Back to Long Tests report for BioC 3.20

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

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.1 LTS)x86_644.4.1 (2024-06-14) -- "Race for Your Life" 4763
palomino8Windows Server 2022 Datacenterx644.4.1 (2024-06-14 ucrt) -- "Race for Your Life" 4505
lconwaymacOS 12.7.1 Montereyx86_644.4.1 (2024-06-14) -- "Race for Your Life" 4538
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 1.12.0  (landing page)
Pierrick Roger
Snapshot Date: 2024-11-02 09:55 -0400 (Sat, 02 Nov 2024)
git_url: https://git.bioconductor.org/packages/biodbHmdb
git_branch: RELEASE_3_20
git_last_commit: 0eb718c
git_last_commit_date: 2024-10-29 11:06:39 -0400 (Tue, 29 Oct 2024)
nebbiolo2Linux (Ubuntu 24.04.1 LTS) / x86_64  WARNINGS  
palomino8Windows Server 2022 Datacenter / x64  ERROR  
lconwaymacOS 12.7.1 Monterey / x86_64  WARNINGS  

CHECK results for biodbHmdb on palomino8

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: 1.12.0
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_1.12.0.tar.gz
StartedAt: 2024-11-02 16:02:40 -0400 (Sat, 02 Nov 2024)
EndedAt: 2024-11-02 16:49:40 -0400 (Sat, 02 Nov 2024)
EllapsedTime: 2820.5 seconds
RetCode: 1
Status:   ERROR  
CheckDir: biodbHmdb.Rcheck
Warnings: NA

Tests output

biodbHmdb.Rcheck/tests/testthat.Rout.fail


R version 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64

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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 [2024-11-02 16:04:14.994][biodb::testContext]
biodb.INFO [2024-11-02 16:04:14.997][biodb::testContext] ********************************************************************************
biodb.INFO [2024-11-02 16:04:14.998][biodb::testContext] Test context - Generic long tests
biodb.INFO [2024-11-02 16:04:14.999][biodb::testContext] ********************************************************************************
biodb.INFO [2024-11-02 16:04:15.001][biodb::testContext]
biodb.INFO [2024-11-02 16:04:15.007][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.14.0.
biodb.DEBUG[2024-11-02 16:04:15.009][self$loadDefinitions] Load definitions from file "F:/biocbuild/bbs-3.20-bioc/R/library/biodb/definitions.yml".
biodb.DEBUG[2024-11-02 16:04:15.017][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-11-02 16:04:15.018][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-11-02 16:04:15.020][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-11-02 16:04:15.021][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-02 16:04:15.022][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-02 16:04:15.023][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-02 16:04:15.024][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-11-02 16:04:15.040][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-11-02 16:04:15.041][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-02 16:04:15.042][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-02 16:04:15.043][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-02 16:04:15.045][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-11-02 16:04:15.046][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-11-02 16:04:15.047][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-02 16:04:15.048][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-02 16:04:15.049][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-02 16:04:15.050][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-11-02 16:04:15.051][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-11-02 16:04:15.052][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-11-02 16:04:15.054][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-02 16:04:15.055][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-02 16:04:15.056][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-02 16:04:15.057][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-11-02 16:04:15.058][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-11-02 16:04:15.059][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-11-02 16:04:15.060][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-02 16:04:15.061][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-02 16:04:15.062][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-02 16:04:15.064][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-11-02 16:04:15.065][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-11-02 16:04:15.066][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-02 16:04:15.067][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-02 16:04:15.068][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-02 16:04:15.069][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-11-02 16:04:15.070][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-11-02 16:04:15.071][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-11-02 16:04:15.072][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-02 16:04:15.074][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-02 16:04:15.075][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-02 16:04:15.076][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-11-02 16:04:15.077][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-11-02 16:04:15.078][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-02 16:04:15.079][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-02 16:04:15.080][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-02 16:04:15.081][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-11-02 16:04:15.082][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-11-02 16:04:15.084][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-11-02 16:04:15.085][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-02 16:04:15.086][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-02 16:04:15.087][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-02 16:04:15.088][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-11-02 16:04:15.089][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-11-02 16:04:15.090][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-11-02 16:04:15.092][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-11-02 16:04:15.093][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-11-02 16:04:15.094][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-11-02 16:04:15.095][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-02 16:04:15.096][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-02 16:04:15.097][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-02 16:04:15.098][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-11-02 16:04:15.100][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-11-02 16:04:15.101][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-02 16:04:15.102][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-02 16:04:15.103][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-02 16:04:15.104][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-11-02 16:04:15.105][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-11-02 16:04:15.106][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-02 16:04:15.107][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-02 16:04:15.108][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-02 16:04:15.109][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-11-02 16:04:15.111][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-11-02 16:04:15.112][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-02 16:04:15.113][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-02 16:04:15.114][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-02 16:04:15.115][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-11-02 16:04:15.116][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-11-02 16:04:15.117][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-02 16:04:15.118][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-02 16:04:15.119][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-02 16:04:15.120][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-11-02 16:04:15.122][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-11-02 16:04:15.123][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-02 16:04:15.124][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-02 16:04:15.125][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-02 16:04:15.126][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-11-02 16:04:15.127][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-11-02 16:04:15.131][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-11-02 16:04:15.132][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-02 16:04:15.133][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-02 16:04:15.134][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-02 16:04:15.135][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-11-02 16:04:15.137][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-11-02 16:04:15.138][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-11-02 16:04:15.139][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-02 16:04:15.140][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-02 16:04:15.141][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-02 16:04:15.144][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-11-02 16:04:15.180][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-11-02 16:04:15.194][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2024-11-02 16:04:15.196][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-11-02 16:04:15.197][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-11-02 16:04:15.198][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-11-02 16:04:15.199][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-11-02 16:04:15.200][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-11-02 16:04:15.202][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-11-02 16:04:15.203][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-11-02 16:04:15.204][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-11-02 16:04:15.205][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-11-02 16:04:15.206][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-11-02 16:04:15.208][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-11-02 16:04:15.209][self$setPropertyValue]
biodb.DEBUG[2024-11-02 16:04:15.210][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-11-02 16:04:15.211][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-11-02 16:04:15.211][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-11-02 16:04:15.211][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-11-02 16:04:15.211][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-11-02 16:04:15.211][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-11-02 16:04:15.212][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-11-02 16:04:15.214][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-02 16:04:15.215][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-02 16:04:15.216][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-11-02 16:04:15.217][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-02 16:04:15.218][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-02 16:04:15.219][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-11-02 16:04:15.220][self$setPropertyValue]
biodb.DEBUG[2024-11-02 16:04:15.222][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-11-02 16:04:15.223][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-11-02 16:04:15.224][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-11-02 16:04:15.225][self$setPropertyValue]
biodb.DEBUG[2024-11-02 16:04:15.226][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-11-02 16:04:15.228][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-11-02 16:04:15.229][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-11-02 16:04:15.231][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-11-02 16:04:15.232][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-11-02 16:04:15.233][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-11-02 16:04:15.234][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-11-02 16:04:15.235][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-11-02 16:04:15.236][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-11-02 16:04:15.238][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-11-02 16:04:15.239][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-11-02 16:04:15.241][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-11-02 16:04:15.242][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-11-02 16:04:15.244][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-11-02 16:04:15.246][self$setPropertyValue]
biodb.DEBUG[2024-11-02 16:04:15.247][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-11-02 16:04:15.248][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-11-02 16:04:15.248][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-11-02 16:04:15.248][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-11-02 16:04:15.248][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-11-02 16:04:15.248][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-11-02 16:04:15.249][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-11-02 16:04:15.250][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-02 16:04:15.252][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-02 16:04:15.253][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-11-02 16:04:15.254][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-02 16:04:15.255][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-02 16:04:15.256][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-11-02 16:04:15.257][self$setPropertyValue]
biodb.DEBUG[2024-11-02 16:04:15.259][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-11-02 16:04:15.260][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-11-02 16:04:15.261][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-11-02 16:04:15.262][self$setPropertyValue]
biodb.DEBUG[2024-11-02 16:04:15.263][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-11-02 16:04:15.265][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-11-02 16:04:15.266][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2024-11-02 16:04:15.268][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-11-02 16:04:15.269][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-11-02 16:04:15.270][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-11-02 16:04:15.271][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-11-02 16:04:15.272][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-11-02 16:04:15.274][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-11-02 16:04:15.275][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-11-02 16:04:15.276][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-11-02 16:04:15.277][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-11-02 16:04:15.278][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-11-02 16:04:15.280][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-11-02 16:04:15.281][self$setPropertyValue]
biodb.DEBUG[2024-11-02 16:04:15.282][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-11-02 16:04:15.283][self$setPropertyValue]
