Back to Long Tests report for BioC 3.20

This page was generated on 2024-05-18 23:55:02 -0400 (Sat, 18 May 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 RC (2024-04-16 r86468) -- "Puppy Cup" 4666
palomino4Windows Server 2022 Datacenterx644.4.0 RC (2024-04-16 r86468 ucrt) -- "Puppy Cup" 4401
merida1macOS 12.7.4 Montereyx86_644.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" 4428
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 8/32HostnameOS / ArchCHECK
biodbHmdb 1.11.0  (landing page)
Pierrick Roger
Snapshot Date: 2024-05-18 09:55:01 -0400 (Sat, 18 May 2024)
git_url: https://git.bioconductor.org/packages/biodbHmdb
git_branch: devel
git_last_commit: c3d59a4
git_last_commit_date: 2024-04-30 11:39:05 -0400 (Tue, 30 Apr 2024)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  ERROR  
palomino4Windows Server 2022 Datacenter / x64  ERROR  
merida1macOS 12.7.4 Monterey / x86_64  ERROR  

CHECK results for biodbHmdb on palomino4


To the developers/maintainers of the biodbHmdb 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: biodbHmdb
Version: 1.11.0
Command: F:\biocbuild\bbs-3.20-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 biodbHmdb_1.11.0.tar.gz
StartedAt: 2024-05-18 16:04:40 -0400 (Sat, 18 May 2024)
EndedAt: 2024-05-18 17:15:53 -0400 (Sat, 18 May 2024)
EllapsedTime: 4272.7 seconds
RetCode: 1
Status:   ERROR  
CheckDir: biodbHmdb.Rcheck
Warnings: NA

