-11 16:01:36.058][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:36.059][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:01:36.060][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-05-11 16:01:36.061][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-05-11 16:01:36.062][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:36.062][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:01:36.063][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-05-11 16:01:36.064][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-05-11 16:01:36.065][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:36.066][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:01:36.067][ef$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-05-11 16:01:36.068][ef$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-05-11 16:01:36.069][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:36.070][ef$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:01:36.070][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-05-11 16:01:36.072][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-05-11 16:01:36.073][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:36.073][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:01:36.083][ef$get] Asked field names are: accession.
biodb.TRACE[2024-05-11 16:01:36.089][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-11 16:01:36.090][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:36.091][ef$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:01:36.096][ef$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-05-11 16:01:36.097][ef$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-05-11 16:01:36.097][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:36.098][ef$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:01:36.103][ef$get] Asked field names are: cofactor.
biodb.TRACE[2024-05-11 16:01:36.104][ef$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-05-11 16:01:36.105][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:36.106][ef$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:01:36.111][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-11 16:01:36.112][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-11 16:01:36.113][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:36.114][ef$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:01:36.130][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/bbs-3.19-bioc-longtests/meat/biodbExpasy.Rcheck/biodbExpasy/testref/entry-expasy.enzyme-1.1.1.54-content.txt".
biodb.DEBUG[2024-05-11 16:01:36.161][biodb$getFactory()$createEntryFromCo ...] Creating Expasy ENZYME database. entries from 1 content(s).
biodb.DEBUG[2024-05-11 16:01:36.162][biodb$getFactory()$createEntryFromCo ...] Parsing 1 Expasy ENZYME database. entries.
biodb.DEBUG[2024-05-11 16:01:36.164][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-11 16:01:36.165][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-11 16:01:36.165][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-11 16:01:36.171][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-11 16:01:36.171][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-11 16:01:36.172][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:01:36.173][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-11 16:01:36.175][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-11 16:01:36.176][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-11 16:01:36.177][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:36.178][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:01:36.179][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-05-11 16:01:36.180][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-05-11 16:01:36.181][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:36.182][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:01:36.183][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-11 16:01:36.184][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-11 16:01:36.185][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:36.186][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:01:36.187][self$getBiodb()$getEntryFields()$get] Asked field names are: COFACTOR.
biodb.TRACE[2024-05-11 16:01:36.188][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-05-11 16:01:36.188][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:36.189][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:01:36.190][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-05-11 16:01:36.191][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-05-11 16:01:36.192][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:36.193][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:01:36.194][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-05-11 16:01:36.195][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-05-11 16:01:36.196][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:36.197][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:01:36.197][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-11 16:01:36.198][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-11 16:01:36.199][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:36.200][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:01:36.201][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-05-11 16:01:36.202][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-05-11 16:01:36.203][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:36.204][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:01:36.205][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-11 16:01:36.206][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-11 16:01:36.206][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:36.207][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:01:36.208][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-11 16:01:36.209][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-11 16:01:36.210][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:36.211][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:01:36.212][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-11 16:01:36.212][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-11 16:01:36.213][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:36.214][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:01:36.215][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-11 16:01:36.216][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-11 16:01:36.217][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:36.218][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:01:36.219][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-11 16:01:36.220][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-11 16:01:36.221][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:36.222][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:01:36.223][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-11 16:01:36.223][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-11 16:01:36.224][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:36.225][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-11 16:01:36.226][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 1.1.1.54.
biodb.TRACE[2024-05-11 16:01:36.249][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-05-11 16:01:36.250][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-05-11 16:01:36.251][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:36.251][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:01:36.252][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-05-11 16:01:36.253][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-05-11 16:01:36.254][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:36.255][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:01:36.256][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-05-11 16:01:36.257][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-05-11 16:01:36.258][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:36.259][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:01:36.259][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-05-11 16:01:36.260][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-05-11 16:01:36.261][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:36.262][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:01:36.263][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-11 16:01:36.264][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-11 16:01:36.265][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:36.266][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:01:36.271][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-05-11 16:01:36.272][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-05-11 16:01:36.273][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:36.274][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:01:36.280][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-11 16:01:36.281][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-11 16:01:36.282][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:36.283][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:01:36.284][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-11 16:01:36.285][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-11 16:01:36.285][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:36.286][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:01:36.287][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-11 16:01:36.288][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-11 16:01:36.289][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:36.290][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:01:36.292][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-11 16:01:36.293][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-11 16:01:36.294][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:36.295][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:01:36.296][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-11 16:01:36.297][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-11 16:01:36.298][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:36.298][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:01:36.299][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-11 16:01:36.300][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-11 16:01:36.301][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:36.302][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:01:36.303][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-05-11 16:01:36.304][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-05-11 16:01:36.305][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:36.306][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:01:36.307][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-05-11 16:01:36.308][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-05-11 16:01:36.309][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:36.310][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:01:36.310][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-05-11 16:01:36.311][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-05-11 16:01:36.312][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:36.313][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:01:36.330][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-11 16:01:36.331][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-11 16:01:36.332][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:36.333][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:01:36.334][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-11 16:01:36.335][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-11 16:01:36.336][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:36.336][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:01:36.337][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-11 16:01:36.338][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-11 16:01:36.339][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:36.340][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:01:36.341][ef$get] Asked field names are: accession.
