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 12/33HostnameOS / ArchCHECK
biodbNci 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/biodbNci
git_branch: RELEASE_3_19
git_last_commit: 0db4525
git_last_commit_date: 2024-04-30 11:41:04 -0400 (Tue, 30 Apr 2024)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK  
palomino3Windows Server 2022 Datacenter / x64  ERROR  
lconwaymacOS 12.7.1 Monterey / x86_64  OK  

CHECK results for biodbNci on palomino3


To the developers/maintainers of the biodbNci 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: biodbNci
Version: 1.8.0
Command: F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --test-dir=longtests --no-stop-on-test-error --no-codoc --no-examples --no-manual --ignore-vignettes --check-subdirs=no biodbNci_1.8.0.tar.gz
StartedAt: 2024-05-11 16:09:02 -0400 (Sat, 11 May 2024)
EndedAt: 2024-05-11 16:11:29 -0400 (Sat, 11 May 2024)
EllapsedTime: 146.9 seconds
RetCode: 1
Status:   ERROR  
CheckDir: biodbNci.Rcheck
Warnings: NA

Tests output

biodbNci.Rcheck/tests/testthat.Rout.fail


R version 4.4.0 (2024-04-24 ucrt) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64

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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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> # Script needed to run testthat automatically from ‘R CMD check’. See
> # testthat::test_dir documentation.
> library(testthat)
> library(biodbNci)
> Sys.setenv(TESTTHAT_REPORTER="summary")
> Sys.setenv(BIODB_LOG_DST="console")
> test_check("biodbNci")
biodb.INFO [2024-05-11 16:10:52.338][biodb::testContext]
biodb.INFO [2024-05-11 16:10:52.341][biodb::testContext] ********************************************************************************
biodb.INFO [2024-05-11 16:10:52.342][biodb::testContext] Test context - Generic long tests
biodb.INFO [2024-05-11 16:10:52.343][biodb::testContext] ********************************************************************************
biodb.INFO [2024-05-11 16:10:52.344][biodb::testContext]
biodb.INFO [2024-05-11 16:10:52.351][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.12.0.
biodb.DEBUG[2024-05-11 16:10:52.353][self$loadDefinitions] Load definitions from file "F:/biocbuild/bbs-3.19-bioc/R/library/biodb/definitions.yml".
biodb.DEBUG[2024-05-11 16:10:52.361][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-05-11 16:10:52.362][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-05-11 16:10:52.364][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-05-11 16:10:52.365][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:10:52.366][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:10:52.367][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:10:52.368][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-05-11 16:10:52.384][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-05-11 16:10:52.386][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:10:52.387][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:10:52.388][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:10:52.389][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-05-11 16:10:52.390][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-05-11 16:10:52.392][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:10:52.393][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:10:52.394][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:10:52.395][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-05-11 16:10:52.396][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-05-11 16:10:52.397][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-05-11 16:10:52.399][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:10:52.400][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:10:52.401][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:10:52.402][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-05-11 16:10:52.403][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-05-11 16:10:52.404][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-05-11 16:10:52.406][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:10:52.407][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:10:52.408][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:10:52.409][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-05-11 16:10:52.410][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-05-11 16:10:52.411][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:10:52.412][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:10:52.414][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:10:52.415][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-05-11 16:10:52.416][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-05-11 16:10:52.417][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-05-11 16:10:52.418][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:10:52.419][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:10:52.421][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:10:52.422][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-05-11 16:10:52.423][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-05-11 16:10:52.424][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:10:52.426][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:10:52.427][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:10:52.429][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-05-11 16:10:52.431][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-05-11 16:10:52.432][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-05-11 16:10:52.434][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:10:52.435][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:10:52.436][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:10:52.437][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-05-11 16:10:52.439][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-05-11 16:10:52.440][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-05-11 16:10:52.441][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-05-11 16:10:52.442][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-05-11 16:10:52.443][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-05-11 16:10:52.445][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:10:52.446][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:10:52.447][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:10:52.448][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-05-11 16:10:52.449][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-05-11 16:10:52.450][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:10:52.451][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:10:52.453][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:10:52.454][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-05-11 16:10:52.455][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-05-11 16:10:52.456][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:10:52.457][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:10:52.458][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:10:52.459][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-05-11 16:10:52.461][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-05-11 16:10:52.462][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:10:52.463][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:10:52.464][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:10:52.465][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-05-11 16:10:52.466][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-05-11 16:10:52.467][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:10:52.468][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:10:52.470][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:10:52.471][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-05-11 16:10:52.472][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-05-11 16:10:52.473][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:10:52.474][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:10:52.475][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:10:52.476][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-05-11 16:10:52.478][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-05-11 16:10:52.482][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-05-11 16:10:52.483][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:10:52.484][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:10:52.485][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:10:52.486][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-05-11 16:10:52.488][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-05-11 16:10:52.489][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-05-11 16:10:52.490][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:10:52.491][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:10:52.492][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:10:52.495][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-05-11 16:10:52.530][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-05-11 16:10:52.544][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2024-05-11 16:10:52.545][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-11 16:10:52.546][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-11 16:10:52.547][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-11 16:10:52.549][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-11 16:10:52.550][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-05-11 16:10:52.551][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-11 16:10:52.552][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-05-11 16:10:52.553][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-11 16:10:52.555][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-05-11 16:10:52.556][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-05-11 16:10:52.557][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-11 16:10:52.558][self$setPropertyValue]
biodb.DEBUG[2024-05-11 16:10:52.559][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-05-11 16:10:52.561][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-05-11 16:10:52.561][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-05-11 16:10:52.561][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-05-11 16:10:52.561][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-05-11 16:10:52.561][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-05-11 16:10:52.562][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-05-11 16:10:52.563][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-11 16:10:52.564][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-11 16:10:52.565][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-11 16:10:52.566][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-11 16:10:52.568][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-11 16:10:52.569][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-11 16:10:52.570][self$setPropertyValue]
biodb.DEBUG[2024-05-11 16:10:52.571][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-11 16:10:52.572][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-11 16:10:52.573][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-05-11 16:10:52.574][self$setPropertyValue]
biodb.DEBUG[2024-05-11 16:10:52.576][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-05-11 16:10:52.578][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-05-11 16:10:52.579][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-05-11 16:10:52.580][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-11 16:10:52.581][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-11 16:10:52.582][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-11 16:10:52.584][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-11 16:10:52.585][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-05-11 16:10:52.586][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-11 16:10:52.587][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-05-11 16:10:52.588][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-11 16:10:52.590][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-05-11 16:10:52.591][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-05-11 16:10:52.592][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-11 16:10:52.593][self$setPropertyValue]
biodb.DEBUG[2024-05-11 16:10:52.594][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-05-11 16:10:52.596][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-05-11 16:10:52.596][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-05-11 16:10:52.596][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-05-11 16:10:52.596][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-05-11 16:10:52.596][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-05-11 16:10:52.597][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-05-11 16:10:52.598][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-11 16:10:52.599][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-11 16:10:52.600][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-11 16:10:52.601][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-11 16:10:52.603][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-11 16:10:52.604][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-11 16:10:52.605][self$setPropertyValue]
biodb.DEBUG[2024-05-11 16:10:52.606][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-11 16:10:52.607][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-11 16:10:52.608][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-05-11 16:10:52.609][self$setPropertyValue]
biodb.DEBUG[2024-05-11 16:10:52.611][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-05-11 16:10:52.613][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-05-11 16:10:52.614][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2024-05-11 16:10:52.615][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-11 16:10:52.616][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-11 16:10:52.618][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-11 16:10:52.619][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-11 16:10:52.620][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-05-11 16:10:52.621][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-11 16:10:52.622][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-05-11 16:10:52.623][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-11 16:10:52.625][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-05-11 16:10:52.626][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-05-11 16:10:52.627][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-11 16:10:52.628][self$setPropertyValue]
biodb.DEBUG[2024-05-11 16:10:52.629][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-05-11 16:10:52.631][self$setPropertyValue]
biodb.DEBUG[2024-05-11 16:10:52.632][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-05-11 16:10:52.633][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-11 16:10:52.634][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-11 16:10:52.635][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-11 16:10:52.636][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-11 16:10:52.637][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-11 16:10:52.639][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-11 16:10:52.640][self$setPropertyValue]
biodb.DEBUG[2024-05-11 16:10:52.641][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-11 16:10:52.642][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-11 16:10:52.643][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-05-11 16:10:52.644][self$setPropertyValue]
biodb.DEBUG[2024-05-11 16:10:52.646][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-05-11 16:10:52.648][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-05-11 16:10:52.649][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-05-11 16:10:52.650][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-11 16:10:52.651][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-11 16:10:52.652][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-11 16:10:52.654][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-11 16:10:52.655][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-05-11 16:10:52.656][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-11 16:10:52.657][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-05-11 16:10:52.658][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-11 16:10:52.660][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-05-11 16:10:52.661][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-05-11 16:10:52.662][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-11 16:10:52.663][self$setPropertyValue]
biodb.DEBUG[2024-05-11 16:10:52.664][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-05-11 16:10:52.666][self$setPropertyValue]
biodb.DEBUG[2024-05-11 16:10:52.667][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-05-11 16:10:52.668][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-11 16:10:52.669][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-11 16:10:52.670][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-11 16:10:52.671][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-11 16:10:52.673][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-11 16:10:52.674][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-11 16:10:52.675][self$setPropertyValue]
biodb.DEBUG[2024-05-11 16:10:52.676][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-11 16:10:52.677][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-11 16:10:52.678][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-05-11 16:10:52.680][self$setPropertyValue]
biodb.DEBUG[2024-05-11 16:10:52.683][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-05-11 16:10:52.684][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:10:52.685][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:10:52.686][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:10:52.687][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-11 16:10:52.688][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-11 16:10:52.689][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:10:52.691][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:10:52.692][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:10:52.693][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-11 16:10:52.694][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 16:10:52.695][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:10:52.696][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:10:52.697][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:10:52.698][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-11 16:10:52.699][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-11 16:10:52.700][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:10:52.701][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:10:52.702][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:10:52.703][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-11 16:10:52.705][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 16:10:52.706][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:10:52.707][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:10:52.708][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:10:52.709][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-11 16:10:52.710][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-11 16:10:52.711][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:10:52.712][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:10:52.713][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:10:52.714][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-11 16:10:52.720][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-11 16:10:52.721][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:10:52.722][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:10:52.723][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:10:52.724][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-11 16:10:52.725][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-11 16:10:52.727][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:10:52.728][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:10:52.729][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:10:52.730][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-11 16:10:52.731][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 16:10:52.732][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:10:52.733][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:10:52.734][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:10:52.735][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-11 16:10:52.736][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-11 16:10:52.737][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:10:52.738][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:10:52.739][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:10:52.741][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-11 16:10:52.742][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 16:10:52.743][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:10:52.744][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:10:52.745][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:10:52.746][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-11 16:10:52.747][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 16:10:52.748][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:10:52.749][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:10:52.750][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:10:52.751][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-11 16:10:52.753][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 16:10:52.754][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:10:52.755][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:10:52.756][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:10:52.757][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-11 