Tests output

biodbHmdb.Rcheck/tests/testthat.Rout.fail


R version 4.4.0 RC (2024-04-16 r86468 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(biodbHmdb)
> Sys.setenv(TESTTHAT_REPORTER="summary")
> Sys.setenv(BIODB_LOG_DST="console")
> test_check("biodbHmdb")
biodb.INFO [2024-05-18 16:06:21.183][biodb::testContext]
biodb.INFO [2024-05-18 16:06:21.186][biodb::testContext] ********************************************************************************
biodb.INFO [2024-05-18 16:06:21.187][biodb::testContext] Test context - Generic long tests
biodb.INFO [2024-05-18 16:06:21.188][biodb::testContext] ********************************************************************************
biodb.INFO [2024-05-18 16:06:21.189][biodb::testContext]
biodb.INFO [2024-05-18 16:06:21.195][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.13.0.
biodb.DEBUG[2024-05-18 16:06:21.198][self$loadDefinitions] Load definitions from file "F:/biocbuild/bbs-3.20-bioc/R/library/biodb/definitions.yml".
biodb.DEBUG[2024-05-18 16:06:21.206][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-05-18 16:06:21.207][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-05-18 16:06:21.208][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-05-18 16:06:21.209][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:06:21.210][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:06:21.212][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-18 16:06:21.213][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-05-18 16:06:21.229][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-05-18 16:06:21.230][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:06:21.231][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:06:21.232][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-18 16:06:21.234][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-05-18 16:06:21.235][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-05-18 16:06:21.236][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:06:21.237][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:06:21.238][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-18 16:06:21.239][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-05-18 16:06:21.240][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-05-18 16:06:21.242][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-05-18 16:06:21.243][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:06:21.244][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:06:21.245][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[2024-05-18 16:06:21.246][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-05-18 16:06:21.247][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-05-18 16:06:21.249][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-05-18 16:06:21.250][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:06:21.251][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:06:21.252][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-18 16:06:21.253][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-05-18 16:06:21.254][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-05-18 16:06:21.255][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:06:21.256][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:06:21.257][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-18 16:06:21.259][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-05-18 16:06:21.260][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-05-18 16:06:21.261][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-05-18 16:06:21.262][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:06:21.263][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:06:21.264][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-18 16:06:21.265][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-05-18 16:06:21.267][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-05-18 16:06:21.268][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:06:21.269][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:06:21.270][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.DEBUG[2024-05-18 16:06:21.271][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-05-18 16:06:21.272][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-05-18 16:06:21.274][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-05-18 16:06:21.275][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:06:21.276][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:06:21.277][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-18 16:06:21.278][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-05-18 16:06:21.279][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-05-18 16:06:21.280][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-05-18 16:06:21.282][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-05-18 16:06:21.283][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-05-18 16:06:21.284][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-05-18 16:06:21.285][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:06:21.286][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:06:21.287][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-18 16:06:21.289][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-05-18 16:06:21.290][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-05-18 16:06:21.291][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:06:21.292][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:06:21.293][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-18 16:06:21.294][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-05-18 16:06:21.295][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-05-18 16:06:21.297][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:06:21.298][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:06:21.299][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-18 16:06:21.300][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-05-18 16:06:21.301][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-05-18 16:06:21.302][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:06:21.303][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:06:21.304][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-18 16:06:21.306][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-05-18 16:06:21.307][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-05-18 16:06:21.308][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:06:21.309][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:06:21.310][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-18 16:06:21.311][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-05-18 16:06:21.313][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-05-18 16:06:21.314][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:06:21.315][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:06:21.316][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-18 16:06:21.317][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-05-18 16:06:21.318][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-05-18 16:06:21.322][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-05-18 16:06:21.323][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:06:21.324][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:06:21.325][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-18 16:06:21.326][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-05-18 16:06:21.327][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-05-18 16:06:21.329][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-05-18 16:06:21.330][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:06:21.331][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:06:21.332][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-18 16:06:21.335][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-05-18 16:06:21.369][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-05-18 16:06:21.383][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2024-05-18 16:06:21.385][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-18 16:06:21.386][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-18 16:06:21.387][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-18 16:06:21.388][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-18 16:06:21.390][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-05-18 16:06:21.391][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-18 16:06:21.392][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-05-18 16:06:21.393][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-18 16:06:21.394][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-05-18 16:06:21.396][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-05-18 16:06:21.397][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-18 16:06:21.398][self$setPropertyValue]
biodb.DEBUG[2024-05-18 16:06:21.399][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-05-18 16:06:21.400][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-05-18 16:06:21.400][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-05-18 16:06:21.400][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-05-18 16:06:21.400][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-05-18 16:06:21.400][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-05-18 16:06:21.402][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-05-18 16:06:21.403][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-18 16:06:21.404][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-18 16:06:21.405][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-18 16:06:21.406][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-18 16:06:21.407][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-18 16:06:21.408][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-18 16:06:21.410][self$setPropertyValue]
biodb.DEBUG[2024-05-18 16:06:21.411][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-18 16:06:21.412][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-18 16:06:21.413][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-05-18 16:06:21.414][self$setPropertyValue]
biodb.DEBUG[2024-05-18 16:06:21.416][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-05-18 16:06:21.418][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-05-18 16:06:21.419][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-05-18 16:06:21.420][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-18 16:06:21.421][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-18 16:06:21.422][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-18 16:06:21.423][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-18 16:06:21.425][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-05-18 16:06:21.426][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-18 16:06:21.427][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-05-18 16:06:21.428][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-18 16:06:21.429][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-05-18 16:06:21.431][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-05-18 16:06:21.432][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-18 16:06:21.433][self$setPropertyValue]
biodb.DEBUG[2024-05-18 16:06:21.434][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-05-18 16:06:21.435][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-05-18 16:06:21.435][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-05-18 16:06:21.435][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-05-18 16:06:21.435][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-05-18 16:06:21.435][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-05-18 16:06:21.437][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-05-18 16:06:21.438][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-18 16:06:21.439][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-18 16:06:21.440][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-18 16:06:21.441][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-18 16:06:21.442][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-18 16:06:21.443][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-18 16:06:21.445][self$setPropertyValue]
biodb.DEBUG[2024-05-18 16:06:21.446][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-18 16:06:21.447][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-18 16:06:21.448][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-05-18 16:06:21.449][self$setPropertyValue]
biodb.DEBUG[2024-05-18 16:06:21.451][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-05-18 16:06:21.453][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-05-18 16:06:21.454][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2024-05-18 16:06:21.455][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-18 16:06:21.456][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-18 16:06:21.457][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-18 16:06:21.459][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-18 16:06:21.460][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-05-18 16:06:21.461][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-18 16:06:21.462][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-05-18 16:06:21.463][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-18 16:06:21.465][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-05-18 16:06:21.466][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-05-18 16:06:21.467][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-18 16:06:21.468][self$setPropertyValue]
biodb.DEBUG[2024-05-18 16:06:21.469][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-05-18 16:06:21.471][self$setPropertyValue]
biodb.DEBUG[2024-05-18 16:06:21.472][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-05-18 16:06:21.473][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-18 16:06:21.474][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-18 16:06:21.475][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-18 16:06:21.476][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-18 16:06:21.477][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-18 16:06:21.479][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-18 16:06:21.480][self$setPropertyValue]
biodb.DEBUG[2024-05-18 16:06:21.481][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-18 16:06:21.482][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-18 16:06:21.483][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-05-18 16:06:21.484][self$setPropertyValue]
biodb.DEBUG[2024-05-18 16:06:21.486][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-05-18 16:06:21.488][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-05-18 16:06:21.489][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-05-18 16:06:21.490][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-18 16:06:21.491][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-18 16:06:21.492][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-18 16:06:21.494][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-18 16:06:21.495][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-05-18 16:06:21.496][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-18 16:06:21.497][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-05-18 16:06:21.498][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-18 16:06:21.500][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-05-18 16:06:21.501][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-05-18 16:06:21.502][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-18 16:06:21.503][self$setPropertyValue]
biodb.DEBUG[2024-05-18 16:06:21.504][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-05-18 16:06:21.505][self$setPropertyValue]
biodb.DEBUG[2024-05-18 16:06:21.507][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-05-18 16:06:21.508][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-18 16:06:21.509][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-18 16:06:21.510][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-18 16:06:21.511][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-18 16:06:21.512][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-18 16:06:21.514][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-18 16:06:21.515][self$setPropertyValue]
biodb.DEBUG[2024-05-18 16:06:21.516][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-18 16:06:21.517][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-18 16:06:21.518][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-05-18 16:06:21.519][self$setPropertyValue]
biodb.DEBUG[2024-05-18 16:06:21.523][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-05-18 16:06:21.524][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:06:21.525][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-18 16:06:21.526][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:06:21.527][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-18 16:06:21.528][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-18 16:06:21.529][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:06:21.530][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-18 16:06:21.532][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:06:21.533][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-18 16:06:21.534][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-18 16:06:21.535][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:06:21.536][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-18 16:06:21.537][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:06:21.538][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-18 16:06:21.539][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-18 16:06:21.540][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:06:21.541][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-18 16:06:21.543][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:06:21.544][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-18 16:06:21.545][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-18 16:06:21.546][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:06:21.547][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-18 16:06:21.548][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:06:21.549][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-18 16:06:21.550][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-18 16:06:21.551][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:06:21.552][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-18 16:06:21.554][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:06:21.559][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-18 16:06:21.561][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-18 16:06:21.562][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:06:21.563][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-18 16:06:21.564][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:06:21.565][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-18 16:06:21.566][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-18 16:06:21.567][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:06:21.568][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-18 16:06:21.569][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:06:21.570][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-18 16:06:21.571][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-18 16:06:21.572][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:06:21.573][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-18 16:06:21.575][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:06:21.576][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-18 16:06:21.577][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-18 16:06:21.578][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:06:21.579][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-18 16:06:21.580][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:06:21.581][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-18 16:06:21.582][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-18 16:06:21.583][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:06:21.584][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-18 16:06:21.585][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:06:21.586][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-18 16:06:21.587][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-18 16:06:21.588][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:06:21.590][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-18 16:06:21.591][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:06:21.592][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-18 16:06:21.593][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-18 16:06:21.594][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:06:21.595][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-18 16:06:21.596][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:06:21.597][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-18 16:06:21.598][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-18 16:06:21.599][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:06:21.600][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-18 16:06:21.601][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:06:21.602][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-18 16:06:21.604][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-18 16:06:21.605][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:06:21.606][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-18 16:06:21.607][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:06:21.608][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-18 16:06:21.609][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-18 16:06:21.610][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:06:21.611][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-18 16:06:21.612][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:06:21.613][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-18 16:06:21.614][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-18 16:06:21.615][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:06:21.616][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-18 