biodb.DEBUG[2024-11-02 16:04:15.284][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-11-02 16:04:15.286][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-02 16:04:15.287][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-02 16:04:15.288][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-11-02 16:04:15.289][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-02 16:04:15.290][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-02 16:04:15.291][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-11-02 16:04:15.292][self$setPropertyValue]
biodb.DEBUG[2024-11-02 16:04:15.294][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-11-02 16:04:15.295][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-11-02 16:04:15.296][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-11-02 16:04:15.297][self$setPropertyValue]
biodb.DEBUG[2024-11-02 16:04:15.298][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-11-02 16:04:15.300][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-11-02 16:04:15.301][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-11-02 16:04:15.303][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-11-02 16:04:15.304][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-11-02 16:04:15.305][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-11-02 16:04:15.306][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-11-02 16:04:15.307][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-11-02 16:04:15.309][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-11-02 16:04:15.310][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-11-02 16:04:15.311][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-11-02 16:04:15.312][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-11-02 16:04:15.313][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-11-02 16:04:15.315][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-11-02 16:04:15.316][self$setPropertyValue]
biodb.DEBUG[2024-11-02 16:04:15.317][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-11-02 16:04:15.318][self$setPropertyValue]
biodb.DEBUG[2024-11-02 16:04:15.319][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-11-02 16:04:15.320][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-02 16:04:15.322][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-02 16:04:15.323][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-11-02 16:04:15.324][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-02 16:04:15.325][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-02 16:04:15.326][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-11-02 16:04:15.327][self$setPropertyValue]
biodb.DEBUG[2024-11-02 16:04:15.328][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-11-02 16:04:15.330][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-11-02 16:04:15.331][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-11-02 16:04:15.332][self$setPropertyValue]
biodb.DEBUG[2024-11-02 16:04:15.335][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-11-02 16:04:15.336][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-11-02 16:04:15.338][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-02 16:04:15.339][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-02 16:04:15.340][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 16:04:15.341][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 16:04:15.342][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-02 16:04:15.343][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-02 16:04:15.344][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-02 16:04:15.345][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 16:04:15.346][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 16:04:15.347][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-02 16:04:15.348][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-02 16:04:15.350][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-02 16:04:15.351][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 16:04:15.352][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 16:04:15.353][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-02 16:04:15.354][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-02 16:04:15.355][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-02 16:04:15.356][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 16:04:15.357][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 16:04:15.358][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-02 16:04:15.359][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-02 16:04:15.360][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-02 16:04:15.361][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 16:04:15.362][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 16:04:15.364][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-02 16:04:15.365][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-02 16:04:15.366][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-02 16:04:15.367][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 16:04:15.368][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 16:04:15.374][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-02 16:04:15.375][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-02 16:04:15.376][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-02 16:04:15.377][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 16:04:15.378][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 16:04:15.379][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-02 16:04:15.380][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-02 16:04:15.382][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-02 16:04:15.383][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 16:04:15.384][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 16:04:15.385][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-02 16:04:15.386][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-02 16:04:15.387][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-02 16:04:15.388][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 16:04:15.389][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 16:04:15.390][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-02 16:04:15.391][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-02 16:04:15.392][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-02 16:04:15.393][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 16:04:15.394][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 16:04:15.395][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-02 16:04:15.396][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-02 16:04:15.397][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-02 16:04:15.398][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 16:04:15.399][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 16:04:15.401][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-02 16:04:15.402][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-02 16:04:15.403][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-02 16:04:15.404][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 16:04:15.405][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 16:04:15.406][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-02 16:04:15.407][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-02 16:04:15.408][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-02 16:04:15.409][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 16:04:15.410][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 16:04:15.411][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-02 16:04:15.412][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-02 16:04:15.414][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-02 16:04:15.415][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 16:04:15.416][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 16:04:15.417][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-02 16:04:15.418][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-02 16:04:15.419][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-02 16:04:15.420][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 16:04:15.421][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 16:04:15.422][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-02 16:04:15.423][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-02 16:04:15.424][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-02 16:04:15.425][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 16:04:15.426][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 16:04:15.427][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-02 16:04:15.428][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-02 16:04:15.430][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-02 16:04:15.431][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 16:04:15.432][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 16:04:15.433][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-02 16:04:15.434][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-02 16:04:15.435][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-11-02 16:04:15.439][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-11-02 16:04:15.441][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-11-02 16:04:15.442][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-11-02 16:04:15.444][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-11-02 16:04:15.445][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-11-02 16:04:15.447][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-11-02 16:04:15.448][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-11-02 16:04:15.450][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-11-02 16:04:15.451][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-11-02 16:04:15.453][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-11-02 16:04:15.454][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-11-02 16:04:15.456][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-11-02 16:04:15.457][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-11-02 16:04:15.459][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-11-02 16:04:15.461][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-11-02 16:04:15.462][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-11-02 16:04:15.464][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-11-02 16:04:15.465][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-11-02 16:04:15.467][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-11-02 16:04:15.468][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-11-02 16:04:15.470][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-11-02 16:04:15.471][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-11-02 16:04:15.473][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-11-02 16:04:15.474][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-11-02 16:04:15.476][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-11-02 16:04:15.478][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-11-02 16:04:15.479][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-11-02 16:04:15.481][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-11-02 16:04:15.482][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-11-02 16:04:15.484][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-11-02 16:04:15.485][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-11-02 16:04:15.487][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-11-02 16:04:15.488][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-11-02 16:04:15.490][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-11-02 16:04:15.491][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-11-02 16:04:15.493][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-11-02 16:04:15.494][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-11-02 16:04:15.496][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-11-02 16:04:15.497][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-11-02 16:04:15.499][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-11-02 16:04:15.500][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-11-02 16:04:15.502][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-11-02 16:04:15.504][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-11-02 16:04:15.505][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-11-02 16:04:15.507][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-11-02 16:04:15.508][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-11-02 16:04:15.510][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-11-02 16:04:15.511][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-11-02 16:04:15.513][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-11-02 16:04:15.514][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-11-02 16:04:15.516][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-11-02 16:04:15.517][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-11-02 16:04:15.519][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-11-02 16:04:15.521][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-11-02 16:04:15.522][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-11-02 16:04:15.524][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-11-02 16:04:15.525][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-11-02 16:04:15.527][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-11-02 16:04:15.528][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-11-02 16:04:15.530][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-11-02 16:04:15.531][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-11-02 16:04:15.533][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-11-02 16:04:15.534][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-11-02 16:04:15.536][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-11-02 16:04:15.537][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-11-02 16:04:15.539][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-11-02 16:04:15.541][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-11-02 16:04:15.542][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-11-02 16:04:15.544][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-11-02 16:04:15.545][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-11-02 16:04:15.547][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-11-02 16:04:15.548][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-11-02 16:04:15.550][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-11-02 16:04:15.551][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-11-02 16:04:15.553][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-11-02 16:04:15.554][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-11-02 16:04:15.556][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-11-02 16:04:15.558][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-11-02 16:04:15.559][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-11-02 16:04:15.561][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-11-02 16:04:15.562][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-11-02 16:04:15.564][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-11-02 16:04:15.604][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-11-02 16:04:15.607][initialize] This is biodb version 1.14.0.