16:10:52.758][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 16:10:52.759][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:10:52.760][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:10:52.762][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:10:52.763][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-11 16:10:52.764][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 16:10:52.765][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:10:52.766][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:10:52.767][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:10:52.768][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-11 16:10:52.769][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 16:10:52.770][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:10:52.771][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:10:52.772][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:10:52.773][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-11 16:10:52.775][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-11 16:10:52.776][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:10:52.777][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:10:52.778][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:10:52.779][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-11 16:10:52.780][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 16:10:52.781][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:10:52.782][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:10:52.783][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-05-11 16:10:52.787][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-05-11 16:10:52.789][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-05-11 16:10:52.791][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-05-11 16:10:52.792][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-05-11 16:10:52.794][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-05-11 16:10:52.795][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-05-11 16:10:52.797][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-05-11 16:10:52.798][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-05-11 16:10:52.800][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-05-11 16:10:52.802][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-05-11 16:10:52.803][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-05-11 16:10:52.805][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-05-11 16:10:52.806][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-05-11 16:10:52.808][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-05-11 16:10:52.809][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-05-11 16:10:52.811][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-05-11 16:10:52.812][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-05-11 16:10:52.814][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-05-11 16:10:52.816][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-05-11 16:10:52.817][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-05-11 16:10:52.819][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-05-11 16:10:52.820][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-05-11 16:10:52.822][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-05-11 16:10:52.823][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-05-11 16:10:52.825][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-05-11 16:10:52.826][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-05-11 16:10:52.828][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-05-11 16:10:52.830][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-05-11 16:10:52.831][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-05-11 16:10:52.833][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-05-11 16:10:52.834][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-05-11 16:10:52.836][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-05-11 16:10:52.837][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-05-11 16:10:52.839][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-05-11 16:10:52.841][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-05-11 16:10:52.842][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-05-11 16:10:52.844][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-05-11 16:10:52.845][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-05-11 16:10:52.847][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-05-11 16:10:52.848][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-05-11 16:10:52.850][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-05-11 16:10:52.852][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-05-11 16:10:52.853][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-05-11 16:10:52.855][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-05-11 16:10:52.856][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-05-11 16:10:52.858][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-05-11 16:10:52.860][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-05-11 16:10:52.861][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-05-11 16:10:52.863][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-05-11 16:10:52.864][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-05-11 16:10:52.866][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-05-11 16:10:52.867][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-05-11 16:10:52.869][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-05-11 16:10:52.870][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-05-11 16:10:52.872][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-05-11 16:10:52.874][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-05-11 16:10:52.875][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-05-11 16:10:52.877][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-05-11 16:10:52.878][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-05-11 16:10:52.880][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-05-11 16:10:52.881][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-05-11 16:10:52.883][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-05-11 16:10:52.885][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-05-11 16:10:52.886][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-05-11 16:10:52.888][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-05-11 16:10:52.889][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-05-11 16:10:52.891][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-05-11 16:10:52.893][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-05-11 16:10:52.894][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-05-11 16:10:52.896][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-05-11 16:10:52.897][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-05-11 16:10:52.899][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-05-11 16:10:52.900][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-05-11 16:10:52.902][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-05-11 16:10:52.904][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-05-11 16:10:52.905][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-05-11 16:10:52.907][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-05-11 16:10:52.908][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-05-11 16:10:52.910][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-05-11 16:10:52.911][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-05-11 16:10:52.913][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-05-11 16:10:52.914][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-05-11 16:10:52.954][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-05-11 16:10:52.957][initialize] This is biodb version 1.12.0.
biodb.DEBUG[2024-05-11 16:10:52.960][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-05-11 16:10:52.961][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-05-11 16:10:52.962][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 16:10:52.963][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:10:52.964][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:10:52.969][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:10:52.970][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-11 16:10:52.971][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-11 16:10:52.972][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-11 16:10:52.973][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 16:10:52.974][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:10:52.975][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:10:52.977][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:10:52.978][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-11 16:10:52.979][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-11 16:10:52.981][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-11 16:10:52.982][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 16:10:52.983][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:10:52.984][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:10:52.986][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:10:52.987][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-11 16:10:52.988][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-11 16:10:52.989][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-11 16:10:52.990][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 16:10:52.991][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:10:52.992][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:10:52.994][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:10:52.995][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-11 16:10:52.996][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-11 16:10:52.997][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-11 16:10:52.998][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 16:10:52.999][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:10:53.000][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:10:53.001][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:10:53.002][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-11 16:10:53.004][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-11 16:10:53.005][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-11 16:10:53.006][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 16:10:53.007][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:10:53.008][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:10:53.009][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:10:53.010][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-11 16:10:53.011][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-11 16:10:53.012][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-11 16:10:53.013][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 16:10:53.014][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:10:53.016][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:10:53.017][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:10:53.018][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-11 16:10:53.019][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-11 16:10:53.020][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-11 16:10:53.021][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 16:10:53.022][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:10:53.023][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:10:53.024][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:10:53.025][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-11 16:10:53.026][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-11 16:10:53.027][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-11 16:10:53.029][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 16:10:53.030][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:10:53.031][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 16:10:53.032][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:10:53.033][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-11 16:10:53.034][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-11 16:10:53.035][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-11 16:10:53.036][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 16:10:53.037][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:10:53.038][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:10:53.039][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:10:53.041][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-11 16:10:53.042][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-11 16:10:53.043][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-11 16:10:53.044][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 16:10:53.045][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:10:53.046][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:10:53.047][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:10:53.048][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-11 16:10:53.049][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-11 16:10:53.050][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-11 16:10:53.052][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 16:10:53.053][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:10:53.054][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 16:10:53.055][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:10:53.056][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-11 16:10:53.057][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-11 16:10:53.058][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-11 16:10:53.059][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 16:10:53.060][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:10:53.061][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 16:10:53.063][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:10:53.064][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-11 16:10:53.065][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-11 16:10:53.066][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-11 16:10:53.067][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 16:10:53.068][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:10:53.069][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 16:10:53.070][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:10:53.071][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-11 16:10:53.072][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-11 16:10:53.073][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-11 16:10:53.074][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 16:10:53.076][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:10:53.077][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:10:53.078][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:10:53.079][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-11 16:10:53.080][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-11 16:10:53.081][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-11 16:10:53.082][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 16:10:53.083][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:10:53.084][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:10:53.085][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:10:53.086][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-11 16:10:53.088][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-11 16:10:53.089][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-11 16:10:53.090][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 16:10:53.091][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:10:53.092][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:10:53.093][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:10:53.094][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-11 16:10:53.095][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-11 16:10:53.096][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-11 16:10:53.097][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 16:10:53.098][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:10:53.100][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:10:53.103][biodb$loadDefinitions] Load definitions from file "F:/biocbuild/bbs-3.19-bioc-longtests/meat/biodbNci.Rcheck/biodbNci/definitions.yml".
biodb.DEBUG[2024-05-11 16:10:53.112][self$getDbsInfo()$define] Define connector nci.cactus.
biodb.DEBUG[2024-05-11 16:10:53.114][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-05-11 16:10:53.115][self$setPropertyValue] Setting property "description" to "National Cancer Institute (USA) CACTUS Database.".
biodb.DEBUG[2024-05-11 16:10:53.116][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-11 16:10:53.118][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-11 16:10:53.119][self$setPropertyValue] Setting property "downloadable" to "TRUE".
biodb.DEBUG[2024-05-11 16:10:53.120][self$setPropertyValue] Setting property "dwnld.ext" to "gz".
biodb.DEBUG[2024-05-11 16:10:53.121][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-05-11 16:10:53.122][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-11 16:10:53.124][self$setPropertyValue] Setting property "entry.content.type" to "sdf".
biodb.DEBUG[2024-05-11 16:10:53.125][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-11 16:10:53.126][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-05-11 16:10:53.127][self$setPropertyValue] Setting property "name" to "NCI CACTUS".
biodb.DEBUG[2024-05-11 16:10:53.129][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-11 16:10:53.130][self$setPropertyValue] Setting property "parsing.expr" to "NSC".
biodb.DEBUG[2024-05-11 16:10:53.130][self$setPropertyValue] Setting property "parsing.expr" to "DTP names".
biodb.DEBUG[2024-05-11 16:10:53.130][self$setPropertyValue] Setting property "parsing.expr" to "Standard InChI".
biodb.DEBUG[2024-05-11 16:10:53.130][self$setPropertyValue] Setting property "parsing.expr" to "c("Standard InChIKey", "^InChIKey=(.*)$")".
biodb.DEBUG[2024-05-11 16:10:53.130][self$setPropertyValue] Setting property "parsing.expr" to "Formula".
biodb.DEBUG[2024-05-11 16:10:53.130][self$setPropertyValue] Setting property "parsing.expr" to "Molecular Weight".
biodb.DEBUG[2024-05-11 16:10:53.130][self$setPropertyValue] Setting property "parsing.expr" to "CAS".
biodb.DEBUG[2024-05-11 16:10:53.131][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-05-11 16:10:53.132][self$setPropertyValue]
biodb.DEBUG[2024-05-11 16:10:53.134][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2024-05-11 16:10:53.135][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-11 16:10:53.136][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-11 16:10:53.137][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-11 16:10:53.138][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-11 16:10:53.139][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-11 16:10:53.140][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-11 16:10:53.142][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/".
biodb.DEBUG[2024-05-11 16:10:53.142][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/".
biodb.DEBUG[2024-05-11 16:10:53.142][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/download/nci/".
biodb.DEBUG[2024-05-11 16:10:53.142][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/download/nci/NCI-Open_2012-05-01.sdf.gz".
biodb.DEBUG[2024-05-11 16:10:53.143][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-11 16:10:53.144][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-11 16:10:53.145][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-05-11 16:10:53.146][self$setPropertyValue]
biodb.DEBUG[2024-05-11 16:10:53.152][self$getEntryFields()$define] Define field nci.cactus.id.
biodb.DEBUG[2024-05-11 16:10:53.200][super$initialize] Initialize connector nci.cactus.
biodb.DEBUG[2024-05-11 16:10:53.201][super$initialize] Register connector nci.cactus with the request scheduler
biodb.DEBUG[2024-05-11 16:10:53.204][private$bdb$getRequestScheduler()$re ...] Register connector nci.cactus.
biodb.DEBUG[2024-05-11 16:10:53.208][private$addConnectorRules] Create new rule for URL "cactus.nci.nih.gov" of connector "nci.cactus".
biodb.DEBUG[2024-05-11 16:10:53.212][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-05-11 16:10:53.213][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-05-11 16:10:53.215][rule$addConnector] Connector "nci.cactus" is already listed in rule "cactus.nci.nih.gov".
biodb.DEBUG[2024-05-11 16:10:53.216][rule$addConnector] Connector "nci.cactus" is already listed in rule "cactus.nci.nih.gov".
biodb.DEBUG[2024-05-11 16:10:53.218][rule$addConnector] Connector "nci.cactus" is already listed in rule "cactus.nci.nih.gov".
biodb.DEBUG[2024-05-11 16:10:53.219][biodb$getFactory()$createConn] Creating new connector nci.cactus for database class nci.cactus .
biodb.INFO [2024-05-11 16:10:53.229][biodb::testThat]
biodb.INFO [2024-05-11 16:10:53.230][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2024-05-11 16:10:53.231][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-11 16:10:53.232][biodb::testThat]
biodb.TRACE[2024-05-11 16:10:53.237][loadFileContents] Loaded 1 files from cache: [1]: "F:/biocbuild/bbs-3.19-bioc-longtests/meat/biodbNci.Rcheck/biodbNci/testref/entry-nci.cactus-749674-content.sdf".
biodb.DEBUG[2024-05-11 16:10:53.239][biodb$getFactory()$createEntryFromCo ...] Creating NCI CACTUS entries from 1 content(s).
biodb.DEBUG[2024-05-11 16:10:53.242][biodb$getFactory()$createEntryFromCo ...] Parsing 1 NCI CACTUS entries.