16:06:21.617][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:06:21.618][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-18 16:06:21.620][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-18 16:06:21.621][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:06:21.622][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-18 16:06:21.623][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-05-18 16:06:21.627][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-05-18 16:06:21.629][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-05-18 16:06:21.630][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-05-18 16:06:21.632][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-05-18 16:06:21.633][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-05-18 16:06:21.635][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-05-18 16:06:21.636][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-05-18 16:06:21.638][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-05-18 16:06:21.639][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-05-18 16:06:21.641][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-05-18 16:06:21.642][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-05-18 16:06:21.644][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-05-18 16:06:21.645][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-05-18 16:06:21.647][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-05-18 16:06:21.649][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-05-18 16:06:21.650][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-05-18 16:06:21.652][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-05-18 16:06:21.653][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-05-18 16:06:21.655][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-05-18 16:06:21.656][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-05-18 16:06:21.658][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-05-18 16:06:21.659][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-05-18 16:06:21.661][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-05-18 16:06:21.662][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-05-18 16:06:21.664][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-05-18 16:06:21.666][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-05-18 16:06:21.667][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-05-18 16:06:21.669][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-05-18 16:06:21.670][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-05-18 16:06:21.672][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-05-18 16:06:21.673][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-05-18 16:06:21.675][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-05-18 16:06:21.676][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-05-18 16:06:21.678][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-05-18 16:06:21.679][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-05-18 16:06:21.681][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-05-18 16:06:21.682][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-05-18 16:06:21.684][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-05-18 16:06:21.686][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-05-18 16:06:21.687][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-05-18 16:06:21.689][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-05-18 16:06:21.690][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-05-18 16:06:21.692][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-05-18 16:06:21.693][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-05-18 16:06:21.695][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-05-18 16:06:21.696][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-05-18 16:06:21.698][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-05-18 16:06:21.699][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-05-18 16:06:21.701][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-05-18 16:06:21.703][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-05-18 16:06:21.704][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-05-18 16:06:21.706][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-05-18 16:06:21.707][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-05-18 16:06:21.709][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-05-18 16:06:21.710][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-05-18 16:06:21.712][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-05-18 16:06:21.713][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-05-18 16:06:21.715][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-05-18 16:06:21.716][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-05-18 16:06:21.718][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-05-18 16:06:21.719][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-05-18 16:06:21.721][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-05-18 16:06:21.723][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-05-18 16:06:21.724][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-05-18 16:06:21.726][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-05-18 16:06:21.727][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-05-18 16:06:21.729][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-05-18 16:06:21.730][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-05-18 16:06:21.732][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-05-18 16:06:21.733][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-05-18 16:06:21.735][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-05-18 16:06:21.737][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-05-18 16:06:21.738][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-05-18 16:06:21.740][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-05-18 16:06:21.741][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-05-18 16:06:21.743][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-05-18 16:06:21.744][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-05-18 16:06:21.746][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-05-18 16:06:21.747][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-05-18 16:06:21.749][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-05-18 16:06:21.750][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-05-18 16:06:21.752][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-05-18 16:06:21.793][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-05-18 16:06:21.795][initialize] This is biodb version 1.13.0.
biodb.DEBUG[2024-05-18 16:06:21.798][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-05-18 16:06:21.800][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-05-18 16:06:21.801][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-18 16:06:21.802][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:06:21.803][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-18 16:06:21.807][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:06:21.808][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-18 16:06:21.810][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-18 16:06:21.811][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-18 16:06:21.812][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-18 16:06:21.813][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:06:21.814][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-18 16:06:21.815][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:06:21.816][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-18 16:06:21.817][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-18 16:06:21.818][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-18 16:06:21.819][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-18 16:06:21.820][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:06:21.822][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-18 16:06:21.823][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:06:21.824][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-18 16:06:21.825][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-18 16:06:21.826][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-18 16:06:21.827][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-18 16:06:21.828][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:06:21.829][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-18 16:06:21.830][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:06:21.831][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-18 16:06:21.832][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-18 16:06:21.834][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-18 16:06:21.835][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-18 16:06:21.836][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:06:21.837][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-18 16:06:21.838][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:06:21.839][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-18 16:06:21.840][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-18 16:06:21.841][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-18 16:06:21.842][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-18 16:06:21.843][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:06:21.844][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-18 16:06:21.845][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:06:21.847][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-18 16:06:21.848][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-18 16:06:21.849][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-18 16:06:21.850][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-18 16:06:21.851][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:06:21.852][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-18 16:06:21.853][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:06:21.854][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-18 16:06:21.855][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-18 16:06:21.856][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-18 16:06:21.857][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-18 16:06:21.858][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:06:21.859][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-18 16:06:21.861][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:06:21.862][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-18 16:06:21.863][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-18 16:06:21.864][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-18 16:06:21.865][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-18 16:06:21.866][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:06:21.867][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-18 16:06:21.869][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:06:21.871][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-18 16:06:21.872][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-18 16:06:21.874][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-18 16:06:21.875][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-18 16:06:21.877][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:06:21.878][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-18 16:06:21.880][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:06:21.882][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-18 16:06:21.883][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-18 16:06:21.885][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-18 16:06:21.886][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-18 16:06:21.888][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:06:21.889][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-18 16:06:21.891][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:06:21.893][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-18 16:06:21.894][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-18 16:06:21.896][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-18 16:06:21.897][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-18 16:06:21.899][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:06:21.900][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-18 16:06:21.902][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:06:21.903][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-18 16:06:21.905][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-18 16:06:21.907][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-18 16:06:21.908][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-18 16:06:21.910][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:06:21.911][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-18 16:06:21.913][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:06:21.915][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-18 16:06:21.916][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-18 16:06:21.918][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-18 16:06:21.919][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-18 16:06:21.921][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:06:21.922][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-18 16:06:21.923][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:06:21.924][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-18 16:06:21.925][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-18 16:06:21.926][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-18 16:06:21.928][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-18 16:06:21.929][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:06:21.930][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-18 16:06:21.931][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:06:21.932][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-18 16:06:21.933][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-18 16:06:21.934][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-18 16:06:21.935][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-18 16:06:21.936][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:06:21.937][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-18 16:06:21.938][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:06:21.939][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-18 16:06:21.941][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-18 16:06:21.942][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-18 16:06:21.943][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-18 16:06:21.944][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:06:21.945][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-18 16:06:21.946][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:06:21.947][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-18 16:06:21.948][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-18 16:06:21.949][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-18 16:06:21.950][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-18 16:06:21.951][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:06:21.952][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-18 16:06:21.954][biodb$getConfig()$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-05-18 16:06:21.955][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:06:21.956][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-18 16:06:21.957][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-18 16:06:21.958][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-18 16:06:21.959][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-18 16:06:21.960][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:06:21.961][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-18 16:06:21.965][biodb$loadDefinitions] Load definitions from file "F:/biocbuild/bbs-3.20-bioc-longtests/meat/biodbHmdb.Rcheck/biodbHmdb/definitions.yml".
biodb.DEBUG[2024-05-18 16:06:21.973][self$getDbsInfo()$define] Define connector hmdb.metabolites.
biodb.DEBUG[2024-05-18 16:06:21.976][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-05-18 16:06:21.977][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2024-05-18 16:06:21.978][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-18 16:06:21.979][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-18 16:06:21.980][self$setPropertyValue] Setting property "downloadable" to "TRUE".
biodb.DEBUG[2024-05-18 16:06:21.982][self$setPropertyValue] Setting property "dwnld.ext" to "zip".
biodb.DEBUG[2024-05-18 16:06:21.983][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-05-18 16:06:21.984][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-18 16:06:21.985][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2024-05-18 16:06:21.986][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-18 16:06:21.988][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-05-18 16:06:21.989][self$setPropertyValue] Setting property "name" to "HMDB Metabolites".
biodb.DEBUG[2024-05-18 16:06:21.990][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-18 16:06:21.991][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/accession".
biodb.DEBUG[2024-05-18 16:06:21.991][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/secondary_accessions/accession".
biodb.DEBUG[2024-05-18 16:06:21.991][self$setPropertyValue] Setting property "parsing.expr" to "//average_molecular_weight".
biodb.DEBUG[2024-05-18 16:06:21.991][self$setPropertyValue] Setting property "parsing.expr" to "//cas_registry_number".
biodb.DEBUG[2024-05-18 16:06:21.991][self$setPropertyValue] Setting property "parsing.expr" to "//chebi_id".
biodb.DEBUG[2024-05-18 16:06:21.991][self$setPropertyValue] Setting property "parsing.expr" to "//chemspider_id".
biodb.DEBUG[2024-05-18 16:06:21.991][self$setPropertyValue] Setting property "parsing.expr" to "//kegg_id".
biodb.DEBUG[2024-05-18 16:06:21.991][self$setPropertyValue] Setting property "parsing.expr" to "//pubchem_compound_id".
biodb.DEBUG[2024-05-18 16:06:21.991][self$setPropertyValue] Setting property "parsing.expr" to "//iupac_name".
biodb.DEBUG[2024-05-18 16:06:21.991][self$setPropertyValue] Setting property "parsing.expr" to "//traditional_iupac".
biodb.DEBUG[2024-05-18 16:06:21.991][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/chemical_formula".
biodb.DEBUG[2024-05-18 16:06:21.991][self$setPropertyValue] Setting property "parsing.expr" to "//inchi".
biodb.DEBUG[2024-05-18 16:06:21.991][self$setPropertyValue] Setting property "parsing.expr" to "//inchikey".
biodb.DEBUG[2024-05-18 16:06:21.991][self$setPropertyValue] Setting property "parsing.expr" to "//monisotopic_molecular_weight".
biodb.DEBUG[2024-05-18 16:06:21.991][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/name".
biodb.DEBUG[2024-05-18 16:06:21.991][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/description".
biodb.DEBUG[2024-05-18 16:06:21.991][self$setPropertyValue] Setting property "parsing.expr" to "//smiles".
biodb.DEBUG[2024-05-18 16:06:21.991][self$setPropertyValue] Setting property "parsing.expr" to "//super_class".
biodb.DEBUG[2024-05-18 16:06:21.993][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-05-18 16:06:21.994][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-05-18 16:06:21.994][self$setPropertyValue] Setting property "searchable.fields" to "description".
biodb.DEBUG[2024-05-18 16:06:21.994][self$setPropertyValue] Setting property "searchable.fields" to "secondary.accessions".
biodb.DEBUG[2024-05-18 16:06:21.995][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2024-05-18 16:06:21.996][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-18 16:06:21.997][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-18 16:06:21.999][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-18 16:06:22.000][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-18 16:06:22.001][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-18 16:06:22.002][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-18 16:06:22.003][self$setPropertyValue] Setting property "urls" to "http://www.hmdb.ca/".
biodb.DEBUG[2024-05-18 16:06:22.003][self$setPropertyValue] Setting property "urls" to "http://www.hmdb.ca/system/downloads/current/hmdb_metabolites.zip".
biodb.DEBUG[2024-05-18 16:06:22.004][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-18 16:06:22.005][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-18 16:06:22.007][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-05-18 16:06:22.008][self$setPropertyValue]
biodb.DEBUG[2024-05-18 16:06:22.039][self$getEntryFields()$define] Define field secondary_accessions.
biodb.DEBUG[2024-05-18 16:06:22.041][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-05-18 16:06:22.043][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-05-18 16:06:22.044][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-05-18 16:06:22.046][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-05-18 16:06:22.067][initialize] Initialize connector hmdb.metabolites.
biodb.DEBUG[2024-05-18 16:06:22.069][initialize] Register connector hmdb.metabolites with the request scheduler
biodb.DEBUG[2024-05-18 16:06:22.073][private$bdb$getRequestScheduler()$re ...] Register connector hmdb.metabolites.
biodb.DEBUG[2024-05-18 16:06:22.076][private$addConnectorRules] Create new rule for URL "www.hmdb.ca" of connector "hmdb.metabolites".
biodb.DEBUG[2024-05-18 16:06:22.080][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-05-18 16:06:22.081][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-05-18 16:06:22.083][rule$addConnector] Connector "hmdb.metabolites" is already listed in rule "www.hmdb.ca".
biodb.DEBUG[2024-05-18 16:06:22.084][biodb$getFactory()$createConn] Creating new connector hmdb.metabolites for database class hmdb.metabolites .
biodb.INFO [2024-05-18 16:06:22.094][biodb::testThat]
biodb.INFO [2024-05-18 16:06:22.095][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2024-05-18 16:06:22.096][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-18 16:06:22.098][biodb::testThat]
biodb.TRACE[2024-05-18 16:06:22.103][loadFileContents] Loaded 1 files from cache: [1]: "F:/biocbuild/bbs-3.20-bioc-longtests/meat/biodbHmdb.Rcheck/biodbHmdb/testref/entry-hmdb.metabolites-HMDB0000001-content.xml".