biodb.TRACE[2024-05-11 16:01:36.342][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-11 16:01:36.343][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:36.344][ef$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:01:36.344][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-11 16:01:36.345][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-11 16:01:36.346][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:36.347][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:01:36.356][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-11 16:01:36.357][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-11 16:01:36.358][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:36.359][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:01:36.360][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-11 16:01:36.361][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-11 16:01:36.362][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:36.362][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:01:36.363][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-11 16:01:36.364][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-11 16:01:36.365][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:36.366][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:01:36.367][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-11 16:01:36.368][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-11 16:01:36.369][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:36.369][ef$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:01:36.370][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-11 16:01:36.371][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-11 16:01:36.372][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:36.373][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:01:36.387][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-05-11 16:01:36.388][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-05-11 16:01:36.389][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:36.390][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:01:36.390][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-05-11 16:01:36.391][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-05-11 16:01:36.393][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:36.393][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:01:36.394][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-05-11 16:01:36.395][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-05-11 16:01:36.396][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:36.397][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:01:36.398][ef$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-05-11 16:01:36.399][ef$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-05-11 16:01:36.400][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:36.401][ef$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:01:36.401][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-05-11 16:01:36.402][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-05-11 16:01:36.403][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:36.404][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:01:36.413][ef$get] Asked field names are: accession.
biodb.TRACE[2024-05-11 16:01:36.414][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-11 16:01:36.415][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:36.416][ef$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:01:36.422][ef$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-05-11 16:01:36.423][ef$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-05-11 16:01:36.424][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:36.426][ef$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:01:36.432][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-11 16:01:36.433][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-11 16:01:36.434][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:36.435][ef$get] fields variable is a list.
biodb.INFO [2024-05-11 16:01:36.445][biodb::testThat]
biodb.INFO [2024-05-11 16:01:36.446][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2024-05-11 16:01:36.446][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-11 16:01:36.447][biodb::testThat]
biodb.DEBUG[2024-05-11 16:01:36.449][private$loadEntries] Creating entries from ids [2]: "1.1.1.1, 1.1.1.54".
biodb.DEBUG[2024-05-11 16:01:36.456][conn$getEntryContent] Get Expasy ENZYME database. entry content(s) for 2 id(s)...
biodb.TRACE[2024-05-11 16:01:36.462][cch$loadFileContent] Trying to load 2 files from cache: [2]: "1.1.1.1, 1.1.1.54".
biodb.INFO [2024-05-11 16:01:36.463][self$getFolderPath] Create cache folder "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280" for "expasy.enzyme-b59b84d962b6741050ba8f70ff4db280".
biodb.TRACE[2024-05-11 16:01:36.464][cch$loadFileContent] file.exist = [2]: "FALSE, FALSE".
biodb.TRACE[2024-05-11 16:01:36.465][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-05-11 16:01:36.466][conn$getEntryContent] 0 Expasy ENZYME database. entry content(s) loaded from cache.
biodb.DEBUG[2024-05-11 16:01:36.467][conn$getEntryContent] 2 entry content(s) need to be fetched from Expasy ENZYME database. database "https://enzyme.expasy.org/".
biodb.DEBUG[2024-05-11 16:01:36.468][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-05-11 16:01:36.469][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-05-11 16:01:36.473][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-11 16:01:36.474][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-11 16:01:36.475][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-11 16:01:36.480][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-11 16:01:36.481][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-11 16:01:36.482][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:01:36.483][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:01:36.484][scheduler$sendRequest] Getting content of get URL request "https://enzyme.expasy.org/EC/1.1.1.1.txt".
biodb.DEBUG[2024-05-11 16:01:36.502][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-11 16:01:36.503][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-11 16:01:36.504][private$doSendRequestOnce] Sent URL is "https://enzyme.expasy.org/EC/1.1.1.1.txt".
biodb.TRACE[2024-05-11 16:01:43.688][getRCurlRequestResult] Using RCurl package for sending request (https://enzyme.expasy.org/EC/1.1.1.1.txt).
biodb.DEBUG[2024-05-11 16:01:44.466][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-05-11 16:01:44.469][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280/a52675cfd2f0c2b41556caa64d9341e3.content"
biodb.TRACE[2024-05-11 16:01:44.481][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280/a52675cfd2f0c2b41556caa64d9341e3.request"
biodb.DEBUG[2024-05-11 16:01:44.483][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-11 16:01:44.484][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-11 16:01:44.484][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-11 16:01:44.489][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-11 16:01:44.490][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-11 16:01:44.491][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:01:44.492][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[2024-05-11 16:01:44.510][scheduler$sendRequest] Getting content of get URL request "https://enzyme.expasy.org/EC/1.1.1.54.txt".
biodb.DEBUG[2024-05-11 16:01:44.531][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-11 16:01:44.532][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-11 16:01:44.545][private$doSendRequestOnce] Sent URL is "https://enzyme.expasy.org/EC/1.1.1.54.txt".
biodb.TRACE[2024-05-11 16:01:45.281][getRCurlRequestResult] Using RCurl package for sending request (https://enzyme.expasy.org/EC/1.1.1.54.txt).
biodb.DEBUG[2024-05-11 16:01:45.826][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-05-11 16:01:45.828][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280/a9b93566a091cbe35a06e4b3871f95c9.content"
biodb.TRACE[2024-05-11 16:01:45.831][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280/a9b93566a091cbe35a06e4b3871f95c9.request"
biodb.TRACE[2024-05-11 16:01:45.833][private$doSaveContentToFile] Saving to cache [2]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280/1.1.1.1.txt, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280/1.1.1.54.txt"
biodb.DEBUG[2024-05-11 16:01:45.835][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-05-11 16:01:45.836][self$createEntryFromContent] Creating Expasy ENZYME database. entries from 2 content(s).