biodb.DEBUG[2024-05-11 16:10:53.249][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-11 16:10:53.250][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-11 16:10:53.251][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-11 16:10:53.267][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-11 16:10:53.268][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 16:10:53.269][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:10:53.270][FUN] Functions in observer BiodbConfig: [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 16:10:53.285][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-11 16:10:53.287][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-11 16:10:53.288][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:10:53.289][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:10:53.290][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-11 16:10:53.301][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-11 16:10:53.303][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:10:53.304][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:10:53.306][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-11 16:10:53.308][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-11 16:10:53.309][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:10:53.310][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:10:53.333][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-11 16:10:53.334][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-11 16:10:53.335][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:10:53.336][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:10:53.338][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-11 16:10:53.340][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-11 16:10:53.341][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:10:53.342][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:10:53.343][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-11 16:10:53.345][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-11 16:10:53.346][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:10:53.347][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:10:53.349][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-05-11 16:10:53.350][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-11 16:10:53.352][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:10:53.353][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:10:53.354][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-05-11 16:10:53.355][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-11 16:10:53.357][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:10:53.358][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:10:53.360][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-11 16:10:53.361][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-11 16:10:53.362][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:10:53.363][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:10:53.365][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-11 16:10:53.366][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-11 16:10:53.367][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:10:53.368][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:10:53.370][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-05-11 16:10:53.372][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-05-11 16:10:53.373][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:10:53.374][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:10:53.375][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-05-11 16:10:53.376][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-05-11 16:10:53.378][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:10:53.379][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:10:53.380][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-11 16:10:53.381][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-11 16:10:53.392][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:10:53.394][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:10:53.395][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-05-11 16:10:53.396][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-05-11 16:10:53.397][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:10:53.399][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:10:53.400][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-11 16:10:53.401][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-11 16:10:53.402][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:10:53.403][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:10:53.405][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-11 16:10:53.406][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-11 16:10:53.407][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:10:53.408][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:10:53.410][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-11 16:10:53.411][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-11 16:10:53.412][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:10:53.413][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:10:53.442][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-11 16:10:53.444][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-11 16:10:53.445][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:10:53.446][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:10:53.448][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-11 16:10:53.449][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-11 16:10:53.450][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:10:53.451][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:10:53.453][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-11 16:10:53.454][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-11 16:10:53.455][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:10:53.456][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-11 16:10:53.457][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 749674.
biodb.TRACE[2024-05-11 16:10:53.461][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-05-11 16:10:53.462][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-05-11 16:10:53.463][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:10:53.464][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:10:53.466][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-05-11 16:10:53.467][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-05-11 16:10:53.468][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:10:53.469][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:10:53.470][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-05-11 16:10:53.472][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-05-11 16:10:53.473][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:10:53.474][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:10:53.475][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-05-11 16:10:53.477][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-05-11 16:10:53.478][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:10:53.480][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:10:53.502][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-11 16:10:53.503][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-11 16:10:53.505][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:10:53.506][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:10:53.520][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-05-11 16:10:53.522][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-05-11 16:10:53.523][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:10:53.524][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:10:53.532][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-11 16:10:53.533][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-11 16:10:53.534][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:10:53.535][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:10:53.536][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-11 16:10:53.538][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-11 16:10:53.539][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:10:53.540][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:10:53.541][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-11 16:10:53.543][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-11 16:10:53.544][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:10:53.545][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:10:53.548][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-11 16:10:53.549][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-11 16:10:53.556][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:10:53.557][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:10:53.558][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-11 16:10:53.560][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-11 16:10:53.561][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:10:53.562][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:10:53.563][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-11 16:10:53.564][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-11 16:10:53.566][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:10:53.567][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:10:53.568][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-05-11 16:10:53.570][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-05-11 16:10:53.571][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:10:53.572][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:10:53.573][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-05-11 16:10:53.574][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-05-11 16:10:53.576][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:10:53.577][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:10:53.578][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-05-11 16:10:53.579][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-05-11 16:10:53.581][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:10:53.582][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:10:53.595][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-11 16:10:53.596][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-11 16:10:53.597][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:10:53.598][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:10:53.599][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-11 16:10:53.601][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-11 16:10:53.602][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:10:53.603][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:10:53.604][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-11 16:10:53.606][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-11 16:10:53.607][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:10:53.608][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:10:53.609][ef$get] Asked field names are: accession.
biodb.TRACE[2024-05-11 16:10:53.610][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-11 16:10:53.612][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:10:53.613][ef$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:10:53.614][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-11 16:10:53.615][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-11 16:10:53.616][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:10:53.618][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:10:53.629][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-11 16:10:53.631][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-11 16:10:53.632][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:10:53.633][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:10:53.634][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-11 16:10:53.636][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-11 16:10:53.637][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:10:53.638][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:10:53.639][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-11 16:10:53.641][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-11 16:10:53.642][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:10:53.643][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:10:53.644][ef$get] Asked field names are: formula.
biodb.TRACE[2024-05-11 16:10:53.646][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-11 16:10:53.647][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:10:53.648][ef$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:10:53.649][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-11 16:10:53.651][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-11 16:10:53.652][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:10:53.653][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:10:53.664][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-11 16:10:53.665][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-11 16:10:53.667][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:10:53.668][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:10:53.669][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-11 16:10:53.670][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-11 16:10:53.671][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:10:53.673][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:10:53.674][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-11 16:10:53.675][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-11 16:10:53.676][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:10:53.678][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:10:53.679][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-11 16:10:53.680][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-11 16:10:53.681][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:10:53.682][ef$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:10:53.684][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-11 16:10:53.685][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-11 16:10:53.686][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:10:53.687][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:10:53.698][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-05-11 16:10:53.700][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-11 16:10:53.701][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:10:53.702][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:10:53.703][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-05-11 16:10:53.705][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-11 16:10:53.706][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:10:53.707][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:10:53.708][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-05-11 16:10:53.709][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-11 16:10:53.711][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:10:53.712][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:10:53.713][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-05-11 16:10:53.714][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-11 16:10:53.716][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:10:53.717][ef$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:10:53.718][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-05-11 16:10:53.719][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-11 16:10:53.720][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:10:53.721][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:10:53.732][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-11 16:10:53.734][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-11 16:10:53.735][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:10:53.736][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:10:53.737][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-11 16:10:53.739][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-11 16:10:53.745][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:10:53.746][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:10:53.747][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-11 16:10:53.749][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-11 16:10:53.750][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:10:53.751][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:10:53.752][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-11 16:10:53.753][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-11 16:10:53.755][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:10:53.756][ef$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:10:53.757][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-11 16:10:53.758][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-11 16:10:53.759][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:10:53.761][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:10:53.772][ef$get] Asked field names are: accession.
biodb.TRACE[2024-05-11 16:10:53.773][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-11 16:10:53.774][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:10:53.775][ef$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:10:53.782][ef$get] Asked field names are: formula.
biodb.TRACE[2024-05-11 16:10:53.783][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-11 16:10:53.785][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:10:53.786][ef$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:10:53.792][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-05-11 16:10:53.794][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-11 16:10:53.795][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:10:53.796][ef$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:10:53.803][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-11 16:10:53.804][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-11 16:10:53.805][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:10:53.806][ef$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:10:53.813][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-11 16:10:53.814][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-11 16:10:53.815][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:10:53.816][ef$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:10:53.834][loadFileContents] Loaded 1 files from cache: [1]: "F:/biocbuild/bbs-3.19-bioc-longtests/meat/biodbNci.Rcheck/biodbNci/testref/entry-nci.cactus-750690-content.sdf".
biodb.DEBUG[2024-05-11 16:10:53.863][biodb$getFactory()$createEntryFromCo ...] Creating NCI CACTUS entries from 1 content(s).
biodb.DEBUG[2024-05-11 16:10:53.865][biodb$getFactory()$createEntryFromCo ...] Parsing 1 NCI CACTUS entries.
biodb.DEBUG[2024-05-11 16:10:53.867][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-11 16:10:53.868][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-11 16:10:53.869][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-11 16:10:53.876][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-11 16:10:53.877][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 16:10:53.879][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:10:53.880][FUN] Functions in observer BiodbConfig: [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 16:10:53.889][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-11 16:10:53.890][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-11 16:10:53.892][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:10:53.893][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:10:53.899][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-11 16:10:53.900][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-11 16:10:53.901][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:10:53.903][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:10:53.920][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-05-11 16:10:53.921][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-05-11 16:10:53.922][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:10:53.923][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:10:53.925][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-05-11 16:10:53.926][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-05-11 16:10:53.927][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:10:53.928][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:10:53.930][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-11 16:10:53.931][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-11 16:10:53.933][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:10:53.934][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:10:53.935][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-11 16:10:53.936][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-11 16:10:53.938][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:10:53.939][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:10:53.940][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-11 16:10:53.942][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-11 16:10:53.943][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:10:53.944][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:10:53.945][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-11 16:10:53.946][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-11 16:10:53.948][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:10:53.949][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:10:53.951][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-11 16:10:53.952][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-11 16:10:53.953][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:10:53.954][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:10:53.955][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-11 16:10:53.957][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-11 16:10:53.958][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:10:53.959][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:10:53.960][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-11 16:10:53.962][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-11 16:10:53.963][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:10:53.964][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:10:53.965][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-11 