biodb.DEBUG[2024-05-18 16:06:22.105][biodb$getFactory()$createEntryFromCo ...] Creating HMDB Metabolites entries from 1 content(s).
biodb.DEBUG[2024-05-18 16:06:22.109][biodb$getFactory()$createEntryFromCo ...] Parsing 1 HMDB Metabolites entries.
biodb.DEBUG[2024-05-18 16:06:22.115][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-18 16:06:22.116][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-18 16:06:22.118][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-18 16:06:22.133][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-18 16:06:22.135][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-18 16:06:22.136][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:06:22.137][FUN] Functions in observer BiodbConfig: [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[2024-05-18 16:06:22.147][ef$get] Asked field names are: accession.
biodb.TRACE[2024-05-18 16:06:22.149][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-18 16:06:22.150][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:06:22.151][ef$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:06:22.153][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-18 16:06:22.164][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-18 16:06:22.166][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:06:22.167][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:06:22.168][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-05-18 16:06:22.170][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-05-18 16:06:22.171][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:06:22.172][ef$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:06:22.195][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-05-18 16:06:22.196][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-05-18 16:06:22.198][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:06:22.199][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:06:22.200][ef$get] Asked field names are: average.mass.
biodb.TRACE[2024-05-18 16:06:22.202][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-05-18 16:06:22.203][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:06:22.204][ef$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:06:22.206][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-05-18 16:06:22.207][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-05-18 16:06:22.208][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:06:22.209][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:06:22.211][ef$get] Asked field names are: cas.id.
biodb.TRACE[2024-05-18 16:06:22.212][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-05-18 16:06:22.213][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:06:22.214][ef$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:06:22.216][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-05-18 16:06:22.217][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-05-18 16:06:22.218][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:06:22.220][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:06:22.221][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-18 16:06:22.222][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-18 16:06:22.223][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:06:22.225][ef$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:06:22.226][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-18 16:06:22.228][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-18 16:06:22.229][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:06:22.230][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:06:22.231][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2024-05-18 16:06:22.232][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2024-05-18 16:06:22.234][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:06:22.235][ef$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:06:22.236][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2024-05-18 16:06:22.248][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2024-05-18 16:06:22.250][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:06:22.251][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:06:22.252][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-18 16:06:22.253][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-18 16:06:22.255][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:06:22.256][ef$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:06:22.257][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-18 16:06:22.259][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-18 16:06:22.260][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:06:22.261][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:06:22.262][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-18 16:06:22.264][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-18 16:06:22.265][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:06:22.266][ef$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:06:22.268][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-18 16:06:22.269][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-18 16:06:22.270][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:06:22.271][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:06:22.273][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-05-18 16:06:22.274][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-05-18 16:06:22.275][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:06:22.276][ef$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:06:22.278][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-05-18 16:06:22.279][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-05-18 16:06:22.280][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:06:22.282][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:06:22.283][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-05-18 16:06:22.284][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-05-18 16:06:22.285][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:06:22.286][ef$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:06:22.288][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-05-18 16:06:22.289][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-05-18 16:06:22.291][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:06:22.292][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:06:22.293][ef$get] Asked field names are: formula.
biodb.TRACE[2024-05-18 16:06:22.294][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-18 16:06:22.296][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:06:22.297][ef$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:06:22.298][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-18 16:06:22.299][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-18 16:06:22.301][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:06:22.302][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:06:22.303][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-05-18 16:06:22.304][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-18 16:06:22.306][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:06:22.307][ef$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:06:22.308][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-05-18 16:06:22.310][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-18 16:06:22.311][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:06:22.312][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:06:22.313][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-18 16:06:22.315][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-18 16:06:22.316][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:06:22.317][ef$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:06:22.319][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-18 16:06:22.320][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-18 16:06:22.321][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:06:22.322][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:06:22.324][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-18 16:06:22.325][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-18 16:06:22.326][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:06:22.327][ef$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:06:22.329][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-18 16:06:22.330][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-18 16:06:22.331][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:06:22.332][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:06:22.334][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-18 16:06:22.335][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-18 16:06:22.336][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:06:22.337][ef$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:06:22.339][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-18 16:06:22.340][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-18 16:06:22.341][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:06:22.342][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:06:22.344][ef$get] Asked field names are: description.
biodb.TRACE[2024-05-18 16:06:22.345][ef$get] Realnames of fields are: description.
biodb.TRACE[2024-05-18 16:06:22.346][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:06:22.347][ef$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:06:22.349][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-05-18 16:06:22.350][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-05-18 16:06:22.351][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:06:22.352][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:06:22.354][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-05-18 16:06:22.355][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-18 16:06:22.356][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:06:22.357][ef$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:06:22.359][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-05-18 16:06:22.360][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-18 16:06:22.361][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:06:22.362][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:06:22.364][ef$get] Asked field names are: super.class.
biodb.TRACE[2024-05-18 16:06:22.365][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2024-05-18 16:06:22.366][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:06:22.367][ef$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:06:22.369][self$getBiodb()$getEntryFields()$get] Asked field names are: super.class.
biodb.TRACE[2024-05-18 16:06:22.370][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2024-05-18 16:06:22.371][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:06:22.372][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:06:22.374][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-18 16:06:22.375][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-18 16:06:22.376][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:06:22.377][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:06:22.379][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-18 16:06:22.380][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-18 16:06:22.381][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:06:22.382][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:06:22.384][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-18 16:06:22.385][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-18 16:06:22.386][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:06:22.387][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:06:22.420][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-05-18 16:06:22.422][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-05-18 16:06:22.423][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:06:22.424][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:06:22.425][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-05-18 16:06:22.427][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-05-18 16:06:22.428][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:06:22.429][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:06:22.430][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-05-18 16:06:22.432][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-05-18 16:06:22.433][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:06:22.434][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:06:22.435][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-05-18 16:06:22.436][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-05-18 16:06:22.438][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:06:22.439][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:06:22.440][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-05-18 16:06:22.441][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-05-18 16:06:22.442][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:06:22.444][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:06:22.445][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-05-18 16:06:22.446][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-05-18 16:06:22.447][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:06:22.448][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:06:22.450][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-18 16:06:22.451][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-18 16:06:22.452][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:06:22.453][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:06:22.455][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-18 16:06:22.456][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-18 16:06:22.457][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:06:22.458][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:06:22.459][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-18 16:06:22.461][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-18 16:06:22.462][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:06:22.463][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:06:22.464][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2024-05-18 16:06:22.466][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2024-05-18 16:06:22.467][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:06:22.468][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:06:22.469][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2024-05-18 16:06:22.470][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2024-05-18 16:06:22.472][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:06:22.473][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:06:22.474][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2024-05-18 16:06:22.475][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2024-05-18 16:06:22.476][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:06:22.478][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:06:22.479][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-05-18 16:06:22.480][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-05-18 16:06:22.481][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:06:22.483][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:06:22.484][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-05-18 16:06:22.485][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-05-18 16:06:22.486][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:06:22.487][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:06:22.489][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-05-18 16:06:22.490][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-05-18 16:06:22.491][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:06:22.492][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:06:22.493][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-05-18 16:06:22.495][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-05-18 16:06:22.496][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:06:22.497][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:06:22.498][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-05-18 16:06:22.500][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-05-18 16:06:22.501][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:06:22.502][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:06:22.503][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-05-18 16:06:22.504][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-05-18 16:06:22.506][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:06:22.507][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:06:22.508][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2024-05-18 16:06:22.509][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2024-05-18 16:06:22.510][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:06:22.512][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:06:22.513][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2024-05-18 16:06:22.514][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2024-05-18 16:06:22.515][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:06:22.516][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:06:22.518][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2024-05-18 16:06:22.519][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2024-05-18 16:06:22.520][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:06:22.521][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:06:22.523][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-05-18 16:06:22.524][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-05-18 16:06:22.525][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:06:22.526][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:06:22.527][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-05-18 16:06:22.529][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-05-18 16:06:22.530][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:06:22.531][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:06:22.532][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-05-18 16:06:22.533][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-05-18 16:06:22.535][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:06:22.536][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:06:22.537][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-18 16:06:22.538][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-18 16:06:22.540][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:06:22.541][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:06:22.542][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-18 16:06:22.543][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-18 16:06:22.544][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:06:22.546][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:06:22.547][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-18 16:06:22.548][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-18 16:06:22.549][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:06:22.550][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:06:22.552][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-05-18 16:06:22.553][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-18 16:06:22.554][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:06:22.555][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:06:22.557][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-05-18 16:06:22.558][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-18 16:06:22.559][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:06:22.560][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:06:22.561][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-05-18 16:06:22.563][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-18 16:06:22.564][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:06:22.565][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:06:22.566][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-18 16:06:22.568][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-18 16:06:22.569][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:06:22.570][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:06:22.571][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-18 16:06:22.572][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-18 16:06:22.574][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:06:22.575][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:06:22.576][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-18 16:06:22.578][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-18 16:06:22.579][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:06:22.580][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:06:22.581][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-18 16:06:22.583][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-18 16:06:22.584][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:06:22.590][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:06:22.591][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-18 16:06:22.593][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-18 16:06:22.594][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:06:22.595][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:06:22.596][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-18 16:06:22.598][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-18 16:06:22.599][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:06:22.600][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:06:22.601][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-18 16:06:22.603][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-18 16:06:22.604][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:06:22.605][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:06:22.606][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-18 16:06:22.607][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-18 16:06:22.609][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:06:22.610][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:06:22.611][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-18 