biodb.DEBUG[2024-05-11 16:01:45.837][self$createEntryFromContent] Parsing 2 Expasy ENZYME database. entries.
biodb.DEBUG[2024-05-11 16:01:45.838][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-11 16:01:45.839][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-11 16:01:45.840][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-11 16:01:45.845][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-11 16:01:45.846][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-11 16:01:45.847][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:01:45.847][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-11 16:01:45.850][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-11 16:01:45.851][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-11 16:01:45.852][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:45.852][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:01:45.853][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-05-11 16:01:45.854][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-05-11 16:01:45.855][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:45.856][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:01:45.857][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-11 16:01:45.858][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-11 16:01:45.859][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:45.860][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:01:45.861][self$getBiodb()$getEntryFields()$get] Asked field names are: COFACTOR.
biodb.TRACE[2024-05-11 16:01:45.862][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-05-11 16:01:45.862][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:45.863][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:01:45.864][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-11 16:01:45.865][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-11 16:01:45.866][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:45.867][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:01:45.868][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-11 16:01:45.869][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-11 16:01:45.869][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:45.870][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:01:45.871][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-11 16:01:45.872][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-11 16:01:45.873][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:45.874][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:01:45.875][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-11 16:01:45.876][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-11 16:01:45.876][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:45.877][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:01:45.878][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-11 16:01:45.879][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-11 16:01:45.880][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:45.881][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:01:45.882][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-05-11 16:01:45.882][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-05-11 16:01:45.883][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:45.884][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:01:45.885][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-05-11 16:01:45.886][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-05-11 16:01:45.887][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:45.888][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:01:45.888][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-11 16:01:45.889][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-11 16:01:45.890][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:45.891][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:01:45.892][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-05-11 16:01:45.893][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-05-11 16:01:45.894][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:45.894][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:01:45.895][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-11 16:01:45.896][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-11 16:01:45.897][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:45.898][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:01:45.899][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-11 16:01:45.899][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-11 16:01:45.900][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:45.901][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:01:45.902][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-11 16:01:45.903][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-11 16:01:45.904][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:45.909][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-11 16:01:45.912][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-11 16:01:45.913][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-11 16:01:45.914][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-11 16:01:45.919][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-11 16:01:45.919][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-11 16:01:45.920][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:01:45.921][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-11 16:01:45.923][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-11 16:01:45.924][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-11 16:01:45.925][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:45.925][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:01:45.926][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-05-11 16:01:45.927][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-05-11 16:01:45.928][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:45.929][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:01:45.930][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-11 16:01:45.931][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-11 16:01:45.932][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:45.932][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:01:45.933][self$getBiodb()$getEntryFields()$get] Asked field names are: COFACTOR.
biodb.TRACE[2024-05-11 16:01:45.934][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-05-11 16:01:45.935][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:45.936][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:01:45.937][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-05-11 16:01:45.938][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-05-11 16:01:45.939][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:45.940][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:01:45.940][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-05-11 16:01:45.941][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-05-11 16:01:45.942][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:45.943][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:01:45.944][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-11 16:01:45.945][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-11 16:01:45.946][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:45.946][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:01:45.947][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-05-11 16:01:45.948][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-05-11 16:01:45.949][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:45.950][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:01:45.951][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-11 16:01:45.952][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-11 16:01:45.953][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:45.953][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:01:45.954][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-11 16:01:45.955][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-11 16:01:45.956][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:45.957][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:01:45.958][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-11 16:01:45.959][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-11 16:01:45.960][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:45.960][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:01:45.962][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-11 16:01:45.962][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-11 16:01:45.963][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:45.964][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:01:45.965][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-11 16:01:45.966][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-11 16:01:45.967][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:45.968][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:01:45.968][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-11 16:01:45.969][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-11 16:01:45.970][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:45.971][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:01:45.972][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-11 16:01:45.973][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-11 16:01:45.974][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:45.974][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:01:45.975][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-11 16:01:45.976][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-11 16:01:45.977][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:45.978][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:01:45.979][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-11 16:01:45.980][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-11 16:01:45.980][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:45.981][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-11 16:01:45.982][self$createEntryFromContent] Accession numbers: 1.1.1.1, 1.1.1.54.
biodb.TRACE[2024-05-11 16:01:45.983][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2024-05-11 16:01:45.984][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2024-05-11 16:01:45.985][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:45.986][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:01:45.987][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2024-05-11 16:01:45.988][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2024-05-11 16:01:45.988][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:45.989][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:01:45.990][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2024-05-11 16:01:45.991][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2024-05-11 16:01:45.992][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:45.993][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:01:45.998][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2024-05-11 16:01:45.999][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2024-05-11 16:01:46.000][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:46.001][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:01:46.002][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2024-05-11 16:01:46.003][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2024-05-11 16:01:46.003][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:46.004][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:01:46.005][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2024-05-11 16:01:46.006][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2024-05-11 16:01:46.007][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:46.008][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-05-11 16:01:46.016][biodb::testThat]
biodb.INFO [2024-05-11 16:01:46.017][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2024-05-11 16:01:46.018][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-11 16:01:46.019][biodb::testThat]
biodb.TRACE[2024-05-11 16:01:46.021][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-11 16:01:46.022][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-11 16:01:46.023][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:46.024][ef$get] fields variable is a list.