biodb.DEBUG[2024-11-02 16:04:15.610][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-11-02 16:04:15.611][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 16:04:15.612][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 16:04:15.613][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-11-02 16:04:15.614][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-02 16:04:15.619][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-02 16:04:15.620][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-02 16:04:15.621][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-02 16:04:15.622][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 16:04:15.623][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 16:04:15.624][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-02 16:04:15.625][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-02 16:04:15.626][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-02 16:04:15.627][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-02 16:04:15.628][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-02 16:04:15.630][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 16:04:15.631][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 16:04:15.632][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-02 16:04:15.633][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-02 16:04:15.634][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-02 16:04:15.635][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-02 16:04:15.636][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-02 16:04:15.637][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 16:04:15.638][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 16:04:15.639][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-02 16:04:15.640][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-02 16:04:15.641][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-02 16:04:15.642][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-02 16:04:15.643][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-02 16:04:15.644][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 16:04:15.645][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 16:04:15.646][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-02 16:04:15.648][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-02 16:04:15.649][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-02 16:04:15.650][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-02 16:04:15.651][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-02 16:04:15.652][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 16:04:15.653][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 16:04:15.654][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-02 16:04:15.655][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-02 16:04:15.656][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-02 16:04:15.657][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-02 16:04:15.658][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-02 16:04:15.659][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 16:04:15.660][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 16:04:15.661][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-02 16:04:15.662][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-02 16:04:15.663][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-02 16:04:15.664][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-02 16:04:15.665][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-02 16:04:15.666][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 16:04:15.668][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 16:04:15.669][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-02 16:04:15.670][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-02 16:04:15.671][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-02 16:04:15.672][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-02 16:04:15.673][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-02 16:04:15.674][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 16:04:15.675][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 16:04:15.676][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-02 16:04:15.677][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-02 16:04:15.678][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-02 16:04:15.679][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-02 16:04:15.680][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-02 16:04:15.681][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 16:04:15.682][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 16:04:15.683][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-02 16:04:15.684][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-02 16:04:15.686][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-02 16:04:15.687][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-02 16:04:15.688][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-02 16:04:15.689][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 16:04:15.690][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 16:04:15.691][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-02 16:04:15.692][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-02 16:04:15.693][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-02 16:04:15.694][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-02 16:04:15.695][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-02 16:04:15.696][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 16:04:15.697][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 16:04:15.698][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-02 16:04:15.699][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-02 16:04:15.700][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-02 16:04:15.701][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-02 16:04:15.702][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-02 16:04:15.703][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 16:04:15.705][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 16:04:15.706][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-02 16:04:15.707][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-02 16:04:15.708][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-02 16:04:15.709][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-02 16:04:15.710][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-02 16:04:15.711][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 16:04:15.712][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 16:04:15.713][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-02 16:04:15.714][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-02 16:04:15.715][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-02 16:04:15.716][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-02 16:04:15.717][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-02 16:04:15.718][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 16:04:15.719][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 16:04:15.720][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-02 16:04:15.722][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-02 16:04:15.723][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-02 16:04:15.724][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-02 16:04:15.725][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-02 16:04:15.727][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 16:04:15.728][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 16:04:15.729][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-02 16:04:15.730][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-02 16:04:15.731][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-02 16:04:15.732][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-02 16:04:15.734][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-02 16:04:15.735][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 16:04:15.736][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 16:04:15.737][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-02 16:04:15.738][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-02 16:04:15.739][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-02 16:04:15.740][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-02 16:04:15.741][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-02 16:04:15.742][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 16:04:15.743][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 16:04:15.744][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-02 16:04:15.745][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-02 16:04:15.747][biodb$getConfig()$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-11-02 16:04:15.748][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-02 16:04:15.749][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-02 16:04:15.750][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-02 16:04:15.751][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 16:04:15.752][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 16:04:15.753][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-02 16:04:15.754][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-02 16:04:15.758][biodb$loadDefinitions] Load definitions from file "F:/biocbuild/bbs-3.20-bioc-longtests/meat/biodbHmdb.Rcheck/biodbHmdb/definitions.yml".
biodb.DEBUG[2024-11-02 16:04:15.767][self$getDbsInfo()$define] Define connector hmdb.metabolites.
biodb.DEBUG[2024-11-02 16:04:15.769][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-11-02 16:04:15.770][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2024-11-02 16:04:15.772][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-11-02 16:04:15.773][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-11-02 16:04:15.774][self$setPropertyValue] Setting property "downloadable" to "TRUE".
biodb.DEBUG[2024-11-02 16:04:15.775][self$setPropertyValue] Setting property "dwnld.ext" to "zip".
biodb.DEBUG[2024-11-02 16:04:15.777][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-11-02 16:04:15.778][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-11-02 16:04:15.779][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2024-11-02 16:04:15.780][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-11-02 16:04:15.781][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-11-02 16:04:15.783][self$setPropertyValue] Setting property "name" to "HMDB Metabolites".
biodb.DEBUG[2024-11-02 16:04:15.784][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-11-02 16:04:15.785][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/accession".
biodb.DEBUG[2024-11-02 16:04:15.785][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/secondary_accessions/accession".
biodb.DEBUG[2024-11-02 16:04:15.785][self$setPropertyValue] Setting property "parsing.expr" to "//average_molecular_weight".
biodb.DEBUG[2024-11-02 16:04:15.785][self$setPropertyValue] Setting property "parsing.expr" to "//cas_registry_number".
biodb.DEBUG[2024-11-02 16:04:15.785][self$setPropertyValue] Setting property "parsing.expr" to "//chebi_id".
biodb.DEBUG[2024-11-02 16:04:15.785][self$setPropertyValue] Setting property "parsing.expr" to "//chemspider_id".
biodb.DEBUG[2024-11-02 16:04:15.785][self$setPropertyValue] Setting property "parsing.expr" to "//kegg_id".
biodb.DEBUG[2024-11-02 16:04:15.785][self$setPropertyValue] Setting property "parsing.expr" to "//pubchem_compound_id".
biodb.DEBUG[2024-11-02 16:04:15.785][self$setPropertyValue] Setting property "parsing.expr" to "//iupac_name".
biodb.DEBUG[2024-11-02 16:04:15.785][self$setPropertyValue] Setting property "parsing.expr" to "//traditional_iupac".
biodb.DEBUG[2024-11-02 16:04:15.785][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/chemical_formula".
biodb.DEBUG[2024-11-02 16:04:15.785][self$setPropertyValue] Setting property "parsing.expr" to "//inchi".
biodb.DEBUG[2024-11-02 16:04:15.785][self$setPropertyValue] Setting property "parsing.expr" to "//inchikey".
biodb.DEBUG[2024-11-02 16:04:15.785][self$setPropertyValue] Setting property "parsing.expr" to "//monisotopic_molecular_weight".
biodb.DEBUG[2024-11-02 16:04:15.785][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/name".
biodb.DEBUG[2024-11-02 16:04:15.785][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/description".
biodb.DEBUG[2024-11-02 16:04:15.785][self$setPropertyValue] Setting property "parsing.expr" to "//smiles".
biodb.DEBUG[2024-11-02 16:04:15.785][self$setPropertyValue] Setting property "parsing.expr" to "//super_class".
biodb.DEBUG[2024-11-02 16:04:15.786][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-11-02 16:04:15.788][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-11-02 16:04:15.788][self$setPropertyValue] Setting property "searchable.fields" to "description".
biodb.DEBUG[2024-11-02 16:04:15.788][self$setPropertyValue] Setting property "searchable.fields" to "secondary.accessions".
biodb.DEBUG[2024-11-02 16:04:15.789][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2024-11-02 16:04:15.790][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-02 16:04:15.791][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-02 16:04:15.792][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-11-02 16:04:15.793][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-02 16:04:15.795][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-02 16:04:15.796][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-11-02 16:04:15.797][self$setPropertyValue] Setting property "urls" to "http://www.hmdb.ca/".
biodb.DEBUG[2024-11-02 16:04:15.797][self$setPropertyValue] Setting property "urls" to "http://www.hmdb.ca/system/downloads/current/hmdb_metabolites.zip".
biodb.DEBUG[2024-11-02 16:04:15.798][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-11-02 16:04:15.799][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-11-02 16:04:15.800][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-11-02 16:04:15.801][self$setPropertyValue]
biodb.DEBUG[2024-11-02 16:04:15.833][self$getEntryFields()$define] Define field secondary_accessions.
biodb.DEBUG[2024-11-02 16:04:15.835][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-11-02 16:04:15.837][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-11-02 16:04:15.839][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-11-02 16:04:15.841][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-11-02 16:04:15.862][initialize] Initialize connector hmdb.metabolites.
biodb.DEBUG[2024-11-02 16:04:15.864][initialize] Register connector hmdb.metabolites with the request scheduler
biodb.DEBUG[2024-11-02 16:04:15.870][private$bdb$getRequestScheduler()$re ...] Register connector hmdb.metabolites.