16:10:53.967][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-11 16:10:53.968][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:10:53.969][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:10:53.970][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-11 16:10:53.972][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-11 16:10:53.973][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:10:53.974][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:10:53.975][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-11 16:10:53.976][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-11 16:10:53.977][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:10:53.979][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:10:53.980][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-11 16:10:53.981][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-11 16:10:53.982][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:10:53.983][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:10:53.986][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-05-11 16:10:53.987][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-11 16:10:53.988][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:10:53.989][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:10:53.990][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-05-11 16:10:53.992][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-11 16:10:53.993][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:10:53.994][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:10:53.996][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-11 16:10:53.997][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-11 16:10:53.998][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:10:54.000][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:10:54.001][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-11 16:10:54.002][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-11 16:10:54.003][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:10:54.005][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:10:54.006][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-05-11 16:10:54.008][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-05-11 16:10:54.009][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:10:54.010][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:10:54.011][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-05-11 16:10:54.013][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-05-11 16:10:54.014][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:10:54.015][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:10:54.016][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-11 16:10:54.018][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-11 16:10:54.019][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:10:54.020][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:10:54.021][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-05-11 16:10:54.023][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-05-11 16:10:54.024][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:10:54.025][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:10:54.026][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-11 16:10:54.027][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-11 16:10:54.029][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:10:54.030][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:10:54.031][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-11 16:10:54.032][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-11 16:10:54.034][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:10:54.035][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:10:54.036][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-11 16:10:54.037][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-11 16:10:54.038][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:10:54.040][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:10:54.041][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-11 16:10:54.042][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-11 16:10:54.043][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:10:54.045][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:10:54.046][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-11 16:10:54.047][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-11 16:10:54.048][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:10:54.050][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:10:54.051][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-11 16:10:54.052][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-11 16:10:54.053][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:10:54.054][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-11 16:10:54.056][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 750690.
biodb.TRACE[2024-05-11 16:10:54.078][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-05-11 16:10:54.080][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-05-11 16:10:54.081][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:10:54.082][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:10:54.083][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-05-11 16:10:54.085][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-05-11 16:10:54.086][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:10:54.087][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:10:54.088][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-05-11 16:10:54.090][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-05-11 16:10:54.091][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:10:54.092][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:10:54.093][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-05-11 16:10:54.094][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-05-11 16:10:54.096][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:10:54.097][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:10:54.099][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-11 16:10:54.101][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-11 16:10:54.102][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:10:54.103][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:10:54.110][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-05-11 16:10:54.111][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-05-11 16:10:54.113][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:10:54.114][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:10:54.121][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-11 16:10:54.122][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-11 16:10:54.123][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:10:54.124][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:10:54.125][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-11 16:10:54.127][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-11 16:10:54.128][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:10:54.129][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:10:54.130][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-11 16:10:54.132][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-11 16:10:54.133][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:10:54.134][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:10:54.137][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-11 16:10:54.138][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-11 16:10:54.139][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:10:54.140][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:10:54.141][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-11 16:10:54.143][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-11 16:10:54.144][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:10:54.145][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:10:54.146][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-11 16:10:54.148][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-11 16:10:54.149][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:10:54.150][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:10:54.151][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-05-11 16:10:54.153][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-05-11 16:10:54.154][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:10:54.155][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:10:54.156][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-05-11 16:10:54.157][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-05-11 16:10:54.159][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:10:54.160][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:10:54.161][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-05-11 16:10:54.162][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-05-11 16:10:54.163][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:10:54.165][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:10:54.185][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-11 16:10:54.186][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-11 16:10:54.187][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:10:54.188][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:10:54.190][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-11 16:10:54.191][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-11 16:10:54.192][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:10:54.193][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:10:54.194][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-11 16:10:54.196][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-11 16:10:54.197][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:10:54.198][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:10:54.199][ef$get] Asked field names are: accession.
biodb.TRACE[2024-05-11 16:10:54.201][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-11 16:10:54.202][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:10:54.203][ef$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:10:54.204][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-11 16:10:54.205][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-11 16:10:54.207][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:10:54.208][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:10:54.219][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-05-11 16:10:54.220][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-05-11 16:10:54.221][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:10:54.223][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:10:54.224][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-05-11 16:10:54.230][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-05-11 16:10:54.231][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:10:54.232][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:10:54.234][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-05-11 16:10:54.235][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-05-11 16:10:54.236][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:10:54.237][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:10:54.239][ef$get] Asked field names are: cas.id.
biodb.TRACE[2024-05-11 16:10:54.240][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-05-11 16:10:54.241][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:10:54.242][ef$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:10:54.244][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-05-11 16:10:54.245][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-05-11 16:10:54.246][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:10:54.248][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:10:54.259][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-11 16:10:54.260][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-11 16:10:54.261][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:10:54.263][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:10:54.264][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-11 16:10:54.265][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-11 16:10:54.266][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:10:54.267][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:10:54.269][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-11 16:10:54.270][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-11 16:10:54.271][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:10:54.273][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:10:54.274][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-11 16:10:54.275][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-11 16:10:54.276][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:10:54.277][ef$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:10:54.279][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-11 16:10:54.280][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-11 16:10:54.281][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:10:54.282][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:10:54.294][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-11 16:10:54.295][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-11 16:10:54.296][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:10:54.297][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:10:54.298][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-11 16:10:54.300][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-11 16:10:54.301][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:10:54.302][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:10:54.303][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-11 16:10:54.305][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-11 16:10:54.306][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:10:54.307][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:10:54.308][ef$get] Asked field names are: formula.
biodb.TRACE[2024-05-11 16:10:54.310][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-11 16:10:54.311][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:10:54.312][ef$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:10:54.313][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-11 16:10:54.314][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-11 16:10:54.316][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:10:54.317][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:10:54.328][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-11 16:10:54.329][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-11 16:10:54.331][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:10:54.332][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:10:54.333][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-11 16:10:54.334][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-11 16:10:54.335][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:10:54.337][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:10:54.338][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-11 16:10:54.339][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-11 16:10:54.340][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:10:54.341][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:10:54.343][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-11 16:10:54.344][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-11 16:10:54.345][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:10:54.346][ef$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:10:54.348][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-11 16:10:54.349][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-11 16:10:54.350][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:10:54.351][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:10:54.362][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-05-11 16:10:54.364][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-11 16:10:54.365][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:10:54.366][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:10:54.367][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-05-11 16:10:54.369][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-11 16:10:54.370][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:10:54.371][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:10:54.372][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-05-11 16:10:54.373][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-11 16:10:54.375][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:10:54.376][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:10:54.377][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-05-11 16:10:54.378][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-11 16:10:54.380][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:10:54.381][ef$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:10:54.382][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-05-11 16:10:54.383][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-11 16:10:54.385][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:10:54.386][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:10:54.397][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-11 16:10:54.399][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-11 16:10:54.400][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:10:54.401][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:10:54.402][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-11 16:10:54.403][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-11 16:10:54.405][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:10:54.406][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:10:54.407][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-11 16:10:54.408][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-11 16:10:54.410][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:10:54.415][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:10:54.417][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-11 16:10:54.418][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-11 16:10:54.419][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:10:54.420][ef$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:10:54.422][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-11 16:10:54.423][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-11 16:10:54.424][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:10:54.425][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:10:54.436][ef$get] Asked field names are: accession.
biodb.TRACE[2024-05-11 16:10:54.438][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-11 16:10:54.439][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:10:54.440][ef$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:10:54.447][ef$get] Asked field names are: cas.id.
biodb.TRACE[2024-05-11 16:10:54.448][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-05-11 16:10:54.449][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:10:54.450][ef$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:10:54.457][ef$get] Asked field names are: formula.
biodb.TRACE[2024-05-11 16:10:54.458][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-11 16:10:54.459][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:10:54.460][ef$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:10:54.467][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-05-11 16:10:54.469][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-11 16:10:54.470][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:10:54.471][ef$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:10:54.478][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-11 16:10:54.479][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-11 16:10:54.480][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:10:54.482][ef$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:10:54.489][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-11 16:10:54.490][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-11 16:10:54.491][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:10:54.492][ef$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:10:54.499][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-11 16:10:54.500][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-11 16:10:54.501][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:10:54.503][ef$get] fields variable is a list.
biodb.INFO [2024-05-11 16:10:54.515][biodb::testThat]
biodb.INFO [2024-05-11 16:10:54.516][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2024-05-11 16:10:54.517][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-11 16:10:54.518][biodb::testThat]
biodb.DEBUG[2024-05-11 16:10:54.521][private$loadEntries] Creating entries from ids [2]: "749674, 750690".
biodb.DEBUG[2024-05-11 16:10:54.527][conn$getEntryContent] Get NCI CACTUS entry content(s) for 2 id(s)...
biodb.INFO [2024-05-11 16:10:54.534][self$getFolderPath] Create cache folder "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/nci.cactus-8efc65070d01b214e760b1d4932ee427" for "nci.cactus-8efc65070d01b214e760b1d4932ee427".
biodb.DEBUG[2024-05-11 16:10:54.942][self$isDownloaded] Database nci.cactus has not yet been downloaded.
biodb.INFO [2024-05-11 16:10:54.944][self$download] Downloading whole database of nci.cactus.
biodb.INFO [2024-05-11 16:10:54.945][private$doDownload] Downloading NCI CACTUS database at "https://cactus.nci.nih.gov/download/nci/NCI-Open_2012-05-01.sdf.gz" ...
biodb.DEBUG[2024-05-11 16:10:54.969][sched$downloadFile] Downloading file "https://cactus.nci.nih.gov/download/nci/NCI-Open_2012-05-01.sdf.gz".
trying URL 'https://cactus.nci.nih.gov/download/nci/NCI-Open_2012-05-01.sdf.gz'
Content type 'application/x-gzip' length 206737123 bytes (197.2 MB)
=======================
downloaded 94.3 MB