biodb.DEBUG[2024-05-11 16:01:46.025][function(conn, opt)] Testing searchForEntries() with entry "1.1.1.1" and field "name".
biodb.TRACE[2024-05-11 16:01:46.055][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-11 16:01:46.056][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-11 16:01:46.057][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:46.058][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:01:46.058][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-11 16:01:46.059][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-11 16:01:46.060][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:46.061][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:01:46.062][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-11 16:01:46.063][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-11 16:01:46.064][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:46.065][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-11 16:01:46.068][function(conn, opt)] With value "alcohol dehydrogenase".
biodb.DEBUG[2024-05-11 16:01:46.070][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://enzyme.expasy.org/enzyme-byname.html?alcohol dehydrogenase".
biodb.DEBUG[2024-05-11 16:01:46.072][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-11 16:01:46.073][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-11 16:01:46.074][private$doSendRequestOnce] Sent URL is "https://enzyme.expasy.org/enzyme-byname.html?alcohol%20dehydrogenase".
biodb.TRACE[2024-05-11 16:01:46.726][getRCurlRequestResult] Using RCurl package for sending request (https://enzyme.expasy.org/enzyme-byname.html?alcohol%20dehydrogenase).
biodb.DEBUG[2024-05-11 16:01:47.399][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-05-11 16:01:47.401][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280/f603fa2a57aec59588edc37541c6f6d5.content"
biodb.TRACE[2024-05-11 16:01:47.405][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280/f603fa2a57aec59588edc37541c6f6d5.request"
biodb.DEBUG[2024-05-11 16:01:47.410][function(conn, opt)] With found IDs [1]: "1.1.1.1".
biodb.INFO [2024-05-11 16:01:47.426][biodb::testThat]
biodb.INFO [2024-05-11 16:01:47.427][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2024-05-11 16:01:47.428][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-11 16:01:47.428][biodb::testThat]
biodb.TRACE[2024-05-11 16:01:47.450][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-11 16:01:47.451][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-11 16:01:47.452][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:47.453][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:01:47.454][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-11 16:01:47.455][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-11 16:01:47.456][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:47.457][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:01:47.458][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-11 16:01:47.459][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-11 16:01:47.459][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:47.460][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-11 16:01:47.492][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://enzyme.expasy.org/enzyme-byname.html?alcohol dehydrogenase".
biodb.DEBUG[2024-05-11 16:01:47.494][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-05-11 16:01:47.507][cch$loadFileContent] Trying to load 1 files from cache: [1]: "f603fa2a57aec59588edc37541c6f6d5".
biodb.TRACE[2024-05-11 16:01:47.509][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-05-11 16:01:47.510][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280/f603fa2a57aec59588edc37541c6f6d5.content".
biodb.INFO [2024-05-11 16:01:47.528][biodb::testThat]
biodb.INFO [2024-05-11 16:01:47.529][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2024-05-11 16:01:47.530][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-11 16:01:47.530][biodb::testThat]
biodb.TRACE[2024-05-11 16:01:47.540][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-05-11 16:01:47.541][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-05-11 16:01:47.542][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:47.543][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:01:47.543][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-05-11 16:01:47.544][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-05-11 16:01:47.545][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:47.546][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:01:47.547][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-05-11 16:01:47.548][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-05-11 16:01:47.549][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:47.550][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:01:47.551][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-05-11 16:01:47.551][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-05-11 16:01:47.552][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:47.553][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:01:47.586][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-05-11 16:01:47.587][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-05-11 16:01:47.588][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:47.589][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:01:47.590][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-05-11 16:01:47.590][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-05-11 16:01:47.591][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:47.592][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:01:47.593][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-05-11 16:01:47.594][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-05-11 16:01:47.595][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:47.596][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:01:47.596][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-05-11 16:01:47.597][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-05-11 16:01:47.598][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:47.599][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-05-11 16:01:47.605][biodb::testThat]
biodb.INFO [2024-05-11 16:01:47.606][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2024-05-11 16:01:47.607][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-11 16:01:47.608][biodb::testThat]
biodb.INFO [2024-05-11 16:01:47.617][biodb::testThat]
biodb.INFO [2024-05-11 16:01:47.618][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2024-05-11 16:01:47.619][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-11 16:01:47.620][biodb::testThat]
biodb.INFO [2024-05-11 16:01:47.627][biodb::testThat]
biodb.INFO [2024-05-11 16:01:47.628][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2024-05-11 16:01:47.629][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-11 16:01:47.630][biodb::testThat]
biodb.DEBUG[2024-05-11 16:01:47.642][function(conn, opt)] Trying to download "https://enzyme.expasy.org/cgi-bin/enzyme/enzyme-search-ec?field1=1&field2=1&field3=1&field4=1".
biodb.DEBUG[2024-05-11 16:01:48.263][getUrlContent] Use RCurl for downloading content of URL https://enzyme.expasy.org/cgi-bin/enzyme/enzyme-search-ec?field1=1&field2=1&field3=1&field4=1.
biodb.INFO [2024-05-11 16:01:48.902][biodb::testThat]
biodb.INFO [2024-05-11 16:01:48.903][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2024-05-11 16:01:48.904][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-11 16:01:48.905][biodb::testThat]
biodb.DEBUG[2024-05-11 16:01:50.495][getUrlContent] Use RCurl for downloading content of URL https://enzyme.expasy.org/images/1.1.1.1/image.png.