biodb.DEBUG[2024-11-02 16:04:15.874][private$addConnectorRules] Create new rule for URL "www.hmdb.ca" of connector "hmdb.metabolites".
biodb.DEBUG[2024-11-02 16:04:15.878][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-11-02 16:04:15.879][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-11-02 16:04:15.881][rule$addConnector] Connector "hmdb.metabolites" is already listed in rule "www.hmdb.ca".
biodb.DEBUG[2024-11-02 16:04:15.882][biodb$getFactory()$createConn] Creating new connector hmdb.metabolites for database class hmdb.metabolites .
biodb.INFO [2024-11-02 16:04:15.892][biodb::testThat]
biodb.INFO [2024-11-02 16:04:15.893][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2024-11-02 16:04:15.895][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-11-02 16:04:15.896][biodb::testThat]
biodb.TRACE[2024-11-02 16:04:15.902][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[2024-11-02 16:04:15.904][biodb$getFactory()$createEntryFromCo ...] Creating HMDB Metabolites entries from 1 content(s).
biodb.DEBUG[2024-11-02 16:04:15.907][biodb$getFactory()$createEntryFromCo ...] Parsing 1 HMDB Metabolites entries.
biodb.DEBUG[2024-11-02 16:04:15.914][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-02 16:04:15.915][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-02 16:04:15.916][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-02 16:04:15.933][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 16:04:15.934][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 16:04:15.935][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-02 16:04:15.936][FUN] Functions in observer BiodbConfig: [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[2024-11-02 16:04:15.947][ef$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 16:04:15.949][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 16:04:15.950][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:04:15.951][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:04:15.953][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 16:04:15.964][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 16:04:15.966][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:04:15.967][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:04:15.968][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-11-02 16:04:15.970][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-11-02 16:04:15.971][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:04:15.972][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:04:15.995][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-11-02 16:04:15.997][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-11-02 16:04:15.998][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:04:15.999][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:04:16.001][ef$get] Asked field names are: average.mass.
biodb.TRACE[2024-11-02 16:04:16.002][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-11-02 16:04:16.003][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:04:16.004][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:04:16.006][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-11-02 16:04:16.007][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-11-02 16:04:16.008][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:04:16.009][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:04:16.011][ef$get] Asked field names are: cas.id.
biodb.TRACE[2024-11-02 16:04:16.012][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-11-02 16:04:16.013][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:04:16.014][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:04:16.016][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-11-02 16:04:16.017][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-11-02 16:04:16.018][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:04:16.020][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:04:16.021][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-02 16:04:16.022][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-02 16:04:16.023][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:04:16.025][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:04:16.026][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-02 16:04:16.028][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-02 16:04:16.029][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:04:16.030][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:04:16.031][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2024-11-02 16:04:16.033][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2024-11-02 16:04:16.034][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:04:16.035][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:04:16.036][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2024-11-02 16:04:16.038][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2024-11-02 16:04:16.039][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:04:16.040][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:04:16.041][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-02 16:04:16.043][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-02 16:04:16.054][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:04:16.056][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:04:16.057][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-02 16:04:16.059][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-02 16:04:16.060][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:04:16.061][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:04:16.062][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-11-02 16:04:16.064][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-11-02 16:04:16.065][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:04:16.066][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:04:16.068][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-11-02 16:04:16.069][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-11-02 16:04:16.070][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:04:16.071][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:04:16.073][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-11-02 16:04:16.074][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-11-02 16:04:16.075][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:04:16.076][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:04:16.078][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-11-02 16:04:16.079][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-11-02 16:04:16.080][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:04:16.081][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:04:16.083][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-11-02 16:04:16.084][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-11-02 16:04:16.085][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:04:16.086][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:04:16.088][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-11-02 16:04:16.089][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-11-02 16:04:16.090][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:04:16.091][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:04:16.093][ef$get] Asked field names are: formula.
biodb.TRACE[2024-11-02 16:04:16.094][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-02 16:04:16.095][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:04:16.096][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:04:16.098][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-11-02 16:04:16.099][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-02 16:04:16.100][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:04:16.101][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:04:16.103][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-11-02 16:04:16.104][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-02 16:04:16.105][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:04:16.106][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:04:16.108][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-11-02 16:04:16.109][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-02 16:04:16.110][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:04:16.111][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:04:16.113][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-02 16:04:16.114][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-02 16:04:16.115][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:04:16.116][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:04:16.118][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-02 16:04:16.119][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-02 16:04:16.120][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:04:16.121][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:04:16.123][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-02 16:04:16.124][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-02 16:04:16.125][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:04:16.126][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:04:16.128][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-02 16:04:16.129][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-02 16:04:16.130][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:04:16.131][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:04:16.133][ef$get] Asked field names are: name.
biodb.TRACE[2024-11-02 16:04:16.134][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-11-02 16:04:16.135][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:04:16.136][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:04:16.138][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-02 16:04:16.139][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-02 16:04:16.140][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:04:16.141][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:04:16.142][ef$get] Asked field names are: description.
biodb.TRACE[2024-11-02 16:04:16.144][ef$get] Realnames of fields are: description.
biodb.TRACE[2024-11-02 16:04:16.145][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:04:16.146][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:04:16.148][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-11-02 16:04:16.149][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-11-02 16:04:16.150][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:04:16.151][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:04:16.152][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-11-02 16:04:16.154][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-02 16:04:16.155][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:04:16.156][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:04:16.158][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-11-02 16:04:16.159][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-02 16:04:16.160][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:04:16.161][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:04:16.163][ef$get] Asked field names are: super.class.
biodb.TRACE[2024-11-02 16:04:16.164][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2024-11-02 16:04:16.165][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:04:16.166][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:04:16.168][self$getBiodb()$getEntryFields()$get] Asked field names are: super.class.