16:06:22.612][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-18 16:06:22.614][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:06:22.615][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:06:22.616][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-18 16:06:22.617][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-18 16:06:22.619][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:06:22.620][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:06:22.621][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-18 16:06:22.622][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-18 16:06:22.623][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:06:22.625][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:06:22.626][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-18 16:06:22.627][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-18 16:06:22.628][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:06:22.629][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:06:22.631][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-18 16:06:22.632][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-18 16:06:22.633][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:06:22.634][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:06:22.636][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-18 16:06:22.637][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-18 16:06:22.638][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:06:22.639][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:06:22.641][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-18 16:06:22.642][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-18 16:06:22.643][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:06:22.644][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:06:22.645][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-05-18 16:06:22.647][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-05-18 16:06:22.648][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:06:22.649][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:06:22.650][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-05-18 16:06:22.652][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-05-18 16:06:22.653][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:06:22.654][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:06:22.655][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-05-18 16:06:22.656][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-05-18 16:06:22.658][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:06:22.659][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:06:22.660][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-05-18 16:06:22.661][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-18 16:06:22.663][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:06:22.664][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:06:22.665][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-05-18 16:06:22.666][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-18 16:06:22.667][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:06:22.669][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:06:22.670][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-05-18 16:06:22.671][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-18 16:06:22.672][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:06:22.673][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:06:22.675][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2024-05-18 16:06:22.676][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-18 16:06:22.677][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:06:22.678][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:06:22.680][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-18 16:06:22.681][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-18 16:06:22.682][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:06:22.683][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:06:22.684][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-18 16:06:22.686][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-18 16:06:22.687][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:06:22.688][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:06:22.689][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-18 16:06:22.691][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-18 16:06:22.692][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:06:22.693][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:06:22.694][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2024-05-18 16:06:22.696][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-18 16:06:22.697][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:06:22.698][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:06:22.714][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-18 16:06:22.716][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-18 16:06:22.717][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:06:22.718][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:06:22.719][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-18 16:06:22.721][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-18 16:06:22.722][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:06:22.723][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:06:22.724][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-18 16:06:22.726][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-18 16:06:22.727][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:06:22.728][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:06:22.729][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-18 16:06:22.731][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-18 16:06:22.732][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:06:22.733][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:06:22.734][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-18 16:06:22.736][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-18 16:06:22.737][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:06:22.738][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:06:22.739][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-05-18 16:06:22.741][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-05-18 16:06:22.742][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:06:22.743][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:06:22.744][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-05-18 16:06:22.746][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-05-18 16:06:22.747][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:06:22.748][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:06:22.749][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-18 16:06:22.750][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-18 16:06:22.752][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:06:22.753][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:06:22.754][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-05-18 16:06:22.760][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-05-18 16:06:22.761][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:06:22.763][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:06:22.764][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-18 16:06:22.765][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-18 16:06:22.766][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:06:22.767][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:06:22.769][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-18 16:06:22.770][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-18 16:06:22.771][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:06:22.772][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:06:22.774][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-18 16:06:22.775][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-18 16:06:22.776][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:06:22.777][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:06:22.779][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-18 16:06:22.780][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-18 16:06:22.781][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:06:22.782][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:06:22.784][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-18 16:06:22.785][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-18 16:06:22.786][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:06:22.787][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:06:22.789][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-18 16:06:22.790][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-18 16:06:22.791][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:06:22.792][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-18 16:06:22.793][biodb$getFactory()$createEntryFromCo ...] Accession numbers: HMDB0000001.
biodb.TRACE[2024-05-18 16:06:22.797][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-05-18 16:06:22.798][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-05-18 16:06:22.799][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:06:22.800][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:06:22.802][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-05-18 16:06:22.803][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-05-18 16:06:22.804][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:06:22.805][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:06:22.806][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-05-18 16:06:22.808][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-05-18 16:06:22.809][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:06:22.810][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:06:22.811][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-05-18 16:06:22.812][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-05-18 16:06:22.814][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:06:22.815][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:06:22.837][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-18 16:06:22.840][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-18 16:06:22.841][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:06:22.843][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:06:22.862][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-05-18 16:06:22.864][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-05-18 16:06:22.865][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:06:22.866][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:06:22.874][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-18 16:06:22.875][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-18 16:06:22.877][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:06:22.878][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:06:22.879][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-18 16:06:22.880][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-18 16:06:22.882][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:06:22.883][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:06:22.884][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-18 16:06:22.885][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-18 16:06:22.886][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:06:22.888][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:06:22.891][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-18 16:06:22.892][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-18 16:06:22.893][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:06:22.894][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:06:22.896][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-18 16:06:22.897][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-18 16:06:22.898][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:06:22.899][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:06:22.900][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-18 16:06:22.902][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-18 16:06:22.904][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:06:22.906][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:06:22.907][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-05-18 16:06:22.909][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-05-18 16:06:22.910][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:06:22.911][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:06:22.912][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-05-18 16:06:22.914][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-05-18 16:06:22.915][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:06:22.916][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:06:22.917][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-05-18 16:06:22.918][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-05-18 16:06:22.920][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:06:22.921][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:06:22.934][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-18 16:06:22.935][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-18 16:06:22.936][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:06:22.938][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:06:22.939][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-18 16:06:22.940][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-18 16:06:22.941][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:06:22.942][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:06:22.944][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-18 16:06:22.945][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-18 16:06:22.946][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:06:22.947][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:06:22.949][ef$get] Asked field names are: accession.
biodb.TRACE[2024-05-18 16:06:22.950][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-18 16:06:22.951][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:06:22.952][ef$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:06:22.954][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-18 16:06:22.955][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-18 16:06:22.956][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:06:22.963][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:06:22.974][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-05-18 16:06:22.976][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-05-18 16:06:22.977][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:06:22.978][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:06:22.980][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-05-18 16:06:22.981][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-05-18 16:06:22.982][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:06:22.983][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:06:22.985][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-05-18 16:06:22.986][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-05-18 16:06:22.987][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:06:22.988][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:06:22.990][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-05-18 16:06:22.991][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-05-18 16:06:22.992][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:06:22.993][ef$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:06:22.994][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-05-18 16:06:22.996][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-05-18 16:06:22.997][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:06:22.998][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:06:23.009][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2024-05-18 16:06:23.011][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2024-05-18 16:06:23.012][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:06:23.013][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:06:23.015][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2024-05-18 16:06:23.016][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2024-05-18 16:06:23.017][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:06:23.018][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:06:23.019][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2024-05-18 16:06:23.021][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2024-05-18 16:06:23.022][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:06:23.023][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:06:23.024][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2024-05-18 16:06:23.026][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2024-05-18 16:06:23.027][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:06:23.028][ef$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:06:23.029][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2024-05-18 16:06:23.031][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2024-05-18 16:06:23.032][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:06:23.033][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:06:23.044][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-18 16:06:23.046][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-18 16:06:23.047][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:06:23.048][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:06:23.049][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-18 16:06:23.051][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-18 16:06:23.052][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:06:23.053][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:06:23.054][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-18 16:06:23.055][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-18 16:06:23.057][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:06:23.058][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:06:23.059][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-18 16:06:23.060][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-18 16:06:23.061][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:06:23.063][ef$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:06:23.064][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-18 16:06:23.065][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-18 16:06:23.066][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:06:23.067][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:06:23.079][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-18 16:06:23.080][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-18 16:06:23.082][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:06:23.083][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:06:23.084][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-18 16:06:23.085][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-18 16:06:23.086][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:06:23.088][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:06:23.089][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-18 16:06:23.090][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-18 16:06:23.091][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:06:23.093][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:06:23.094][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-18 16:06:23.095][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-18 16:06:23.096][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:06:23.097][ef$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:06:23.099][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-18 16:06:23.100][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-18 16:06:23.101][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:06:23.102][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:06:23.114][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-18 16:06:23.115][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-18 16:06:23.116][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:06:23.117][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:06:23.119][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-18 16:06:23.120][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-18 16:06:23.121][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:06:23.122][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:06:23.124][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-18 16:06:23.125][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-18 16:06:23.126][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:06:23.127][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:06:23.129][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-18 16:06:23.130][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-18 16:06:23.131][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:06:23.132][ef$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:06:23.134][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-18 16:06:23.135][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-18 16:06:23.136][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:06:23.137][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:06:23.155][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-18 16:06:23.156][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-18 16:06:23.157][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:06:23.159][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:06:23.160][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-18 16:06:23.161][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-18 16:06:23.162][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:06:23.164][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:06:23.165][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-18 16:06:23.166][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-18 16:06:23.167][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:06:23.168][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:06:23.170][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-18 16:06:23.171][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-18 16:06:23.172][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:06:23.173][ef$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:06:23.175][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-18 16:06:23.176][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-18 16:06:23.177][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:06:23.178][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:06:23.190][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-05-18 16:06:23.191][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-05-18 16:06:23.192][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:06:23.194][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:06:23.195][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-05-18 16:06:23.196][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-05-18 16:06:23.197][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:06:23.198][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:06:23.200][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-05-18 16:06:23.201][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-05-18 16:06:23.202][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:06:23.203][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:06:23.205][ef$get] Asked field names are: description.