biodb.INFO [2024-05-11 16:11:27.285][biodb::testThat]
biodb.INFO [2024-05-11 16:11:27.286][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2024-05-11 16:11:27.288][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-11 16:11:27.289][biodb::testThat]
biodb.INFO [2024-05-11 16:11:27.298][biodb::testThat]
biodb.INFO [2024-05-11 16:11:27.300][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2024-05-11 16:11:27.301][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-11 16:11:27.302][biodb::testThat]
biodb.WARN [2024-05-11 16:11:27.328][self$searchForEntries] This database is not searchable by field "name".
biodb.WARN [2024-05-11 16:11:27.347][self$searchForEntries] This database is not searchable by field "name".
biodb.INFO [2024-05-11 16:11:27.359][biodb::testThat]
biodb.INFO [2024-05-11 16:11:27.360][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2024-05-11 16:11:27.362][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-11 16:11:27.363][biodb::testThat]
biodb.DEBUG[2024-05-11 16:11:27.379][private$loadEntries] Creating entries from ids [1]: "749674".
biodb.DEBUG[2024-05-11 16:11:27.428][conn$getEntryContent] Get NCI CACTUS entry content(s) for 1 id(s)...
biodb.DEBUG[2024-05-11 16:11:27.430][self$isDownloaded] Database nci.cactus has not yet been downloaded.
biodb.INFO [2024-05-11 16:11:27.432][self$download] Downloading whole database of nci.cactus.
biodb.INFO [2024-05-11 16:11:27.433][private$doDownload] Downloading NCI CACTUS database at "https://cactus.nci.nih.gov/download/nci/NCI-Open_2012-05-01.sdf.gz" ...
biodb.DEBUG[2024-05-11 16:11:27.450][sched$downloadFile] Downloading file "https://cactus.nci.nih.gov/download/nci/NCI-Open_2012-05-01.sdf.gz".
trying URL 'https://cactus.nci.nih.gov/download/nci/NCI-Open_2012-05-01.sdf.gz'
Content type 'application/x-gzip' length 206737123 bytes (197.2 MB)