biodb.TRACE[2024-05-11 16:01:50.778][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-11 16:01:50.779][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-11 16:01:50.780][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:50.785][ef$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:01:50.786][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-11 16:01:50.787][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-11 16:01:50.788][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:50.789][ef$get] fields variable is a list.
biodb.INFO [2024-05-11 16:01:50.790][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-05-11 16:01:50.791][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector expasy.enzyme from the request scheduler
biodb.INFO [2024-05-11 16:01:50.792][self$deleteConn] Connector "expasy.enzyme" deleted.
biodb.DEBUG[2024-05-11 16:01:50.793][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-05-11 16:01:50.793][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-11 16:01:50.794][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-11 16:01:50.795][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-11 16:01:50.795][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-11 16:01:50.796][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:01:50.797][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2024-05-11 16:01:50.805][biodb::testContext]
biodb.INFO [2024-05-11 16:01:50.806][biodb::testContext] ********************************************************************************
biodb.INFO [2024-05-11 16:01:50.806][biodb::testContext] Test context - Example long tests
biodb.INFO [2024-05-11 16:01:50.807][biodb::testContext] ********************************************************************************
biodb.INFO [2024-05-11 16:01:50.817][biodb::testContext]
biodb.INFO [2024-05-11 16:01:50.819][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.12.0.
biodb.DEBUG[2024-05-11 16:01:50.821][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2024-05-11 16:01:50.824][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-05-11 16:01:50.825][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-05-11 16:01:50.826][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-05-11 16:01:50.826][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:01:50.827][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:01:50.828][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:01:50.828][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-05-11 16:01:50.829][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-05-11 16:01:50.830][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:01:50.831][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:01:50.831][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:01:50.832][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-05-11 16:01:50.833][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-05-11 16:01:50.834][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:01:50.834][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:01:50.835][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:01:50.836][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-05-11 16:01:50.837][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-05-11 16:01:50.837][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-05-11 16:01:50.838][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:01:50.839][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:01:50.840][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:01:50.840][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-05-11 16:01:50.841][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-05-11 16:01:50.842][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-05-11 16:01:50.843][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:01:50.844][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:01:50.844][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:01:50.845][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-05-11 16:01:50.846][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-05-11 16:01:50.847][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:01:50.848][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:01:50.849][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:01:50.849][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-05-11 16:01:50.850][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-05-11 16:01:50.851][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-05-11 16:01:50.852][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:01:50.853][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:01:50.853][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:01:50.854][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-05-11 16:01:50.855][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-05-11 16:01:50.856][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:01:50.857][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:01:50.857][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:01:50.858][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-05-11 16:01:50.859][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-05-11 16:01:50.860][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-05-11 16:01:50.861][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:01:50.861][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:01:50.862][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:01:50.863][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-05-11 16:01:50.864][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-05-11 16:01:50.865][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-05-11 16:01:50.865][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-05-11 16:01:50.866][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-05-11 16:01:50.867][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-05-11 16:01:50.868][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:01:50.868][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:01:50.869][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:01:50.870][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-05-11 16:01:50.871][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-05-11 16:01:50.872][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:01:50.872][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:01:50.873][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:01:50.874][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-05-11 16:01:50.875][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-05-11 16:01:50.875][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:01:50.876][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:01:50.877][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:01:50.878][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-05-11 16:01:50.878][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-05-11 16:01:50.879][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:01:50.880][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:01:50.881][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:01:50.882][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-05-11 16:01:50.882][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-05-11 16:01:50.883][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:01:50.884][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:01:50.885][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:01:50.885][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-05-11 16:01:50.886][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-05-11 16:01:50.887][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:01:50.888][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:01:50.888][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:01:50.889][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-05-11 16:01:50.890][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-05-11 16:01:50.907][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-05-11 16:01:50.908][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:01:50.909][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:01:50.910][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:01:50.911][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-05-11 16:01:50.911][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-05-11 16:01:50.912][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-05-11 16:01:50.913][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:01:50.914][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:01:50.915][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:01:50.915][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-05-11 16:01:50.917][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-05-11 16:01:50.918][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2024-05-11 16:01:50.919][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-11 16:01:50.919][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-11 16:01:50.920][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-11 16:01:50.921][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-11 16:01:50.922][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-05-11 16:01:50.923][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-11 16:01:50.923][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-05-11 16:01:50.924][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-11 16:01:50.925][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-05-11 16:01:50.926][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-05-11 16:01:50.928][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-11 16:01:50.928][self$setPropertyValue]
biodb.DEBUG[2024-05-11 16:01:50.929][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-05-11 16:01:50.930][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-05-11 16:01:50.930][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-05-11 16:01:50.930][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-05-11 16:01:50.930][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-05-11 16:01:50.930][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-05-11 16:01:50.931][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-05-11 16:01:50.932][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-11 16:01:50.933][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-11 16:01:50.933][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-11 16:01:50.934][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-11 16:01:50.939][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-11 16:01:50.940][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-11 16:01:50.941][self$setPropertyValue]
biodb.DEBUG[2024-05-11 16:01:50.941][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-11 16:01:50.942][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-11 16:01:50.943][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-05-11 16:01:50.944][self$setPropertyValue]
biodb.DEBUG[2024-05-11 16:01:50.945][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-05-11 16:01:50.946][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-05-11 16:01:50.947][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-05-11 16:01:50.948][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-11 16:01:50.948][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-11 16:01:50.949][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-11 16:01:50.950][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-11 16:01:50.951][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-05-11 16:01:50.952][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-11 16:01:50.952][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-05-11 16:01:50.953][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-11 16:01:50.954][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-05-11 16:01:50.955][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-05-11 16:01:50.956][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-11 16:01:50.957][self$setPropertyValue]
biodb.DEBUG[2024-05-11 16:01:50.957][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-05-11 16:01:50.958][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-05-11 16:01:50.958][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-05-11 16:01:50.958][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-05-11 16:01:50.958][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-05-11 16:01:50.958][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-05-11 16:01:50.959][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-05-11 16:01:50.960][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-11 16:01:50.961][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-11 16:01:50.961][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-11 16:01:50.962][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-11 16:01:50.963][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-11 16:01:50.964][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-11 16:01:50.964][self$setPropertyValue]