biodb.TRACE[2024-05-18 16:06:23.206][ef$get] Realnames of fields are: description.
biodb.TRACE[2024-05-18 16:06:23.207][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:06:23.209][ef$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:06:23.210][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-05-18 16:06:23.211][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-05-18 16:06:23.212][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:06:23.213][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:06:23.225][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-18 16:06:23.226][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-18 16:06:23.227][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:06:23.228][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:06:23.230][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-18 16:06:23.231][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-18 16:06:23.232][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:06:23.233][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:06:23.235][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-18 16:06:23.236][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-18 16:06:23.237][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:06:23.238][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:06:23.240][ef$get] Asked field names are: formula.
biodb.TRACE[2024-05-18 16:06:23.241][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-18 16:06:23.242][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:06:23.243][ef$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:06:23.244][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-18 16:06:23.246][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-18 16:06:23.247][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:06:23.248][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:06:23.259][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-05-18 16:06:23.261][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-05-18 16:06:23.262][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:06:23.263][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:06:23.264][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-05-18 16:06:23.266][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-05-18 16:06:23.267][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:06:23.268][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:06:23.269][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-05-18 16:06:23.271][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-05-18 16:06:23.272][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:06:23.273][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:06:23.274][ef$get] Asked field names are: average.mass.
biodb.TRACE[2024-05-18 16:06:23.276][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-05-18 16:06:23.277][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:06:23.278][ef$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:06:23.279][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-05-18 16:06:23.281][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-05-18 16:06:23.283][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:06:23.284][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:06:23.302][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-18 16:06:23.304][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-18 16:06:23.305][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:06:23.306][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:06:23.308][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-18 16:06:23.309][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-18 16:06:23.310][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:06:23.311][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:06:23.312][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-18 16:06:23.314][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-18 16:06:23.315][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:06:23.316][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:06:23.317][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-18 16:06:23.319][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-18 16:06:23.320][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:06:23.321][ef$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:06:23.322][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-18 16:06:23.324][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-18 16:06:23.325][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:06:23.326][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:06:23.337][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2024-05-18 16:06:23.339][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2024-05-18 16:06:23.340][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:06:23.346][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:06:23.347][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2024-05-18 16:06:23.348][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2024-05-18 16:06:23.350][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:06:23.351][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:06:23.352][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2024-05-18 16:06:23.353][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2024-05-18 16:06:23.355][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:06:23.356][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:06:23.357][ef$get] Asked field names are: comp.super.class.
biodb.TRACE[2024-05-18 16:06:23.358][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2024-05-18 16:06:23.359][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:06:23.361][ef$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:06:23.362][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2024-05-18 16:06:23.363][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2024-05-18 16:06:23.364][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:06:23.365][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:06:23.377][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-05-18 16:06:23.378][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-05-18 16:06:23.379][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:06:23.381][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:06:23.382][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-05-18 16:06:23.383][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-05-18 16:06:23.384][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:06:23.386][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:06:23.387][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-05-18 16:06:23.388][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-05-18 16:06:23.389][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:06:23.390][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:06:23.392][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-05-18 16:06:23.393][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-05-18 16:06:23.394][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:06:23.395][ef$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:06:23.397][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-05-18 16:06:23.398][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-05-18 16:06:23.399][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:06:23.400][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:06:23.412][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-05-18 16:06:23.413][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-05-18 16:06:23.414][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:06:23.415][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:06:23.417][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-05-18 16:06:23.418][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-05-18 16:06:23.419][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:06:23.420][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:06:23.421][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-05-18 16:06:23.423][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-05-18 16:06:23.424][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:06:23.425][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:06:23.426][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-05-18 16:06:23.428][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-05-18 16:06:23.429][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:06:23.430][ef$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:06:23.431][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-05-18 16:06:23.432][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-05-18 16:06:23.434][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:06:23.435][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:06:23.446][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-05-18 16:06:23.447][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-18 16:06:23.449][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:06:23.450][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:06:23.451][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-05-18 16:06:23.452][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-18 16:06:23.454][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:06:23.455][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:06:23.456][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-05-18 16:06:23.457][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-18 16:06:23.458][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:06:23.460][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:06:23.461][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-05-18 16:06:23.462][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-18 16:06:23.463][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:06:23.464][ef$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:06:23.466][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-05-18 16:06:23.467][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-18 16:06:23.468][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:06:23.469][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:06:23.480][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-05-18 16:06:23.482][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-18 16:06:23.483][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:06:23.484][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:06:23.486][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-05-18 16:06:23.487][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-18 16:06:23.488][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:06:23.489][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:06:23.490][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-05-18 16:06:23.492][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-18 16:06:23.493][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:06:23.494][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:06:23.495][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-05-18 16:06:23.497][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-18 16:06:23.498][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:06:23.499][ef$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:06:23.500][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-05-18 16:06:23.501][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-18 16:06:23.503][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:06:23.504][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:06:23.515][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-18 16:06:23.516][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-18 16:06:23.517][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:06:23.518][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:06:23.520][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-18 16:06:23.521][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-18 16:06:23.522][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:06:23.523][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:06:23.529][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-18 16:06:23.531][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-18 16:06:23.532][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:06:23.533][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:06:23.534][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-18 16:06:23.536][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-18 16:06:23.537][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:06:23.538][ef$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:06:23.539][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-18 16:06:23.540][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-18 16:06:23.542][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:06:23.543][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:06:23.554][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-05-18 16:06:23.555][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-05-18 16:06:23.557][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:06:23.558][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:06:23.559][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-05-18 16:06:23.560][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-05-18 16:06:23.562][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:06:23.563][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:06:23.564][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-05-18 16:06:23.565][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-05-18 16:06:23.567][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:06:23.568][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:06:23.569][ef$get] Asked field names are: cas.id.
biodb.TRACE[2024-05-18 16:06:23.570][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-05-18 16:06:23.571][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:06:23.573][ef$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:06:23.574][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-05-18 16:06:23.575][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-05-18 16:06:23.577][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:06:23.578][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:06:23.590][ef$get] Asked field names are: accession.
biodb.TRACE[2024-05-18 16:06:23.592][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-18 16:06:23.593][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:06:23.594][ef$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:06:23.601][ef$get] Asked field names are: average.mass.
biodb.TRACE[2024-05-18 16:06:23.602][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-05-18 16:06:23.603][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:06:23.605][ef$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:06:23.611][ef$get] Asked field names are: cas.id.
biodb.TRACE[2024-05-18 16:06:23.613][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-05-18 16:06:23.615][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:06:23.617][ef$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:06:23.624][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-18 16:06:23.625][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-18 16:06:23.626][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:06:23.628][ef$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:06:23.635][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2024-05-18 16:06:23.636][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2024-05-18 16:06:23.637][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:06:23.639][ef$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:06:23.646][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-05-18 16:06:23.647][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-05-18 16:06:23.648][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:06:23.650][ef$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:06:23.657][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-05-18 16:06:23.658][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-05-18 16:06:23.659][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:06:23.660][ef$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:06:23.668][ef$get] Asked field names are: comp.super.class.
biodb.TRACE[2024-05-18 16:06:23.669][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2024-05-18 16:06:23.670][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:06:23.671][ef$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:06:23.678][ef$get] Asked field names are: description.
biodb.TRACE[2024-05-18 16:06:23.680][ef$get] Realnames of fields are: description.
biodb.TRACE[2024-05-18 16:06:23.681][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:06:23.682][ef$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:06:23.689][ef$get] Asked field names are: formula.
biodb.TRACE[2024-05-18 16:06:23.690][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-18 16:06:23.691][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:06:23.693][ef$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:06:23.699][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-05-18 16:06:23.701][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-18 16:06:23.702][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:06:23.703][ef$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:06:23.710][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-18 16:06:23.711][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-18 16:06:23.712][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:06:23.713][ef$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:06:23.720][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-18 16:06:23.722][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-18 16:06:23.723][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:06:23.724][ef$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:06:23.731][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-18 16:06:23.737][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-18 16:06:23.738][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:06:23.740][ef$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:06:23.747][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-18 16:06:23.748][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-18 16:06:23.749][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:06:23.750][ef$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:06:23.757][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-18 16:06:23.759][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-18 16:06:23.760][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:06:23.761][ef$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:06:23.768][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-05-18 16:06:23.770][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-05-18 16:06:23.771][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:06:23.772][ef$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:06:23.779][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-05-18 16:06:23.780][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-18 16:06:23.781][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:06:23.783][ef$get] fields variable is a list.
biodb.INFO [2024-05-18 16:06:23.795][biodb::testThat]
biodb.INFO [2024-05-18 16:06:23.797][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2024-05-18 16:06:23.798][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-18 16:06:23.799][biodb::testThat]
biodb.DEBUG[2024-05-18 16:06:23.812][private$loadEntries] Creating entries from ids [1]: "HMDB0000001".
biodb.DEBUG[2024-05-18 16:06:23.818][conn$getEntryContent] Get HMDB Metabolites entry content(s) for 1 id(s)...
biodb.INFO [2024-05-18 16:06:23.825][self$getFolderPath] Create cache folder "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34" for "hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34".
biodb.DEBUG[2024-05-18 16:06:23.827][self$isDownloaded] Database hmdb.metabolites has not yet been downloaded.
biodb.INFO [2024-05-18 16:06:23.828][self$download] Downloading whole database of hmdb.metabolites.
biodb.INFO [2024-05-18 16:06:23.829][private$doDownload] Downloading HMDB metabolite database at "http://www.hmdb.ca/system/downloads/current/hmdb_metabolites.zip" ...
biodb.DEBUG[2024-05-18 16:06:23.832][sched$downloadFile] Downloading file "http://www.hmdb.ca/system/downloads/current/hmdb_metabolites.zip".
trying URL 'http://www.hmdb.ca/system/downloads/current/hmdb_metabolites.zip'
Content type 'application/zip' length 953913010 bytes (909.7 MB)
==================================================
downloaded 909.7 MB