downloaded 0 bytes

biodb.INFO [2024-05-11 16:11:27.550][biodb::testThat]
biodb.INFO [2024-05-11 16:11:27.551][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2024-05-11 16:11:27.553][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-11 16:11:27.554][biodb::testThat]
biodb.INFO [2024-05-11 16:11:27.564][biodb::testThat]
biodb.INFO [2024-05-11 16:11:27.566][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2024-05-11 16:11:27.567][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-11 16:11:27.568][biodb::testThat]
biodb.INFO [2024-05-11 16:11:27.578][biodb::testThat]
biodb.INFO [2024-05-11 16:11:27.580][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2024-05-11 16:11:27.581][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-11 16:11:27.582][biodb::testThat]
biodb.INFO [2024-05-11 16:11:27.591][biodb::testThat]
biodb.INFO [2024-05-11 16:11:27.592][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2024-05-11 16:11:27.593][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-11 16:11:27.595][biodb::testThat]
biodb.INFO [2024-05-11 16:11:27.603][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-05-11 16:11:27.605][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector nci.cactus from the request scheduler
biodb.INFO [2024-05-11 16:11:27.606][self$deleteConn] Connector "nci.cactus" deleted.
biodb.DEBUG[2024-05-11 16:11:27.607][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-05-11 16:11:27.608][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-11 16:11:27.609][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-11 16:11:27.610][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-11 16:11:27.611][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-11 16:11:27.613][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:11:27.614][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2024-05-11 16:11:27.623][biodb::testContext]
biodb.INFO [2024-05-11 16:11:27.629][biodb::testContext] ********************************************************************************
biodb.INFO [2024-05-11 16:11:27.631][biodb::testContext] Test context - Example long tests
biodb.INFO [2024-05-11 16:11:27.632][biodb::testContext] ********************************************************************************
biodb.INFO [2024-05-11 16:11:27.633][biodb::testContext]
biodb.INFO [2024-05-11 16:11:27.636][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.12.0.
biodb.DEBUG[2024-05-11 16:11:27.638][self$loadDefinitions] Load definitions from file "F:/biocbuild/bbs-3.19-bioc/R/library/biodb/definitions.yml".
biodb.DEBUG[2024-05-11 16:11:27.644][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-05-11 16:11:27.645][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-05-11 16:11:27.646][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-05-11 16:11:27.647][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:11:27.649][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:11:27.650][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:11:27.651][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-05-11 16:11:27.652][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-05-11 16:11:27.653][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:11:27.654][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:11:27.656][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:11:27.657][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-05-11 16:11:27.658][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-05-11 16:11:27.659][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:11:27.660][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:11:27.661][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:11:27.663][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-05-11 16:11:27.664][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-05-11 16:11:27.665][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-05-11 16:11:27.666][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:11:27.667][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:11:27.668][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:11:27.670][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-05-11 16:11:27.671][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-05-11 16:11:27.672][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-05-11 16:11:27.673][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:11:27.674][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:11:27.676][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:11:27.677][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-05-11 16:11:27.678][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-05-11 16:11:27.679][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:11:27.680][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:11:27.681][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:11:27.683][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-05-11 16:11:27.684][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-05-11 16:11:27.685][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-05-11 16:11:27.686][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:11:27.687][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:11:27.688][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:11:27.689][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-05-11 16:11:27.691][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-05-11 16:11:27.692][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:11:27.693][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:11:27.694][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:11:27.695][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-05-11 16:11:27.696][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-05-11 16:11:27.698][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-05-11 16:11:27.699][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:11:27.700][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:11:27.701][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:11:27.702][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-05-11 16:11:27.703][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-05-11 16:11:27.705][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-05-11 16:11:27.706][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-05-11 16:11:27.707][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-05-11 16:11:27.708][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-05-11 16:11:27.709][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:11:27.710][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:11:27.712][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:11:27.713][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-05-11 16:11:27.714][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-05-11 16:11:27.715][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:11:27.716][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:11:27.717][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:11:27.718][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-05-11 16:11:27.720][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-05-11 16:11:27.721][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:11:27.722][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:11:27.723][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:11:27.724][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-05-11 16:11:27.726][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-05-11 16:11:27.727][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:11:27.728][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:11:27.729][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:11:27.731][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-05-11 16:11:27.733][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-05-11 16:11:27.734][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:11:27.735][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:11:27.736][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:11:27.737][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-05-11 16:11:27.739][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-05-11 16:11:27.740][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:11:27.741][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:11:27.742][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:11:27.743][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-05-11 16:11:27.745][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-05-11 16:11:27.749][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-05-11 16:11:27.750][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:11:27.751][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:11:27.752][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:11:27.753][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-05-11 16:11:27.754][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-05-11 16:11:27.756][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-05-11 16:11:27.757][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:11:27.758][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:11:27.759][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:11:27.760][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-05-11 16:11:27.762][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-05-11 16:11:27.763][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2024-05-11 16:11:27.765][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-11 16:11:27.766][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-11 16:11:27.767][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-11 16:11:27.769][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-11 16:11:27.771][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-05-11 16:11:27.772][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-11 16:11:27.773][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-05-11 16:11:27.774][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-11 16:11:27.775][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-05-11 16:11:27.777][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-05-11 16:11:27.778][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-11 16:11:27.779][self$setPropertyValue]
biodb.DEBUG[2024-05-11 16:11:27.780][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-05-11 16:11:27.781][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-05-11 16:11:27.781][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-05-11 16:11:27.781][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-05-11 16:11:27.781][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-05-11 16:11:27.781][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-05-11 16:11:27.783][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-05-11 16:11:27.784][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-11 16:11:27.785][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-11 16:11:27.786][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-11 16:11:27.787][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-11 16:11:27.788][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-11 16:11:27.790][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-11 16:11:27.791][self$setPropertyValue]
biodb.DEBUG[2024-05-11 16:11:27.792][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-11 16:11:27.793][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-11 16:11:27.794][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-05-11 16:11:27.795][self$setPropertyValue]
biodb.DEBUG[2024-05-11 16:11:27.797][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-05-11 16:11:27.804][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-05-11 16:11:27.805][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-05-11 16:11:27.806][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-11 16:11:27.807][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-11 16:11:27.809][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-11 16:11:27.810][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-11 16:11:27.811][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-05-11 16:11:27.812][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-11 16:11:27.813][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-05-11 16:11:27.815][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-11 16:11:27.816][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-05-11 16:11:27.817][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-05-11 16:11:27.818][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-11 16:11:27.820][self$setPropertyValue]
biodb.DEBUG[2024-05-11 16:11:27.821][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-05-11 16:11:27.822][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-05-11 16:11:27.822][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-05-11 16:11:27.822][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-05-11 16:11:27.822][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-05-11 16:11:27.822][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-05-11 16:11:27.823][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-05-11 16:11:27.825][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-11 16:11:27.826][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-11 16:11:27.827][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-11 16:11:27.828][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-11 16:11:27.829][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-11 16:11:27.830][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-11 16:11:27.831][self$setPropertyValue]
biodb.DEBUG[2024-05-11 16:11:27.833][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-11 16:11:27.834][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-11 16:11:27.835][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-05-11 16:11:27.836][self$setPropertyValue]
biodb.DEBUG[2024-05-11 16:11:27.837][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-05-11 16:11:27.839][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-05-11 16:11:27.841][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2024-05-11 16:11:27.842][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-11 16:11:27.843][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-11 16:11:27.844][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-11 16:11:27.846][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-11 16:11:27.847][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-05-11 16:11:27.848][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-11 16:11:27.849][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-05-11 16:11:27.851][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-11 16:11:27.852][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-05-11 16:11:27.853][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-05-11 16:11:27.854][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-11 16:11:27.856][self$setPropertyValue]
biodb.DEBUG[2024-05-11 16:11:27.857][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-05-11 16:11:27.858][self$setPropertyValue]
biodb.DEBUG[2024-05-11 16:11:27.859][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-05-11 16:11:27.860][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-11 16:11:27.861][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-11 16:11:27.863][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-11 16:11:27.864][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-11 16:11:27.865][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-11 16:11:27.866][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-11 16:11:27.867][self$setPropertyValue]
biodb.DEBUG[2024-05-11 16:11:27.868][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-11 16:11:27.870][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-11 16:11:27.871][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-05-11 16:11:27.872][self$setPropertyValue]
biodb.DEBUG[2024-05-11 16:11:27.873][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-05-11 16:11:27.875][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-05-11 16:11:27.877][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-05-11 16:11:27.878][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-11 16:11:27.880][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-11 16:11:27.882][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-11 16:11:27.883][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-11 16:11:27.884][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-05-11 16:11:27.885][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-11 16:11:27.887][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-05-11 16:11:27.888][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-11 16:11:27.889][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-05-11 16:11:27.890][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-05-11 16:11:27.891][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-11 16:11:27.893][self$setPropertyValue]
biodb.DEBUG[2024-05-11 16:11:27.894][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-05-11 16:11:27.895][self$setPropertyValue]
biodb.DEBUG[2024-05-11 16:11:27.896][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-05-11 16:11:27.898][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-11 16:11:27.899][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-11 16:11:27.900][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-11 16:11:27.901][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-11 16:11:27.902][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-11 16:11:27.903][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-11 16:11:27.904][self$setPropertyValue]
biodb.DEBUG[2024-05-11 16:11:27.906][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-11 16:11:27.907][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-11 16:11:27.908][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-05-11 16:11:27.909][self$setPropertyValue]
biodb.DEBUG[2024-05-11 16:11:27.911][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-05-11 16:11:27.912][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:11:27.913][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:11:27.914][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:11:27.915][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-11 16:11:27.916][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-11 16:11:27.917][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:11:27.918][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:11:27.919][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:11:27.921][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-11 16:11:27.922][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-11 16:11:27.923][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:11:27.924][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:11:27.925][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:11:27.926][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-11 16:11:27.927][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 16:11:27.928][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:11:27.929][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:11:27.931][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:11:27.932][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-11 16:11:27.933][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 16:11:27.934][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:11:27.935][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:11:27.936][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:11:27.937][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-11 16:11:27.938][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-11 16:11:27.939][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:11:27.940][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:11:27.942][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:11:27.943][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-11 16:11:27.944][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-11 16:11:27.945][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:11:27.946][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:11:27.947][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:11:27.948][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-11 16:11:27.949][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 16:11:27.950][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:11:27.951][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:11:27.953][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:11:27.954][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-11 16:11:27.955][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 16:11:27.956][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:11:27.957][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:11:27.958][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:11:27.959][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-11 16:11:27.960][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 16:11:27.961][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:11:27.963][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:11:27.968][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:11:27.969][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-11 16:11:27.971][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 16:11:27.972][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:11:27.973][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:11:27.974][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:11:27.975][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-11 16:11:27.976][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 16:11:27.977][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:11:27.978][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:11:27.979][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:11:27.980][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-11 16:11:27.981][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 16:11:27.983][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:11:27.984][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:11:27.985][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:11:27.986][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-11 16:11:27.987][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-11 16:11:27.989][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:11:27.990][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:11:27.991][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:11:27.992][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-11 16:11:27.993][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 16:11:27.994][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:11:27.996][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:11:27.997][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:11:27.998][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-11 