biodb.DEBUG[2024-05-11 16:01:50.965][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-11 16:01:50.966][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-11 16:01:50.967][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-05-11 16:01:50.967][self$setPropertyValue]
biodb.DEBUG[2024-05-11 16:01:50.968][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-05-11 16:01:50.970][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-05-11 16:01:50.971][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2024-05-11 16:01:50.972][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-11 16:01:50.973][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-11 16:01:50.973][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-11 16:01:50.974][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-11 16:01:50.975][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-05-11 16:01:50.976][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-11 16:01:50.977][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-05-11 16:01:50.978][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-11 16:01:50.979][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-05-11 16:01:50.979][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-05-11 16:01:50.980][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-11 16:01:50.981][self$setPropertyValue]
biodb.DEBUG[2024-05-11 16:01:50.982][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-05-11 16:01:50.983][self$setPropertyValue]
biodb.DEBUG[2024-05-11 16:01:50.984][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-05-11 16:01:50.984][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-11 16:01:50.985][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-11 16:01:50.986][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-11 16:01:50.987][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-11 16:01:50.987][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-11 16:01:50.988][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-11 16:01:50.989][self$setPropertyValue]
biodb.DEBUG[2024-05-11 16:01:50.990][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-11 16:01:50.990][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-11 16:01:50.991][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-05-11 16:01:50.992][self$setPropertyValue]
biodb.DEBUG[2024-05-11 16:01:50.993][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-05-11 16:01:50.994][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-05-11 16:01:50.995][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-05-11 16:01:50.996][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-11 16:01:50.997][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-11 16:01:50.997][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-11 16:01:50.998][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-11 16:01:50.999][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-05-11 16:01:51.000][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-11 16:01:51.001][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-05-11 16:01:51.001][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-11 16:01:51.002][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-05-11 16:01:51.003][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-05-11 16:01:51.004][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-11 16:01:51.005][self$setPropertyValue]
biodb.DEBUG[2024-05-11 16:01:51.006][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-05-11 16:01:51.006][self$setPropertyValue]
biodb.DEBUG[2024-05-11 16:01:51.007][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-05-11 16:01:51.008][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-11 16:01:51.009][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-11 16:01:51.009][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-11 16:01:51.010][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-11 16:01:51.011][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-11 16:01:51.012][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-11 16:01:51.012][self$setPropertyValue]
biodb.DEBUG[2024-05-11 16:01:51.013][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-11 16:01:51.014][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-11 16:01:51.015][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-05-11 16:01:51.015][self$setPropertyValue]
biodb.DEBUG[2024-05-11 16:01:51.016][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-05-11 16:01:51.017][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:01:51.018][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:01:51.019][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:01:51.019][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-11 16:01:51.020][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-11 16:01:51.021][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:01:51.021][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:01:51.022][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:01:51.023][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-11 16:01:51.024][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-11 16:01:51.024][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:01:51.025][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:01:51.026][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:01:51.027][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-11 16:01:51.027][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-11 16:01:51.028][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:01:51.029][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:01:51.029][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:01:51.030][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-11 16:01:51.031][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-11 16:01:51.032][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:01:51.032][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:01:51.033][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:01:51.034][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-11 16:01:51.034][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-11 16:01:51.039][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:01:51.040][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:01:51.041][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:01:51.041][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-11 16:01:51.042][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-11 16:01:51.043][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:01:51.043][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:01:51.044][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:01:51.045][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-11 16:01:51.045][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-11 16:01:51.046][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:01:51.047][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[2024-05-11 16:01:51.048][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:01:51.048][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-11 16:01:51.049][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-11 16:01:51.050][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:01:51.050][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:01:51.051][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:01:51.052][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-11 16:01:51.053][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-11 16:01:51.053][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:01:51.054][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:01:51.055][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:01:51.055][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-11 16:01:51.056][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-11 16:01:51.057][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:01:51.057][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[2024-05-11 16:01:51.058][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:01:51.059][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-11 16:01:51.060][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-11 16:01:51.060][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:01:51.061][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[2024-05-11 16:01:51.062][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:01:51.062][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-11 16:01:51.063][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-11 16:01:51.064][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:01:51.065][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:01:51.065][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:01:51.066][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-11 16:01:51.067][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-11 16:01:51.068][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:01:51.068][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:01:51.069][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:01:51.070][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-11 16:01:51.071][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-11 16:01:51.071][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:01:51.072][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:01:51.073][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:01:51.074][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-11 16:01:51.074][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-11 16:01:51.075][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:01:51.076][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:01:51.077][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:01:51.077][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-11 16:01:51.078][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-11 16:01:51.079][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:01:51.079][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:01:51.080][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:01:51.081][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-11 16:01:51.082][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-11 16:01:51.082][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:01:51.083][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:01:51.084][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-05-11 16:01:51.085][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-05-11 16:01:51.086][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-05-11 16:01:51.087][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-05-11 16:01:51.089][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-05-11 16:01:51.090][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-05-11 16:01:51.091][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-05-11 16:01:51.092][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-05-11 16:01:51.093][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-05-11 16:01:51.094][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-05-11 16:01:51.095][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-05-11 16:01:51.096][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-05-11 16:01:51.098][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-05-11 16:01:51.099][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-05-11 16:01:51.100][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-05-11 16:01:51.101][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-05-11 16:01:51.102][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-05-11 16:01:51.103][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-05-11 16:01:51.104][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-05-11 16:01:51.105][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-05-11 16:01:51.107][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-05-11 16:01:51.108][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-05-11 16:01:51.109][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-05-11 16:01:51.110][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-05-11 16:01:51.111][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-05-11 16:01:51.112][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-05-11 16:01:51.113][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-05-11 16:01:51.115][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-05-11 16:01:51.116][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-05-11 