biodb.TRACE[2024-11-02 16:04:16.169][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2024-11-02 16:04:16.170][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:04:16.171][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:04:16.173][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 16:04:16.174][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 16:04:16.175][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:04:16.177][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:04:16.178][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 16:04:16.179][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 16:04:16.180][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:04:16.181][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:04:16.183][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 16:04:16.184][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 16:04:16.185][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:04:16.186][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:04:16.220][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-11-02 16:04:16.222][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-11-02 16:04:16.223][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:04:16.224][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:04:16.225][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-11-02 16:04:16.226][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-11-02 16:04:16.228][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:04:16.229][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:04:16.230][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-11-02 16:04:16.231][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-11-02 16:04:16.232][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:04:16.234][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:04:16.235][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-11-02 16:04:16.236][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-11-02 16:04:16.237][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:04:16.239][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:04:16.240][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-11-02 16:04:16.241][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-11-02 16:04:16.242][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:04:16.243][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:04:16.245][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-11-02 16:04:16.246][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-11-02 16:04:16.247][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:04:16.248][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:04:16.249][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-02 16:04:16.251][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-02 16:04:16.252][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:04:16.253][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:04:16.254][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-02 16:04:16.255][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-02 16:04:16.257][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:04:16.258][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:04:16.259][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-02 16:04:16.260][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-02 16:04:16.261][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:04:16.263][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:04:16.264][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2024-11-02 16:04:16.265][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2024-11-02 16:04:16.266][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:04:16.267][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:04:16.269][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2024-11-02 16:04:16.270][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2024-11-02 16:04:16.271][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:04:16.272][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:04:16.273][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2024-11-02 16:04:16.275][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2024-11-02 16:04:16.276][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:04:16.277][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:04:16.278][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-11-02 16:04:16.280][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-11-02 16:04:16.281][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:04:16.282][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:04:16.283][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-11-02 16:04:16.284][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-11-02 16:04:16.286][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:04:16.287][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:04:16.288][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-11-02 16:04:16.289][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-11-02 16:04:16.290][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:04:16.292][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:04:16.293][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-11-02 16:04:16.294][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-11-02 16:04:16.295][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:04:16.297][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:04:16.298][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-11-02 16:04:16.299][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-11-02 16:04:16.300][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:04:16.301][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:04:16.303][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-11-02 16:04:16.304][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-11-02 16:04:16.305][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:04:16.306][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:04:16.308][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2024-11-02 16:04:16.309][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2024-11-02 16:04:16.310][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:04:16.311][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:04:16.312][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2024-11-02 16:04:16.314][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2024-11-02 16:04:16.315][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:04:16.316][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:04:16.317][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2024-11-02 16:04:16.318][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2024-11-02 16:04:16.320][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:04:16.321][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:04:16.322][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-11-02 16:04:16.323][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-11-02 16:04:16.324][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:04:16.326][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:04:16.327][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-11-02 16:04:16.328][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-11-02 16:04:16.329][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:04:16.330][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:04:16.332][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-11-02 16:04:16.333][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-11-02 16:04:16.334][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:04:16.335][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:04:16.336][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-11-02 16:04:16.338][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-02 16:04:16.339][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:04:16.340][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:04:16.341][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-11-02 16:04:16.342][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-02 16:04:16.343][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:04:16.345][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:04:16.346][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-11-02 16:04:16.347][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-02 16:04:16.348][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:04:16.349][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:04:16.351][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-11-02 16:04:16.352][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-02 16:04:16.353][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:04:16.354][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:04:16.356][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-11-02 16:04:16.357][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-02 16:04:16.358][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:04:16.359][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:04:16.360][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-11-02 16:04:16.362][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-02 16:04:16.363][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:04:16.364][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:04:16.365][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-02 16:04:16.367][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-02 16:04:16.368][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:04:16.369][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:04:16.370][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-02 16:04:16.371][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-02 16:04:16.372][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:04:16.374][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:04:16.375][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-02 16:04:16.376][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-02 16:04:16.377][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:04:16.378][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:04:16.380][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-02 16:04:16.381][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-02 16:04:16.382][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:04:16.383][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:04:16.384][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-02 16:04:16.386][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-02 16:04:16.387][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:04:16.388][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:04:16.389][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-02 16:04:16.391][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-02 16:04:16.396][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:04:16.398][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:04:16.399][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-02 16:04:16.400][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-02 16:04:16.402][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:04:16.403][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:04:16.404][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-02 16:04:16.405][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-02 16:04:16.406][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:04:16.407][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:04:16.409][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-02 16:04:16.410][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-02 16:04:16.411][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:04:16.412][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:04:16.414][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-02 16:04:16.415][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-02 16:04:16.416][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:04:16.417][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:04:16.418][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-02 16:04:16.420][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-02 16:04:16.421][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:04:16.422][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:04:16.423][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-02 16:04:16.424][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-02 16:04:16.425][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:04:16.427][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:04:16.428][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-11-02 16:04:16.429][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-11-02 16:04:16.430][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:04:16.431][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:04:16.433][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-11-02 16:04:16.434][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-11-02 16:04:16.435][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:04:16.436][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:04:16.437][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-11-02 16:04:16.439][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-11-02 16:04:16.440][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:04:16.441][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:04:16.442][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-11-02 16:04:16.444][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-11-02 16:04:16.445][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:04:16.446][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:04:16.447][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-11-02 16:04:16.448][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-11-02 16:04:16.450][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:04:16.451][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:04:16.452][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-11-02 16:04:16.453][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-11-02 16:04:16.454][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:04:16.455][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:04:16.457][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-11-02 16:04:16.458][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-02 16:04:16.459][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:04:16.460][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:04:16.461][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-11-02 16:04:16.463][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-02 16:04:16.464][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:04:16.465][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:04:16.466][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-11-02 16:04:16.467][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-02 16:04:16.469][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:04:16.470][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:04:16.471][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2024-11-02 16:04:16.472][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-02 16:04:16.473][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:04:16.474][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:04:16.476][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-02 16:04:16.477][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-02 16:04:16.478][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:04:16.479][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:04:16.480][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-02 16:04:16.482][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-02 16:04:16.483][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:04:16.484][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:04:16.485][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-02 16:04:16.487][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-02 16:04:16.488][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:04:16.489][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:04:16.490][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2024-11-02 16:04:16.492][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-02 16:04:16.493][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:04:16.494][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:04:16.510][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-02 16:04:16.512][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-02 16:04:16.513][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:04:16.514][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:04:16.515][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-02 16:04:16.517][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-02 16:04:16.518][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:04:16.519][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:04:16.520][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-02 16:04:16.521][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-02 16:04:16.523][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:04:16.524][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:04:16.525][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-02 16:04:16.526][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-02 16:04:16.527][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:04:16.528][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:04:16.530][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-02 16:04:16.531][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-02 16:04:16.532][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:04:16.533][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:04:16.535][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-11-02 16:04:16.536][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-11-02 16:04:16.537][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:04:16.538][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:04:16.540][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-11-02 16:04:16.541][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-11-02 16:04:16.542][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:04:16.543][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:04:16.544][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 16:04:16.546][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 16:04:16.547][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:04:16.548][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:04:16.549][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-11-02 16:04:16.550][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-11-02 16:04:16.551][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:04:16.553][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:04:16.554][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 16:04:16.555][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 16:04:16.556][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:04:16.557][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:04:16.559][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 16:04:16.564][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 16:04:16.566][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:04:16.567][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:04:16.568][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 16:04:16.570][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 16:04:16.571][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:04:16.572][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:04:16.573][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 16:04:16.575][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 16:04:16.576][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:04:16.577][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:04:16.578][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 16:04:16.580][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 16:04:16.581][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:04:16.582][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:04:16.583][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 16:04:16.585][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 16:04:16.586][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:04:16.587][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-02 16:04:16.588][biodb$getFactory()$createEntryFromCo ...] Accession numbers: HMDB0000001.
biodb.TRACE[2024-11-02 16:04:16.591][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-11-02 16:04:16.593][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-11-02 16:04:16.594][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:04:16.595][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:04:16.596][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-11-02 16:04:16.598][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-11-02 16:04:16.599][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:04:16.600][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:04:16.601][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-11-02 16:04:16.603][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-11-02 16:04:16.604][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:04:16.605][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:04:16.606][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-11-02 16:04:16.607][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-11-02 16:04:16.609][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:04:16.610][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:04:16.632][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 16:04:16.633][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 16:04:16.635][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:04:16.636][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:04:16.653][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-11-02 16:04:16.656][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-11-02 16:04:16.658][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:04:16.660][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:04:16.667][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 16:04:16.669][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 16:04:16.670][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:04:16.671][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:04:16.672][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 16:04:16.673][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 16:04:16.675][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:04:16.676][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:04:16.677][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 16:04:16.678][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 16:04:16.679][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:04:16.680][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:04:16.683][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 16:04:16.685][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 16:04:16.686][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:04:16.687][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:04:16.688][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 16:04:16.690][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 16:04:16.691][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:04:16.692][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:04:16.693][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 16:04:16.696][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 16:04:16.697][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:04:16.698][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:04:16.700][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-11-02 16:04:16.701][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-11-02 16:04:16.702][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:04:16.704][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:04:16.705][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-11-02 16:04:16.706][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-11-02 16:04:16.707][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:04:16.708][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:04:16.709][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-11-02 16:04:16.711][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-11-02 16:04:16.712][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:04:16.713][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:04:16.725][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 16:04:16.727][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 16:04:16.729][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:04:16.730][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:04:16.732][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 16:04:16.733][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 16:04:16.734][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:04:16.735][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:04:16.737][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 16:04:16.738][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 16:04:16.739][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:04:16.740][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:04:16.742][ef$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 16:04:16.743][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 16:04:16.744][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:04:16.745][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:04:16.746][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 16:04:16.748][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 16:04:16.749][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:04:16.750][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:04:16.767][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-11-02 16:04:16.769][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-11-02 16:04:16.770][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:04:16.771][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:04:16.772][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-11-02 16:04:16.773][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-11-02 16:04:16.775][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:04:16.776][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:04:16.777][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-11-02 16:04:16.778][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-11-02 16:04:16.779][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:04:16.781][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:04:16.782][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-11-02 16:04:16.783][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-11-02 16:04:16.784][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:04:16.785][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:04:16.787][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-11-02 16:04:16.788][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-11-02 16:04:16.789][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:04:16.790][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:04:16.801][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2024-11-02 16:04:16.803][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2024-11-02 16:04:16.804][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:04:16.805][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:04:16.806][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2024-11-02 16:04:16.808][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2024-11-02 16:04:16.809][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:04:16.810][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:04:16.811][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2024-11-02 16:04:16.812][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2024-11-02 16:04:16.813][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:04:16.815][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:04:16.816][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2024-11-02 16:04:16.817][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2024-11-02 16:04:16.818][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:04:16.819][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:04:16.821][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2024-11-02 16:04:16.822][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2024-11-02 16:04:16.823][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:04:16.824][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:04:16.835][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-11-02 16:04:16.836][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-11-02 16:04:16.838][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:04:16.839][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:04:16.840][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-11-02 16:04:16.841][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-11-02 16:04:16.842][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:04:16.843][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:04:16.845][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-11-02 16:04:16.846][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-11-02 16:04:16.847][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:04:16.848][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:04:16.849][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-11-02 16:04:16.851][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-11-02 16:04:16.852][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:04:16.853][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:04:16.854][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-11-02 16:04:16.855][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-11-02 16:04:16.856][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:04:16.857][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:04:16.868][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-02 16:04:16.870][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-02 16:04:16.871][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:04:16.872][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:04:16.873][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-02 16:04:16.875][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-02 16:04:16.876][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:04:16.877][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:04:16.878][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-02 16:04:16.879][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-02 16:04:16.881][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:04:16.882][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:04:16.883][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-02 16:04:16.884][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-02 16:04:16.885][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:04:16.886][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:04:16.888][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-02 16:04:16.889][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-02 16:04:16.890][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:04:16.891][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:04:16.902][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-02 16:04:16.904][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-02 16:04:16.905][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:04:16.906][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:04:16.907][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-02 16:04:16.909][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-02 16:04:16.910][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:04:16.911][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:04:16.912][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-02 16:04:16.913][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-02 16:04:16.914][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:04:16.916][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:04:16.917][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-02 16:04:16.918][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-02 16:04:16.919][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:04:16.920][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:04:16.922][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-02 16:04:16.923][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-02 16:04:16.924][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:04:16.925][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:04:16.936][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-02 16:04:16.938][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-02 16:04:16.939][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:04:16.940][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:04:16.941][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-02 16:04:16.943][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-02 16:04:16.944][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:04:16.950][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:04:16.951][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-02 16:04:16.952][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-02 16:04:16.954][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:04:16.955][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:04:16.956][ef$get] Asked field names are: name.