16:11:27.999][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 16:11:28.000][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:11:28.001][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:11:28.002][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:11:28.003][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-11 16:11:28.004][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 16:11:28.005][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:11:28.007][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:11:28.008][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:11:28.009][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-11 16:11:28.010][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 16:11:28.011][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:11:28.012][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:11:28.014][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-05-11 16:11:28.015][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-05-11 16:11:28.017][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-05-11 16:11:28.018][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-05-11 16:11:28.020][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-05-11 16:11:28.022][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-05-11 16:11:28.024][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-05-11 16:11:28.025][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-05-11 16:11:28.027][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-05-11 16:11:28.029][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-05-11 16:11:28.030][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-05-11 16:11:28.032][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-05-11 16:11:28.033][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-05-11 16:11:28.035][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-05-11 16:11:28.037][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-05-11 16:11:28.039][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-05-11 16:11:28.040][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-05-11 16:11:28.042][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-05-11 16:11:28.043][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-05-11 16:11:28.045][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-05-11 16:11:28.046][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-05-11 16:11:28.048][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-05-11 16:11:28.050][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-05-11 16:11:28.051][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-05-11 16:11:28.053][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-05-11 16:11:28.055][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-05-11 16:11:28.057][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-05-11 16:11:28.059][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-05-11 16:11:28.060][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-05-11 16:11:28.062][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-05-11 16:11:28.063][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-05-11 16:11:28.065][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-05-11 16:11:28.066][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-05-11 16:11:28.068][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-05-11 16:11:28.070][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-05-11 16:11:28.071][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-05-11 16:11:28.073][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-05-11 16:11:28.074][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-05-11 16:11:28.076][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-05-11 16:11:28.077][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-05-11 16:11:28.079][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-05-11 16:11:28.081][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-05-11 16:11:28.082][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-05-11 16:11:28.084][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-05-11 16:11:28.085][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-05-11 16:11:28.087][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-05-11 16:11:28.089][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-05-11 16:11:28.090][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-05-11 16:11:28.092][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-05-11 16:11:28.093][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-05-11 16:11:28.095][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-05-11 16:11:28.096][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-05-11 16:11:28.098][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-05-11 16:11:28.100][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-05-11 16:11:28.101][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-05-11 16:11:28.103][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-05-11 16:11:28.104][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-05-11 16:11:28.106][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-05-11 16:11:28.107][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-05-11 16:11:28.109][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-05-11 16:11:28.111][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-05-11 16:11:28.112][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-05-11 16:11:28.114][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-05-11 16:11:28.115][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-05-11 16:11:28.117][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-05-11 16:11:28.124][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-05-11 16:11:28.125][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-05-11 16:11:28.127][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-05-11 16:11:28.129][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-05-11 16:11:28.130][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-05-11 16:11:28.132][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-05-11 16:11:28.133][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-05-11 16:11:28.135][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-05-11 16:11:28.136][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-05-11 16:11:28.138][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-05-11 16:11:28.139][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-05-11 16:11:28.141][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-05-11 16:11:28.143][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-05-11 16:11:28.144][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-05-11 16:11:28.146][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-05-11 16:11:28.147][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-05-11 16:11:28.149][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-05-11 16:11:28.150][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-05-11 16:11:28.152][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-05-11 16:11:28.154][initialize] This is biodb version 1.12.0.
biodb.DEBUG[2024-05-11 16:11:28.156][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-05-11 16:11:28.157][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-05-11 16:11:28.158][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-11 16:11:28.159][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:11:28.160][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:11:28.161][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:11:28.162][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-11 16:11:28.163][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-11 16:11:28.164][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-11 16:11:28.166][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 16:11:28.167][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:11:28.168][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:11:28.169][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:11:28.170][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-11 16:11:28.171][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-11 16:11:28.172][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-11 16:11:28.173][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 16:11:28.174][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:11:28.175][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:11:28.176][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:11:28.178][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-11 16:11:28.179][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-11 16:11:28.180][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-11 16:11:28.181][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 16:11:28.182][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:11:28.183][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:11:28.184][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:11:28.185][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-11 16:11:28.186][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-11 16:11:28.187][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-11 16:11:28.188][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-11 16:11:28.190][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:11:28.191][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:11:28.192][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:11:28.193][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-11 16:11:28.194][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-11 16:11:28.195][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-11 16:11:28.196][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 16:11:28.197][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:11:28.198][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:11:28.200][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:11:28.201][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-11 16:11:28.202][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-11 16:11:28.203][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-11 16:11:28.204][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 16:11:28.205][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:11:28.206][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:11:28.207][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:11:28.208][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-11 16:11:28.209][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-11 16:11:28.211][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-11 16:11:28.212][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 16:11:28.213][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:11:28.214][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:11:28.215][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:11:28.216][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-11 16:11:28.217][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-11 16:11:28.218][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-11 16:11:28.219][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 16:11:28.220][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:11:28.222][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 16:11:28.223][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:11:28.224][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-11 16:11:28.225][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-11 16:11:28.226][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-11 16:11:28.227][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 16:11:28.228][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:11:28.229][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:11:28.230][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:11:28.231][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-11 16:11:28.233][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-11 16:11:28.234][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-11 16:11:28.235][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 16:11:28.236][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:11:28.237][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 16:11:28.238][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:11:28.239][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-11 16:11:28.240][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-11 16:11:28.241][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-11 16:11:28.242][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-11 16:11:28.244][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:11:28.245][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:11:28.246][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:11:28.247][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-11 16:11:28.248][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-11 16:11:28.249][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-11 16:11:28.250][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 16:11:28.251][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:11:28.252][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 16:11:28.253][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:11:28.254][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-11 16:11:28.255][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-11 16:11:28.256][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-11 16:11:28.258][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 16:11:28.259][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:11:28.260][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:11:28.261][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:11:28.262][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-11 16:11:28.263][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-11 16:11:28.264][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-11 16:11:28.265][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 16:11:28.266][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:11:28.267][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 16:11:28.268][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:11:28.269][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-11 16:11:28.271][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-11 16:11:28.272][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-11 16:11:28.273][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-11 16:11:28.274][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:11:28.275][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 16:11:28.276][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:11:28.282][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-11 16:11:28.283][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-11 16:11:28.285][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-11 16:11:28.286][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 16:11:28.287][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:11:28.288][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:11:28.289][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:11:28.290][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-11 16:11:28.291][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-11 16:11:28.292][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-11 16:11:28.293][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-11 16:11:28.294][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:11:28.295][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 16:11:28.299][biodb$loadDefinitions] Load definitions from file "F:/biocbuild/bbs-3.19-bioc-longtests/meat/biodbNci.Rcheck/biodbNci/definitions.yml".
biodb.DEBUG[2024-05-11 16:11:28.301][self$getDbsInfo()$define] Define connector nci.cactus.
biodb.DEBUG[2024-05-11 16:11:28.303][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-05-11 16:11:28.304][self$setPropertyValue] Setting property "description" to "National Cancer Institute (USA) CACTUS Database.".
biodb.DEBUG[2024-05-11 16:11:28.305][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-11 16:11:28.306][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-11 16:11:28.308][self$setPropertyValue] Setting property "downloadable" to "TRUE".
biodb.DEBUG[2024-05-11 16:11:28.309][self$setPropertyValue] Setting property "dwnld.ext" to "gz".
biodb.DEBUG[2024-05-11 16:11:28.310][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-05-11 16:11:28.312][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-11 16:11:28.313][self$setPropertyValue] Setting property "entry.content.type" to "sdf".
biodb.DEBUG[2024-05-11 16:11:28.314][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-11 16:11:28.315][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-05-11 16:11:28.316][self$setPropertyValue] Setting property "name" to "NCI CACTUS".
biodb.DEBUG[2024-05-11 16:11:28.318][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-11 16:11:28.319][self$setPropertyValue] Setting property "parsing.expr" to "NSC".
biodb.DEBUG[2024-05-11 16:11:28.319][self$setPropertyValue] Setting property "parsing.expr" to "DTP names".
biodb.DEBUG[2024-05-11 16:11:28.319][self$setPropertyValue] Setting property "parsing.expr" to "Standard InChI".
biodb.DEBUG[2024-05-11 16:11:28.319][self$setPropertyValue] Setting property "parsing.expr" to "c("Standard InChIKey", "^InChIKey=(.*)$")".
biodb.DEBUG[2024-05-11 16:11:28.319][self$setPropertyValue] Setting property "parsing.expr" to "Formula".
biodb.DEBUG[2024-05-11 16:11:28.319][self$setPropertyValue] Setting property "parsing.expr" to "Molecular Weight".
biodb.DEBUG[2024-05-11 16:11:28.319][self$setPropertyValue] Setting property "parsing.expr" to "CAS".
biodb.DEBUG[2024-05-11 16:11:28.320][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-05-11 16:11:28.321][self$setPropertyValue]
biodb.DEBUG[2024-05-11 16:11:28.323][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2024-05-11 16:11:28.324][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-11 16:11:28.325][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-11 16:11:28.326][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-11 16:11:28.327][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-11 16:11:28.328][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-11 16:11:28.329][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-11 16:11:28.331][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/".
biodb.DEBUG[2024-05-11 16:11:28.331][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/".
biodb.DEBUG[2024-05-11 16:11:28.331][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/download/nci/".
biodb.DEBUG[2024-05-11 16:11:28.331][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/download/nci/NCI-Open_2012-05-01.sdf.gz".
biodb.DEBUG[2024-05-11 16:11:28.332][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-11 16:11:28.333][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-11 16:11:28.334][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-05-11 16:11:28.335][self$setPropertyValue]
biodb.DEBUG[2024-05-11 16:11:28.337][self$getEntryFields()$define] Define field nci.cactus.id.
biodb.DEBUG[2024-05-11 16:11:28.341][super$initialize] Initialize connector nci.cactus.
biodb.DEBUG[2024-05-11 16:11:28.342][super$initialize] Register connector nci.cactus with the request scheduler
biodb.DEBUG[2024-05-11 16:11:28.343][private$bdb$getRequestScheduler()$re ...] Register connector nci.cactus.
biodb.DEBUG[2024-05-11 16:11:28.345][private$addConnectorRules] Create new rule for URL "cactus.nci.nih.gov" of connector "nci.cactus".
biodb.DEBUG[2024-05-11 16:11:28.346][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-05-11 16:11:28.348][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-05-11 16:11:28.349][rule$addConnector] Connector "nci.cactus" is already listed in rule "cactus.nci.nih.gov".
biodb.DEBUG[2024-05-11 16:11:28.351][rule$addConnector] Connector "nci.cactus" is already listed in rule "cactus.nci.nih.gov".
biodb.DEBUG[2024-05-11 16:11:28.353][rule$addConnector] Connector "nci.cactus" is already listed in rule "cactus.nci.nih.gov".
biodb.DEBUG[2024-05-11 16:11:28.354][biodb$getFactory()$createConn] Creating new connector nci.cactus for database class nci.cactus .
biodb.INFO [2024-05-11 16:11:28.357][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-05-11 16:11:28.358][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector nci.cactus from the request scheduler
biodb.INFO [2024-05-11 16:11:28.360][self$deleteConn] Connector "nci.cactus" deleted.
biodb.DEBUG[2024-05-11 16:11:28.361][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-05-11 16:11:28.362][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-11 16:11:28.363][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-11 16:11:28.364][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-11 16:11:28.365][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 16:11:28.366][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:11:28.368][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
[ FAIL 2 | WARN 4 | SKIP 0 | PASS 85 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test_long_100_generic.R:37:1'): RT unit is defined when there is an RT value. ──
Error in `utils::download.file(url = url, destfile = dest.file, mode = "wb", 
    method = "auto", cacheOK = FALSE, quiet = FALSE)`: download from 'https://cactus.nci.nih.gov/download/nci/NCI-Open_2012-05-01.sdf.gz' failed
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb (local) `<fn>`(conn = `<NcCctsCn>`, opt = `<named list>`)
 3.   └─conn$getBiodb()$getFactory()$getEntry(...)
 4.     └─private$loadEntries(conn$getId(), missing.ids, drop = FALSE)
 5.       └─conn$getEntryContent(ids)
 6.         └─self$download()
 7.           └─private$doDownload()
 8.             └─sched$downloadFile(url = gz.url, dest.file = tmpFile)
 9.               └─utils::download.file(...)
── Error ('test_long_100_generic.R:37:1'): We can load an entry from the database. ──
Error in `utils::download.file(url = url, destfile = dest.file, mode = "wb", 
    method = "auto", cacheOK = FALSE, quiet = FALSE)`: download from 'https://cactus.nci.nih.gov/download/nci/NCI-Open_2012-05-01.sdf.gz' failed
Backtrace:
     ▆
  1. ├─base::do.call(fct, params)
  2. └─biodb (local) `<fn>`(conn = `<NcCctsCn>`, opt = `<named list>`)
  3.   └─opt$refEntries$getRealEntry(id)
  4.     └─self$getRealEntries(ids = id)
  5.       └─private$bdb$getFactory()$getEntry(...)
  6.         └─private$loadEntries(conn$getId(), missing.ids, drop = FALSE)
  7.           └─conn$getEntryContent(ids)
  8.             └─self$download()
  9.               └─private$doDownload()
 10.                 └─sched$downloadFile(url = gz.url, dest.file = tmpFile)
 11.                   └─utils::download.file(...)