biodb.TRACE[2024-05-18 16:06:34.792][cch$addFilesToCache] Moving files to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/tmp\hmdb.metabolites16d5869ec3879zip".
biodb.TRACE[2024-05-18 16:06:34.793][private$doAddFilesToCache] Destination files are [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/download.zip".
biodb.DEBUG[2024-05-18 16:06:35.190][cch$addFilesToCache] Done adding files.
biodb.DEBUG[2024-05-18 16:06:35.193][self$getDownloadPath] Download path of hmdb.metabolites is "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/download.zip".
biodb.DEBUG[2024-05-18 16:06:35.194][self$download] Downloading of hmdb.metabolites completed.
biodb.TRACE[2024-05-18 16:06:35.198][self$addFilesToCache] Moving files to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/tmp\marker16d5836e357a2marker".
biodb.TRACE[2024-05-18 16:06:35.200][private$doAddFilesToCache] Destination files are [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/downloaded.marker".
biodb.DEBUG[2024-05-18 16:06:35.206][self$addFilesToCache] Done adding files.
biodb.DEBUG[2024-05-18 16:06:35.208][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.INFO [2024-05-18 16:06:35.209][self$download] Extract whole database of hmdb.metabolites.
biodb.INFO [2024-05-18 16:06:35.211][private$doExtractDownload] Extracting content of downloaded',
                    ' HMDB metabolite database...
biodb.DEBUG[2024-05-18 16:06:35.213][self$getDownloadPath] Download path of hmdb.metabolites is "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/download.zip".
biodb.DEBUG[2024-05-18 16:06:35.214][private$doExtractDownload] Unzipping C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/download.zip into C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/tmp...
biodb.DEBUG[2024-05-18 16:07:12.185][private$findXmlDatabaseFile] Found files [1]: "hmdb_metabolites.xml" into C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/download.zip.
biodb.DEBUG[2024-05-18 16:07:12.187][private$findXmlDatabaseFile] Found XML file C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/tmp/hmdb_metabolites.xml in ZIP file.
biodb.DEBUG[2024-05-18 16:07:12.188][private$doExtractDownload] Delete existing entry files in cache system.
biodb.DEBUG[2024-05-18 16:07:12.191][private$doExtractDownload] Extract entries from XML file "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/tmp/hmdb_metabolites.xml", into "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/tmp".
biodb.TRACE[2024-05-18 16:27:56.134][self$addFilesToCache] Moving files to cache [217920]: "C:\Users\biocbuild\AppData\Local\R\cache\R\biodb\tmp/HMDB0000001.xml, C:\Users\biocbuild\AppData\Local\R\cache\R\biodb\tmp/HMDB0000002.xml, C:\Users\biocbuild\AppData\Local\R\cache\R\biodb\tmp/HMDB0000005.xml, C:\Users\biocbuild\AppData\Local\R\cache\R\biodb\tmp/HMDB0000008.xml, C:\Users\biocbuild\AppData\Local\R\cache\R\biodb\tmp/HMDB0000010.xml, C:\Users\biocbuild\AppData\Local\R\cache\R\biodb\tmp/HMDB0000011.xml, C:\Users\biocbuild\AppData\Local\R\cache\R\biodb\tmp/HMDB0000012.xml, C:\Users\biocbuild\AppData\Local\R\cache\R\biodb\tmp/HMDB0000014.xml, C:\Users\biocbuild\AppData\Local\R\cache\R\biodb\tmp/HMDB0000015.xml, C:\Users\biocbuild\AppData\Local\R\cache\R\biodb\tmp/HMDB0000016.xml, ...".
biodb.TRACE[2024-05-18 16:27:57.082][private$doAddFilesToCache] Destination files are [217920]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/HMDB0000001.xml, C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/HMDB0000002.xml, C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/HMDB0000005.xml, C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/HMDB0000008.xml, C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/HMDB0000010.xml, C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/HMDB0000011.xml, C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/HMDB0000012.xml, C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/HMDB0000014.xml, C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/HMDB0000015.xml, C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/HMDB0000016.xml, ...".
biodb.DEBUG[2024-05-18 17:15:26.564][self$addFilesToCache] Done adding files.
biodb.DEBUG[2024-05-18 17:15:26.569][private$doExtractDownload] Delete extracted database.
biodb.TRACE[2024-05-18 17:15:26.579][self$addFilesToCache] Moving files to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/tmp\marker16d5852dd7477marker".
biodb.TRACE[2024-05-18 17:15:26.581][private$doAddFilesToCache] Destination files are [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/extracted.marker".
biodb.DEBUG[2024-05-18 17:15:26.589][self$addFilesToCache] Done adding files.
biodb.TRACE[2024-05-18 17:15:26.592][cch$loadFileContent] Trying to load 1 files from cache: [1]: "HMDB0000001".
biodb.TRACE[2024-05-18 17:15:26.594][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-05-18 17:15:26.596][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-05-18 17:15:26.598][conn$getEntryContent] 0 HMDB Metabolites entry content(s) loaded from cache.
biodb.DEBUG[2024-05-18 17:15:26.600][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2024-05-18 17:15:26.635][self$createEntryFromContent] Creating HMDB Metabolites entries from 1 content(s).
biodb.DEBUG[2024-05-18 17:15:26.637][self$createEntryFromContent] Parsing 1 HMDB Metabolites entries.
biodb.DEBUG[2024-05-18 17:15:26.640][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-18 17:15:26.648][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-18 17:15:26.650][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-18 17:15:26.669][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-18 17:15:26.670][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-18 17:15:26.671][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-18 17:15:26.672][FUN] Functions in observer BiodbConfig: [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[2024-05-18 17:15:26.675][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-05-18 17:15:26.677][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-05-18 17:15:26.678][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 17:15:26.679][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 17:15:26.681][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-05-18 17:15:26.682][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-05-18 17:15:26.683][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 17:15:26.684][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 17:15:26.686][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-18 17:15:26.687][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-18 17:15:26.689][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 17:15:26.690][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 17:15:26.691][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-18 17:15:26.692][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-18 17:15:26.694][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 17:15:26.696][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 17:15:26.697][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-18 17:15:26.698][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-18 17:15:26.699][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 17:15:26.701][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 17:15:26.702][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-18 17:15:26.704][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-18 17:15:26.705][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 17:15:26.706][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 17:15:26.708][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-18 17:15:26.709][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-18 17:15:26.710][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 17:15:26.711][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 17:15:26.713][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-18 17:15:26.714][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-18 17:15:26.715][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 17:15:26.716][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-18 17:15:26.718][self$createEntryFromContent] Accession numbers: NA.
biodb.DEBUG[2024-05-18 17:15:26.719][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.INFO [2024-05-18 17:15:26.757][biodb::testThat]
biodb.INFO [2024-05-18 17:15:26.758][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2024-05-18 17:15:26.759][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-18 17:15:26.760][biodb::testThat]
biodb.TRACE[2024-05-18 17:15:26.765][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-18 17:15:26.766][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-18 17:15:26.767][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-18 17:15:26.768][ef$get] fields variable is a list.
biodb.DEBUG[2024-05-18 17:15:26.772][function(conn, opt)] Testing searchForEntries() with entry "HMDB0000001" and field "name".
biodb.INFO [2024-05-18 17:15:27.187][biodb::testThat]
biodb.INFO [2024-05-18 17:15:27.189][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2024-05-18 17:15:27.190][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-18 17:15:27.191][biodb::testThat]
biodb.INFO [2024-05-18 17:15:27.242][biodb::testThat]
biodb.INFO [2024-05-18 17:15:27.244][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2024-05-18 17:15:27.245][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-18 17:15:27.246][biodb::testThat]
biodb.INFO [2024-05-18 17:15:27.300][biodb::testThat]
biodb.INFO [2024-05-18 17:15:27.301][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2024-05-18 17:15:27.302][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-18 17:15:27.303][biodb::testThat]
biodb.INFO [2024-05-18 17:15:27.314][biodb::testThat]
biodb.INFO [2024-05-18 17:15:27.316][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2024-05-18 17:15:27.317][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-18 17:15:27.318][biodb::testThat]
biodb.INFO [2024-05-18 17:15:27.329][biodb::testThat]
biodb.INFO [2024-05-18 17:15:27.330][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2024-05-18 17:15:27.331][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-18 17:15:27.332][biodb::testThat]
biodb.DEBUG[2024-05-18 17:15:27.336][function(conn, opt)] Trying to download "http://www.hmdb.ca/metabolites/HMDB0000001".
biodb.DEBUG[2024-05-18 17:15:27.984][getUrlContent] Use base::url() for downloading content of URL http://www.hmdb.ca/metabolites/HMDB0000001.
biodb.INFO [2024-05-18 17:15:39.530][biodb::testThat]
biodb.INFO [2024-05-18 17:15:39.531][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2024-05-18 17:15:39.532][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-18 17:15:39.534][biodb::testThat]
biodb.DEBUG[2024-05-18 17:15:39.678][getUrlContent] Use base::url() for downloading content of URL http://www.hmdb.ca/structures/HMDB0000001/image.png.
biodb.TRACE[2024-05-18 17:15:40.142][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-18 17:15:40.144][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-18 17:15:40.145][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-18 17:15:40.146][ef$get] fields variable is a list.
biodb.TRACE[2024-05-18 17:15:40.148][ef$get] Asked field names are: description.
biodb.TRACE[2024-05-18 17:15:40.149][ef$get] Realnames of fields are: description.
biodb.TRACE[2024-05-18 17:15:40.150][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-18 17:15:40.151][ef$get] fields variable is a list.
biodb.TRACE[2024-05-18 17:15:40.152][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-05-18 17:15:40.154][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-05-18 17:15:40.155][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-18 17:15:40.156][ef$get] fields variable is a list.
biodb.TRACE[2024-05-18 17:15:40.158][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-18 17:15:40.159][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-18 17:15:40.160][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-18 17:15:40.161][ef$get] fields variable is a list.
biodb.TRACE[2024-05-18 17:15:40.162][ef$get] Asked field names are: description.
biodb.TRACE[2024-05-18 17:15:40.164][ef$get] Realnames of fields are: description.
biodb.TRACE[2024-05-18 17:15:40.165][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-18 17:15:40.166][ef$get] fields variable is a list.
biodb.TRACE[2024-05-18 17:15:40.167][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-05-18 17:15:40.169][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-05-18 17:15:40.170][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-18 17:15:40.171][ef$get] fields variable is a list.
biodb.INFO [2024-05-18 17:15:40.172][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-05-18 17:15:40.174][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector hmdb.metabolites from the request scheduler
biodb.INFO [2024-05-18 17:15:40.175][self$deleteConn] Connector "hmdb.metabolites" deleted.
biodb.DEBUG[2024-05-18 17:15:40.176][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-05-18 17:15:40.177][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-18 17:15:40.178][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-18 17:15:40.179][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-18 17:15:40.180][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-18 17:15:40.182][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 17:15:40.183][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".
[ FAIL 7 | WARN 131508 | SKIP 0 | PASS 115 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test_long_100_generic.R:42:1'): RT unit is defined when there is an RT value. ──
Error in `eval_bare(expr, quo_get_env(quo))`: attempt to apply non-function
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb (local) `<fn>`(conn = `<HmdbMtbC>`, opt = `<named list>`)
 3.   └─testthat::expect_true(...)
 4.     └─testthat::quasi_label(enquo(object), label, arg = "object")
 5.       └─rlang::eval_bare(expr, quo_get_env(quo))
── Failure ('test_long_100_generic.R:42:1'): We can search for an entry by searchable field ──
!is.null(entry) is not TRUE