biodb.TRACE[2024-11-02 16:04:16.957][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-11-02 16:04:16.958][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:04:16.959][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:04:16.961][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-02 16:04:16.962][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-02 16:04:16.963][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:04:16.964][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:04:16.975][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-11-02 16:04:16.977][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-11-02 16:04:16.978][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:04:16.979][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:04:16.980][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-11-02 16:04:16.981][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-11-02 16:04:16.983][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:04:16.984][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:04:16.985][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-11-02 16:04:16.986][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-11-02 16:04:16.987][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:04:16.988][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:04:16.990][ef$get] Asked field names are: description.
biodb.TRACE[2024-11-02 16:04:16.991][ef$get] Realnames of fields are: description.
biodb.TRACE[2024-11-02 16:04:16.992][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:04:16.993][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:04:16.994][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-11-02 16:04:16.996][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-11-02 16:04:16.997][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:04:16.998][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:04:17.009][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-11-02 16:04:17.010][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-02 16:04:17.011][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:04:17.013][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:04:17.014][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-11-02 16:04:17.015][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-02 16:04:17.016][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:04:17.017][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:04:17.018][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-11-02 16:04:17.020][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-02 16:04:17.021][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:04:17.022][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:04:17.023][ef$get] Asked field names are: formula.
biodb.TRACE[2024-11-02 16:04:17.024][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-02 16:04:17.026][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:04:17.027][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:04:17.028][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-11-02 16:04:17.029][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-02 16:04:17.030][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:04:17.031][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:04:17.042][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-11-02 16:04:17.044][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-11-02 16:04:17.045][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:04:17.046][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:04:17.047][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-11-02 16:04:17.048][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-11-02 16:04:17.049][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:04:17.051][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:04:17.052][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-11-02 16:04:17.053][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-11-02 16:04:17.054][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:04:17.055][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:04:17.057][ef$get] Asked field names are: average.mass.
biodb.TRACE[2024-11-02 16:04:17.058][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-11-02 16:04:17.059][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:04:17.060][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:04:17.061][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-11-02 16:04:17.062][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-11-02 16:04:17.064][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:04:17.065][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:04:17.075][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-02 16:04:17.077][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-02 16:04:17.078][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:04:17.079][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:04:17.080][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-02 16:04:17.082][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-02 16:04:17.083][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:04:17.084][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:04:17.085][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-02 16:04:17.086][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-02 16:04:17.087][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:04:17.089][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:04:17.090][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-02 16:04:17.091][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-02 16:04:17.092][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:04:17.093][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:04:17.094][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-02 16:04:17.096][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-02 16:04:17.097][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:04:17.098][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:04:17.109][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2024-11-02 16:04:17.110][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2024-11-02 16:04:17.111][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:04:17.112][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:04:17.113][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2024-11-02 16:04:17.115][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2024-11-02 16:04:17.116][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:04:17.117][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:04:17.118][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2024-11-02 16:04:17.119][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2024-11-02 16:04:17.120][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:04:17.122][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:04:17.123][ef$get] Asked field names are: comp.super.class.
biodb.TRACE[2024-11-02 16:04:17.124][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2024-11-02 16:04:17.130][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:04:17.131][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:04:17.133][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2024-11-02 16:04:17.134][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2024-11-02 16:04:17.135][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:04:17.136][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:04:17.147][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-11-02 16:04:17.148][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-11-02 16:04:17.149][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:04:17.151][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:04:17.152][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-11-02 16:04:17.153][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-11-02 16:04:17.154][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:04:17.155][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:04:17.156][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-11-02 16:04:17.158][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-11-02 16:04:17.159][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:04:17.160][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:04:17.161][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-11-02 16:04:17.162][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-11-02 16:04:17.164][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:04:17.165][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:04:17.166][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-11-02 16:04:17.167][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-11-02 16:04:17.168][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:04:17.169][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:04:17.180][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-11-02 16:04:17.182][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-11-02 16:04:17.183][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:04:17.184][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:04:17.185][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-11-02 16:04:17.187][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-11-02 16:04:17.188][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:04:17.189][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:04:17.190][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-11-02 16:04:17.191][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-11-02 16:04:17.192][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:04:17.194][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:04:17.195][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-11-02 16:04:17.196][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-11-02 16:04:17.197][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:04:17.198][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:04:17.199][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-11-02 16:04:17.201][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-11-02 16:04:17.202][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:04:17.203][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:04:17.214][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-11-02 16:04:17.215][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-02 16:04:17.216][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:04:17.218][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:04:17.219][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-11-02 16:04:17.220][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-02 16:04:17.221][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:04:17.222][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:04:17.223][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-11-02 16:04:17.225][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-02 16:04:17.226][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:04:17.227][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:04:17.228][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-11-02 16:04:17.229][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-02 16:04:17.230][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:04:17.232][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:04:17.233][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-11-02 16:04:17.234][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-02 16:04:17.235][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:04:17.236][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:04:17.247][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-11-02 16:04:17.249][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-02 16:04:17.250][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:04:17.251][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:04:17.252][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-11-02 16:04:17.253][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-02 16:04:17.255][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:04:17.256][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:04:17.257][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-11-02 16:04:17.258][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-02 16:04:17.259][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:04:17.260][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:04:17.262][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-11-02 16:04:17.263][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-02 16:04:17.264][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:04:17.265][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:04:17.266][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-11-02 16:04:17.268][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-02 16:04:17.269][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:04:17.270][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:04:17.281][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-02 16:04:17.282][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-02 16:04:17.283][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:04:17.284][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:04:17.286][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-02 16:04:17.287][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-02 16:04:17.288][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:04:17.289][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:04:17.290][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-02 16:04:17.292][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-02 16:04:17.293][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:04:17.294][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:04:17.295][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-02 16:04:17.296][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-02 16:04:17.298][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:04:17.299][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:04:17.300][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-02 16:04:17.301][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-02 16:04:17.302][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:04:17.303][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:04:17.319][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-11-02 16:04:17.321][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-11-02 16:04:17.322][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:04:17.323][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:04:17.324][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-11-02 16:04:17.326][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-11-02 16:04:17.327][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:04:17.328][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:04:17.329][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-11-02 16:04:17.330][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-11-02 16:04:17.332][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:04:17.333][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:04:17.334][ef$get] Asked field names are: cas.id.