[ FAIL 2 | WARN 4 | SKIP 0 | PASS 85 ]
Error: Test failures
Execution halted

'R CMD check' output

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --test-dir=longtests --no-stop-on-test-error --no-codoc --no-examples --no-manual --ignore-vignettes --check-subdirs=no biodbNci_1.8.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.19-bioc-longtests/meat/biodbNci.Rcheck'
* using R version 4.4.0 (2024-04-24 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.2.0
    GNU Fortran (GCC) 13.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using options '--no-codoc --no-examples --no-manual --ignore-vignettes --no-stop-on-test-error'
* checking for file 'biodbNci/DESCRIPTION' ... OK
* this is package 'biodbNci' 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 whether package 'biodbNci' can be installed ... OK
* used C++ compiler: 'G__~1.EXE (GCC) 13.2.0'
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* 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 line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... OK
* checking files in 'vignettes' ... SKIPPED
* checking examples ... SKIPPED
* checking for unstated dependencies in 'longtests' ... OK
* checking tests in 'longtests' ...
  Running 'testthat.R'
 ERROR
Running the tests in 'longtests/testthat.R' failed.
Last 13 lines of output:
    1. ├─base::do.call(fct, params)
    2. └─biodb (local) `<fn>`(conn = `<NcCctsCn>`, opt = `<named list>`)
    3.   └─opt$refEntries$getRealEntry(id)
    4.     └─self$getRealEntries(ids = id)
    5.       └─private$bdb$getFactory()$getEntry(...)
    6.         └─private$loadEntries(conn$getId(), missing.ids, drop = FALSE)
    7.           └─conn$getEntryContent(ids)
    8.             └─self$download()
    9.               └─private$doDownload()
   10.                 └─sched$downloadFile(url = gz.url, dest.file = tmpFile)
   11.                   └─utils::download.file(...)
  
  [ FAIL 2 | WARN 4 | SKIP 0 | PASS 85 ]
  Error: Test failures
  Execution halted
* DONE

Status: 1 ERROR
See
  'F:/biocbuild/bbs-3.19-bioc-longtests/meat/biodbNci.Rcheck/00check.log'
for details.

Installation output

biodbNci.Rcheck/00install.out

* installing *source* package 'biodbNci' ...
** using staged installation
** libs
using C++ compiler: 'G__~1.EXE (GCC) 13.2.0'
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.19-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.19-bioc/R/library/testthat/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.19-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.19-bioc/R/library/testthat/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c extractEntries.cpp -o extractEntries.o
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.19-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.19-bioc/R/library/testthat/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c test-100-example.cpp -o test-100-example.o
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.19-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.19-bioc/R/library/testthat/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c test-runner.cpp -o test-runner.o
g++ -std=gnu++17 -shared -s -static-libgcc -o biodbNci.dll tmp.def RcppExports.o extractEntries.o test-100-example.o test-runner.o -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.19-bioc/R/bin/x64 -lR
installing to F:/biocbuild/bbs-3.19-bioc-longtests/meat/biodbNci.Rcheck/00LOCK-biodbNci/00new/biodbNci/libs/x64
** 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 (biodbNci)