16:01:51.117][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-05-11 16:01:51.118][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-05-11 16:01:51.119][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-05-11 16:01:51.120][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-05-11 16:01:51.121][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-05-11 16:01:51.123][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-05-11 16:01:51.124][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-05-11 16:01:51.125][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-05-11 16:01:51.126][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-05-11 16:01:51.127][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-05-11 16:01:51.128][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-05-11 16:01:51.129][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-05-11 16:01:51.130][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-05-11 16:01:51.132][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-05-11 16:01:51.133][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-05-11 16:01:51.138][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-05-11 16:01:51.139][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-05-11 16:01:51.140][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-05-11 16:01:51.141][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-05-11 16:01:51.142][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-05-11 16:01:51.143][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-05-11 16:01:51.144][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-05-11 16:01:51.146][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-05-11 16:01:51.147][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-05-11 16:01:51.148][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-05-11 16:01:51.149][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-05-11 16:01:51.150][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-05-11 16:01:51.151][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-05-11 16:01:51.152][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-05-11 16:01:51.153][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-05-11 16:01:51.154][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-05-11 16:01:51.155][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-05-11 16:01:51.156][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-05-11 16:01:51.158][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-05-11 16:01:51.159][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-05-11 16:01:51.160][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-05-11 16:01:51.161][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-05-11 16:01:51.162][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-05-11 16:01:51.163][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-05-11 16:01:51.164][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-05-11 16:01:51.165][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-05-11 16:01:51.167][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-05-11 16:01:51.168][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-05-11 16:01:51.169][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-05-11 16:01:51.170][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-05-11 16:01:51.171][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-05-11 16:01:51.172][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-05-11 16:01:51.173][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-05-11 16:01:51.174][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-05-11 16:01:51.175][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-05-11 16:01:51.177][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-05-11 16:01:51.178][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-05-11 16:01:51.179][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-05-11 16:01:51.180][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-05-11 16:01:51.181][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-05-11 16:01:51.183][initialize] This is biodb version 1.12.0.
biodb.DEBUG[2024-05-11 16:01:51.184][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-05-11 16:01:51.184][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-05-11 16:01:51.185][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-11 16:01:51.186][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:01:51.186][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:01:51.187][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:01:51.188][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-11 16:01:51.189][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-11 16:01:51.189][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-11 16:01:51.190][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-11 16:01:51.191][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:01:51.192][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:01:51.192][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:01:51.193][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-11 16:01:51.194][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-11 16:01:51.194][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-11 16:01:51.195][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-11 16:01:51.196][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:01:51.197][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:01:51.197][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:01:51.198][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-11 16:01:51.199][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-11 16:01:51.200][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-11 16:01:51.200][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-11 16:01:51.201][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:01:51.202][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:01:51.202][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:01:51.203][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-11 16:01:51.204][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-11 16:01:51.205][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-11 16:01:51.205][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-11 16:01:51.206][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:01:51.207][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:01:51.208][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:01:51.208][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-11 16:01:51.209][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-11 16:01:51.210][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-11 16:01:51.211][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-11 16:01:51.211][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:01:51.212][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:01:51.213][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:01:51.213][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-11 16:01:51.214][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-11 16:01:51.215][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-11 16:01:51.216][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-11 16:01:51.216][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:01:51.217][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:01:51.218][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:01:51.218][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-11 16:01:51.219][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-11 16:01:51.220][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-11 16:01:51.220][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-11 16:01:51.221][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:01:51.222][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:01:51.223][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:01:51.223][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-11 16:01:51.224][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-11 16:01:51.225][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-11 16:01:51.226][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-11 16:01:51.226][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:01:51.227][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:01:51.228][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:01:51.229][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-11 16:01:51.229][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-11 16:01:51.230][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-11 16:01:51.235][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-11 16:01:51.236][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:01:51.237][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:01:51.238][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:01:51.238][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-11 16:01:51.239][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-11 16:01:51.240][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-11 16:01:51.240][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-11 16:01:51.241][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:01:51.242][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:01:51.242][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:01:51.243][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-11 16:01:51.244][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-11 16:01:51.245][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-11 16:01:51.245][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-11 16:01:51.246][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:01:51.247][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:01:51.247][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:01:51.248][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-11 16:01:51.249][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-11 16:01:51.249][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-11 16:01:51.250][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-11 16:01:51.251][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:01:51.252][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:01:51.252][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:01:51.253][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-11 16:01:51.254][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-11 16:01:51.254][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-11 16:01:51.255][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-11 16:01:51.256][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:01:51.257][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:01:51.258][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:01:51.258][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-11 16:01:51.259][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-11 16:01:51.260][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-11 16:01:51.260][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-11 16:01:51.261][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:01:51.262][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:01:51.263][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:01:51.263][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-11 16:01:51.264][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-11 16:01:51.265][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-11 16:01:51.266][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-11 16:01:51.267][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:01:51.267][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:01:51.268][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:01:51.269][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-11 16:01:51.270][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-11 16:01:51.270][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-11 16:01:51.271][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-11 16:01:51.272][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:01:51.273][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:01:51.273][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:01:51.274][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-11 16:01:51.275][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-11 16:01:51.275][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-11 16:01:51.276][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-11 16:01:51.277][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:01:51.278][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:01:51.280][biodb$loadDefinitions] Load definitions from file "/Users/biocbuild/bbs-3.19-bioc-longtests/meat/biodbExpasy.Rcheck/biodbExpasy/definitions.yml".