biodb.TRACE[2024-11-02 16:04:17.335][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-11-02 16:04:17.336][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:04:17.337][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:04:17.339][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-11-02 16:04:17.340][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-11-02 16:04:17.341][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:04:17.342][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:04:17.353][ef$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 16:04:17.355][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 16:04:17.356][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:04:17.357][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:04:17.364][ef$get] Asked field names are: average.mass.
biodb.TRACE[2024-11-02 16:04:17.365][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-11-02 16:04:17.367][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:04:17.368][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:04:17.374][ef$get] Asked field names are: cas.id.
biodb.TRACE[2024-11-02 16:04:17.376][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-11-02 16:04:17.377][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:04:17.378][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:04:17.385][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-02 16:04:17.386][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-02 16:04:17.387][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:04:17.388][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:04:17.395][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2024-11-02 16:04:17.396][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2024-11-02 16:04:17.397][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:04:17.399][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:04:17.405][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-11-02 16:04:17.407][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-11-02 16:04:17.408][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:04:17.409][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:04:17.416][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-11-02 16:04:17.417][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-11-02 16:04:17.418][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:04:17.419][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:04:17.426][ef$get] Asked field names are: comp.super.class.
biodb.TRACE[2024-11-02 16:04:17.428][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2024-11-02 16:04:17.429][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:04:17.430][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:04:17.437][ef$get] Asked field names are: description.
biodb.TRACE[2024-11-02 16:04:17.438][ef$get] Realnames of fields are: description.
biodb.TRACE[2024-11-02 16:04:17.439][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:04:17.440][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:04:17.447][ef$get] Asked field names are: formula.
biodb.TRACE[2024-11-02 16:04:17.449][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-02 16:04:17.450][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:04:17.451][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:04:17.458][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-11-02 16:04:17.460][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-02 16:04:17.461][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:04:17.462][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:04:17.469][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-02 16:04:17.470][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-02 16:04:17.472][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:04:17.473][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:04:17.480][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-02 16:04:17.481][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-02 16:04:17.482][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:04:17.484][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:04:17.490][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-02 16:04:17.492][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-02 16:04:17.493][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:04:17.494][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:04:17.501][ef$get] Asked field names are: name.
biodb.TRACE[2024-11-02 16:04:17.502][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-11-02 16:04:17.503][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:04:17.504][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:04:17.516][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-11-02 16:04:17.517][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-11-02 16:04:17.519][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:04:17.520][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:04:17.526][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-11-02 16:04:17.528][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-11-02 16:04:17.529][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:04:17.530][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:04:17.537][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-11-02 16:04:17.538][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-02 16:04:17.540][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:04:17.541][ef$get] fields variable is a list.
biodb.INFO [2024-11-02 16:04:17.553][biodb::testThat]
biodb.INFO [2024-11-02 16:04:17.554][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2024-11-02 16:04:17.555][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-11-02 16:04:17.556][biodb::testThat]
biodb.DEBUG[2024-11-02 16:04:17.570][private$loadEntries] Creating entries from ids [1]: "HMDB0000001".
biodb.DEBUG[2024-11-02 16:04:17.576][conn$getEntryContent] Get HMDB Metabolites entry content(s) for 1 id(s)...
biodb.INFO [2024-11-02 16:04:17.582][self$getFolderPath] Create cache folder "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34" for "hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34".
biodb.DEBUG[2024-11-02 16:04:17.584][self$isDownloaded] Database hmdb.metabolites has not yet been downloaded.
biodb.INFO [2024-11-02 16:04:17.585][self$download] Downloading whole database of hmdb.metabolites.
biodb.INFO [2024-11-02 16:04:17.587][private$doDownload] Downloading HMDB metabolite database at "http://www.hmdb.ca/system/downloads/current/hmdb_metabolites.zip" ...
biodb.DEBUG[2024-11-02 16:04:17.601][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 24.0 MB

biodb.INFO [2024-11-02 16:05:08.799][biodb::testThat]
biodb.INFO [2024-11-02 16:05:08.800][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2024-11-02 16:05:08.801][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-11-02 16:05:08.803][biodb::testThat]
biodb.TRACE[2024-11-02 16:05:08.806][ef$get] Asked field names are: name.
biodb.TRACE[2024-11-02 16:05:08.808][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-11-02 16:05:08.809][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:08.810][ef$get] fields variable is a list.
biodb.DEBUG[2024-11-02 16:05:08.812][function(conn, opt)] Testing searchForEntries() with entry "HMDB0000001" and field "name".
biodb.DEBUG[2024-11-02 16:05:08.837][private$loadEntries] Creating entries from ids [1]: "HMDB0000001".
biodb.DEBUG[2024-11-02 16:05:08.887][conn$getEntryContent] Get HMDB Metabolites entry content(s) for 1 id(s)...
biodb.DEBUG[2024-11-02 16:05:08.889][self$isDownloaded] Database hmdb.metabolites has not yet been downloaded.
biodb.INFO [2024-11-02 16:05:08.891][self$download] Downloading whole database of hmdb.metabolites.
biodb.INFO [2024-11-02 16:05:08.892][private$doDownload] Downloading HMDB metabolite database at "http://www.hmdb.ca/system/downloads/current/hmdb_metabolites.zip" ...
biodb.DEBUG[2024-11-02 16:05:08.906][sched$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 41.1 MB

biodb.INFO [2024-11-02 16:06:05.514][biodb::testThat]
biodb.INFO [2024-11-02 16:06:05.516][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2024-11-02 16:06:05.517][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-11-02 16:06:05.518][biodb::testThat]
biodb.DEBUG[2024-11-02 16:06:05.534][private$loadEntries] Creating entries from ids [1]: "HMDB0000001".
biodb.DEBUG[2024-11-02 16:06:05.536][conn$getEntryContent] Get HMDB Metabolites entry content(s) for 1 id(s)...
biodb.DEBUG[2024-11-02 16:06:05.538][self$isDownloaded] Database hmdb.metabolites has not yet been downloaded.
biodb.INFO [2024-11-02 16:06:05.540][self$download] Downloading whole database of hmdb.metabolites.
biodb.INFO [2024-11-02 16:06:05.541][private$doDownload] Downloading HMDB metabolite database at "http://www.hmdb.ca/system/downloads/current/hmdb_metabolites.zip" ...
biodb.DEBUG[2024-11-02 16:06:05.543][sched$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[2024-11-02 16:06:27.303][cch$addFilesToCache] Moving files to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/tmp\hmdb.metabolites22e8c6b3b3aaazip".
biodb.TRACE[2024-11-02 16:06:27.305][private$doAddFilesToCache] Destination files are [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/download.zip".
biodb.DEBUG[2024-11-02 16:06:27.603][cch$addFilesToCache] Done adding files.
biodb.DEBUG[2024-11-02 16:06:27.605][self$getDownloadPath] Download path of hmdb.metabolites is "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/download.zip".
biodb.DEBUG[2024-11-02 16:06:27.606][self$download] Downloading of hmdb.metabolites completed.
biodb.TRACE[2024-11-02 16:06:27.609][self$addFilesToCache] Moving files to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/tmp\marker22e8c4a1b4c3bmarker".
biodb.TRACE[2024-11-02 16:06:27.611][private$doAddFilesToCache] Destination files are [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/downloaded.marker".
biodb.DEBUG[2024-11-02 16:06:27.615][self$addFilesToCache] Done adding files.
biodb.DEBUG[2024-11-02 16:06:27.617][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.INFO [2024-11-02 16:06:27.619][self$download] Extract whole database of hmdb.metabolites.
biodb.INFO [2024-11-02 16:06:27.620][private$doExtractDownload] Extracting content of downloaded',
                    ' HMDB metabolite database...
biodb.DEBUG[2024-11-02 16:06:27.622][self$getDownloadPath] Download path of hmdb.metabolites is "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/download.zip".
biodb.DEBUG[2024-11-02 16:06:27.623][private$doExtractDownload] Unzipping C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/download.zip into C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/tmp...