`actual`:   FALSE
`expected`: TRUE 
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb (local) `<fn>`(conn = `<HmdbMtbC>`, opt = `<named list>`)
 3.   └─testthat::expect_true(!is.null(entry))
── Error ('test_long_100_generic.R:42:1'): We can search for an entry by searchable field ──
Error in `entry$getFieldValue(f)`: attempt to apply non-function
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb (local) `<fn>`(conn = `<HmdbMtbC>`, opt = `<named list>`)
── Failure ('test_long_100_generic.R:42:1'): We can search for an entry by name. ──
!is.null(entry) is not TRUE

`actual`:   FALSE
`expected`: TRUE 
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb (local) `<fn>`(conn = `<HmdbMtbC>`, opt = `<named list>`)
 3.   └─testthat::expect_true(!is.null(entry))
── Error ('test_long_100_generic.R:42:1'): We can search for an entry by name. ──
Error in `entry$getFieldValue("name")`: attempt to apply non-function
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb (local) `<fn>`(conn = `<HmdbMtbC>`, opt = `<named list>`)
── Failure ('test_long_100_generic.R:42:1'): We can load an entry from the database. ──
any(vapply(entries, is.null, FUN.VALUE = TRUE)) is not FALSE

`actual`:   TRUE 
`expected`: FALSE
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb (local) `<fn>`(conn = `<HmdbMtbC>`, opt = `<named list>`)
 3.   └─opt$refEntries$getRealEntry(id)
 4.     └─self$getRealEntries(ids = id)
 5.       └─testthat::expect_false(any(vapply(entries, is.null, FUN.VALUE = TRUE)))
── Failure ('test_long_100_generic.R:42:1'): We can load an entry from the database. ──
`e` inherits from `'NULL'` not `'character'`.
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb (local) `<fn>`(conn = `<HmdbMtbC>`, opt = `<named list>`)
 3.   └─testthat::expect_is(e, "BiodbEntry")

[ FAIL 7 | WARN 131508 | SKIP 0 | PASS 115 ]
Error: Test failures
Execution halted

'R CMD check' output

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.20-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 biodbHmdb_1.11.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.20-bioc-longtests/meat/biodbHmdb.Rcheck'
* using R version 4.4.0 RC (2024-04-16 r86468 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 'biodbHmdb/DESCRIPTION' ... OK
* this is package 'biodbHmdb' version '1.11.0'
* 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 'biodbHmdb' can be installed ... WARNING
Found the following significant warnings:
  EntryMaker.hpp:23:21: warning: 'EntryMaker::accession_tag' will be initialized after [-Wreorder]
  EntryMaker.hpp:22:14: warning:   'bool EntryMaker::closed' [-Wreorder]
  EntryMaker.cpp:5:1: warning:   when initialized here [-Wreorder]
See 'F:/biocbuild/bbs-3.20-bioc-longtests/meat/biodbHmdb.Rcheck/00install.out' for details.
* 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 ... NOTE
Namespace in Imports field not imported from: 'zip'
  All declared Imports should be used.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking for missing documentation entries ... WARNING
Undocumented code objects:
  'HmdbMetabolitesConn' 'HmdbMetabolitesEntry' 'hmdbToSqlite'
All user-level objects in a package should have documentation entries.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* 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:
   2. └─biodb (local) `<fn>`(conn = `<HmdbMtbC>`, opt = `<named list>`)
   3.   └─opt$refEntries$getRealEntry(id)
   4.     └─self$getRealEntries(ids = id)
   5.       └─testthat::expect_false(any(vapply(entries, is.null, FUN.VALUE = TRUE)))
  ── Failure ('test_long_100_generic.R:42:1'): We can load an entry from the database. ──
  `e` inherits from `'NULL'` not `'character'`.
  Backtrace:
      ▆
   1. ├─base::do.call(fct, params)
   2. └─biodb (local) `<fn>`(conn = `<HmdbMtbC>`, opt = `<named list>`)
   3.   └─testthat::expect_is(e, "BiodbEntry")
  
  [ FAIL 7 | WARN 131508 | SKIP 0 | PASS 115 ]
  Error: Test failures
  Execution halted
* DONE

Status: 1 ERROR, 2 WARNINGs, 1 NOTE
See
  'F:/biocbuild/bbs-3.20-bioc-longtests/meat/biodbHmdb.Rcheck/00check.log'
for details.

Installation output

biodbHmdb.Rcheck/00install.out

* installing *source* package 'biodbHmdb' ...
** using staged installation
** libs
using C++ compiler: 'G__~1.EXE (GCC) 13.2.0'
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/testthat/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c EntryMaker.cpp -o EntryMaker.o
In file included from EntryMaker.cpp:1:
EntryMaker.hpp: In constructor 'EntryMaker::EntryMaker()':
EntryMaker.hpp:23:21: warning: 'EntryMaker::accession_tag' will be initialized after [-Wreorder]
   23 |         TagDetector accession_tag;
      |                     ^~~~~~~~~~~~~
EntryMaker.hpp:22:14: warning:   'bool EntryMaker::closed' [-Wreorder]
   22 |         bool closed;
      |              ^~~~~~
EntryMaker.cpp:5:1: warning:   when initialized here [-Wreorder]
    5 | EntryMaker::EntryMaker() :
      | ^~~~~~~~~~
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/testthat/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c FileEntryMaker.cpp -o FileEntryMaker.o
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.20-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-3.20-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/testthat/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c StringEnrtryMaker.cpp -o StringEnrtryMaker.o
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/testthat/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c TagDetector.cpp -o TagDetector.o
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/testthat/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c XmlSplitter.cpp -o XmlSplitter.o
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/testthat/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c extractXmlEntries.cpp -o extractXmlEntries.o
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/testthat/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c test-100-TagDetector.cpp -o test-100-TagDetector.o
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/testthat/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c test-150-StringEntryMaker.cpp -o test-150-StringEntryMaker.o
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/testthat/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c test-200-XmlSplitter.cpp -o test-200-XmlSplitter.o
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.20-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 biodbHmdb.dll tmp.def EntryMaker.o FileEntryMaker.o RcppExports.o StringEnrtryMaker.o TagDetector.o XmlSplitter.o extractXmlEntries.o test-100-TagDetector.o test-150-StringEntryMaker.o test-200-XmlSplitter.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-3.20-bioc/R/bin/x64 -lR
installing to F:/biocbuild/bbs-3.20-bioc-longtests/meat/biodbHmdb.Rcheck/00LOCK-biodbHmdb/00new/biodbHmdb/libs/x64
** R
** inst
** byte-compile and prepare package for lazy loading
** help
No man pages found in package  'biodbHmdb' 
*** 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 (biodbHmdb)