biodb.DEBUG[2024-05-11 16:01:51.281][self$getDbsInfo()$define] Define connector expasy.enzyme.
biodb.DEBUG[2024-05-11 16:01:51.282][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-05-11 16:01:51.283][self$setPropertyValue] Setting property "description" to "Write here the description of this database.".
biodb.DEBUG[2024-05-11 16:01:51.284][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-11 16:01:51.285][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-11 16:01:51.286][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-11 16:01:51.287][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-11 16:01:51.287][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-05-11 16:01:51.288][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-11 16:01:51.289][self$setPropertyValue] Setting property "entry.content.type" to "txt".
biodb.DEBUG[2024-05-11 16:01:51.290][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-11 16:01:51.291][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-05-11 16:01:51.292][self$setPropertyValue] Setting property "name" to "Expasy ENZYME database.".
biodb.DEBUG[2024-05-11 16:01:51.292][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-11 16:01:51.293][self$setPropertyValue] Setting property "parsing.expr" to "^ID\s+([0-9.]+)$".
biodb.DEBUG[2024-05-11 16:01:51.293][self$setPropertyValue] Setting property "parsing.expr" to "^CA\s+(.+?)\.?$".
biodb.DEBUG[2024-05-11 16:01:51.293][self$setPropertyValue] Setting property "parsing.expr" to "^CF\s+(.+?)\.?$".
biodb.DEBUG[2024-05-11 16:01:51.293][self$setPropertyValue] Setting property "parsing.expr" to "^DE\s+(.+?)\.?$".
biodb.DEBUG[2024-05-11 16:01:51.294][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-05-11 16:01:51.295][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-05-11 16:01:51.296][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2024-05-11 16:01:51.296][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-11 16:01:51.297][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-11 16:01:51.298][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-11 16:01:51.298][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-11 16:01:51.299][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-11 16:01:51.300][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-11 16:01:51.301][self$setPropertyValue] Setting property "urls" to "https://enzyme.expasy.org/".
biodb.DEBUG[2024-05-11 16:01:51.301][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-11 16:01:51.302][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-11 16:01:51.303][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-05-11 16:01:51.304][self$setPropertyValue]
biodb.DEBUG[2024-05-11 16:01:51.305][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-05-11 16:01:51.307][super$initialize] Initialize connector expasy.enzyme.
biodb.DEBUG[2024-05-11 16:01:51.308][super$initialize] Register connector expasy.enzyme with the request scheduler
biodb.DEBUG[2024-05-11 16:01:51.309][private$bdb$getRequestScheduler()$re ...] Register connector expasy.enzyme.
biodb.DEBUG[2024-05-11 16:01:51.310][private$addConnectorRules] Create new rule for URL "enzyme.expasy.org" of connector "expasy.enzyme".
biodb.DEBUG[2024-05-11 16:01:51.311][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-05-11 16:01:51.312][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-05-11 16:01:51.313][biodb$getFactory()$createConn] Creating new connector expasy.enzyme for database class expasy.enzyme .
biodb.INFO [2024-05-11 16:01:51.313][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-05-11 16:01:51.314][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector expasy.enzyme from the request scheduler
biodb.INFO [2024-05-11 16:01:51.315][self$deleteConn] Connector "expasy.enzyme" deleted.
biodb.DEBUG[2024-05-11 16:01:51.316][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-05-11 16:01:51.317][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-11 16:01:51.317][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-11 16:01:51.318][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-11 16:01:51.319][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-11 16:01:51.319][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:01:51.320][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".
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 86 ]
> 
> proc.time()
   user  system elapsed 
  4.351   0.343  18.185

'R CMD check' output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --test-dir=longtests --no-stop-on-test-error --no-codoc --no-examples --no-manual --ignore-vignettes --check-subdirs=no biodbExpasy_1.8.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.19-bioc-longtests/meat/biodbExpasy.Rcheck’
* using R version 4.4.0 (2024-04-24)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.1
* 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 ‘1.8.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘biodbExpasy’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Title field: should not end in a period.
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... SKIPPED
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... SKIPPED
* checking examples ... SKIPPED
* checking for unstated dependencies in ‘longtests’ ... OK
* checking tests in ‘longtests’ ...
  Running ‘testthat.R’
 OK
* DONE

Status: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.19-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)