biodb.DEBUG[2024-11-02 16:07:03.586][private$findXmlDatabaseFile] Found files [3]: "hmdb.metabolites22e8c57b7f58zip, hmdb.metabolites22e8c7fcd363zip, hmdb_metabolites.xml" into C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/download.zip.
biodb.DEBUG[2024-11-02 16:07:03.588][private$findXmlDatabaseFile] Found XML file C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/tmp/hmdb_metabolites.xml in ZIP file.
biodb.DEBUG[2024-11-02 16:07:03.590][private$doExtractDownload] Delete existing entry files in cache system.
biodb.DEBUG[2024-11-02 16:07:03.592][private$doExtractDownload] Extract entries from XML file "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/tmp/hmdb_metabolites.xml", into "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/tmp".
biodb.TRACE[2024-11-02 16:34:17.032][self$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[2024-11-02 16:34:18.005][private$doAddFilesToCache] Destination files are [217920]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/HMDB0000001.xml, C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/HMDB0000002.xml, C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/HMDB0000005.xml, C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/HMDB0000008.xml, C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/HMDB0000010.xml, C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/HMDB0000011.xml, C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/HMDB0000012.xml, C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/HMDB0000014.xml, C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/HMDB0000015.xml, C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/HMDB0000016.xml, ...".
biodb.DEBUG[2024-11-02 16:49:24.157][self$addFilesToCache] Done adding files.
biodb.DEBUG[2024-11-02 16:49:24.160][private$doExtractDownload] Delete extracted database.
biodb.TRACE[2024-11-02 16:49:24.714][self$addFilesToCache] Moving files to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/tmp\marker22e8c776e5849marker".
biodb.TRACE[2024-11-02 16:49:24.716][private$doAddFilesToCache] Destination files are [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/extracted.marker".
biodb.DEBUG[2024-11-02 16:49:24.722][self$addFilesToCache] Done adding files.
biodb.TRACE[2024-11-02 16:49:24.724][cch$loadFileContent] Trying to load 1 files from cache: [1]: "HMDB0000001".
biodb.TRACE[2024-11-02 16:49:24.726][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-11-02 16:49:24.743][loadFileContents] Loaded 1 files from cache: [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/HMDB0000001.xml".
biodb.DEBUG[2024-11-02 16:49:24.744][conn$getEntryContent] 1 HMDB Metabolites entry content(s) loaded from cache.
biodb.DEBUG[2024-11-02 16:49:24.768][self$createEntryFromContent] Creating HMDB Metabolites entries from 1 content(s).
biodb.DEBUG[2024-11-02 16:49:24.770][self$createEntryFromContent] Parsing 1 HMDB Metabolites entries.
biodb.DEBUG[2024-11-02 16:49:24.773][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-02 16:49:24.774][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-02 16:49:24.775][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-02 16:49:24.784][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 16:49:24.785][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 16:49:24.787][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-02 16:49:24.788][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-02 16:49:24.793][ef$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 16:49:24.795][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 16:49:24.796][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:49:24.797][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:49:24.799][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 16:49:24.800][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 16:49:24.801][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:49:24.802][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:49:24.804][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-11-02 16:49:24.805][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-11-02 16:49:24.806][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:49:24.807][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:49:24.809][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-11-02 16:49:24.810][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-11-02 16:49:24.811][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:49:24.812][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:49:24.814][ef$get] Asked field names are: average.mass.
biodb.TRACE[2024-11-02 16:49:24.815][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-11-02 16:49:24.816][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:49:24.817][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:49:24.819][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-11-02 16:49:24.820][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-11-02 16:49:24.821][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:49:24.823][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:49:24.824][ef$get] Asked field names are: cas.id.
biodb.TRACE[2024-11-02 16:49:24.825][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-11-02 16:49:24.826][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:49:24.827][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:49:24.829][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-11-02 16:49:24.830][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-11-02 16:49:24.832][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:49:24.833][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:49:24.834][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-02 16:49:24.836][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-02 16:49:24.837][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:49:24.838][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:49:24.840][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-02 16:49:24.842][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-02 16:49:24.843][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:49:24.844][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:49:24.846][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2024-11-02 16:49:24.847][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2024-11-02 16:49:24.848][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:49:24.850][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:49:24.851][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2024-11-02 16:49:24.853][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2024-11-02 16:49:24.854][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:49:24.855][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:49:24.857][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-02 16:49:24.858][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-02 16:49:24.860][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:49:24.861][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:49:24.863][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-02 16:49:24.864][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-02 16:49:24.866][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:49:24.867][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:49:24.869][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-11-02 16:49:24.870][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-11-02 16:49:24.872][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:49:24.873][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:49:24.875][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-11-02 16:49:24.877][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-11-02 16:49:24.878][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:49:24.880][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:49:24.881][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-11-02 16:49:24.883][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-11-02 16:49:24.885][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:49:24.886][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:49:24.888][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-11-02 16:49:24.890][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-11-02 16:49:24.891][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:49:24.893][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:49:24.894][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-11-02 16:49:24.896][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-11-02 16:49:24.897][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:49:24.898][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:49:24.900][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-11-02 16:49:24.901][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-11-02 16:49:24.903][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:49:24.904][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:49:24.906][ef$get] Asked field names are: formula.
biodb.TRACE[2024-11-02 16:49:24.907][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-02 16:49:24.908][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:49:24.910][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:49:24.911][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-11-02 16:49:24.913][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-02 16:49:24.914][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:49:24.915][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:49:24.917][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-11-02 16:49:24.918][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-02 16:49:24.919][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:49:24.921][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:49:24.922][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-11-02 16:49:24.924][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-02 16:49:24.925][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:49:24.927][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:49:24.928][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-02 16:49:24.930][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-02 16:49:24.931][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:49:24.932][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:49:24.935][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-02 16:49:24.936][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-02 16:49:24.938][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:49:24.939][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:49:24.940][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-02 16:49:24.942][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-02 16:49:24.943][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:49:24.944][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:49:24.946][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-02 16:49:24.948][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-02 16:49:24.949][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:49:24.950][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:49:24.952][ef$get] Asked field names are: name.
biodb.TRACE[2024-11-02 16:49:24.953][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-11-02 16:49:24.955][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:49:24.956][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:49:24.957][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-02 16:49:24.959][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-02 16:49:24.960][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:49:24.961][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:49:24.963][ef$get] Asked field names are: description.
biodb.TRACE[2024-11-02 16:49:24.964][ef$get] Realnames of fields are: description.
biodb.TRACE[2024-11-02 16:49:24.966][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:49:24.967][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:49:24.969][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-11-02 16:49:24.970][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-11-02 16:49:24.971][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:49:24.973][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:49:24.974][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-11-02 16:49:24.975][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-02 16:49:24.977][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:49:24.978][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:49:24.980][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-11-02 16:49:24.981][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-02 16:49:24.983][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:49:24.984][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:49:24.985][ef$get] Asked field names are: super.class.
biodb.TRACE[2024-11-02 16:49:24.987][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2024-11-02 16:49:24.988][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:49:24.989][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:49:24.991][self$getBiodb()$getEntryFields()$get] Asked field names are: super.class.
biodb.TRACE[2024-11-02 16:49:24.993][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2024-11-02 16:49:24.994][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:49:24.995][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:49:24.997][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 16:49:24.998][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 16:49:25.000][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:49:25.001][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:49:25.002][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 16:49:25.004][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 16:49:25.005][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:49:25.006][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:49:25.008][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 16:49:25.009][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 16:49:25.010][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:49:25.012][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:49:25.013][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-11-02 16:49:25.015][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-11-02 16:49:25.016][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:49:25.017][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:49:25.018][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-11-02 16:49:25.020][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-11-02 16:49:25.021][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:49:25.022][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:49:25.024][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-11-02 16:49:25.025][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-11-02 16:49:25.027][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:49:25.028][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:49:25.029][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-11-02 16:49:25.031][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-11-02 16:49:25.032][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:49:25.033][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:49:25.035][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-11-02 16:49:25.036][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-11-02 16:49:25.037][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:49:25.039][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:49:25.040][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-11-02 16:49:25.042][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-11-02 16:49:25.043][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:49:25.044][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:49:25.046][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-02 16:49:25.047][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-02 16:49:25.048][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:49:25.050][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:49:25.051][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-02 16:49:25.053][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-02 16:49:25.054][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:49:25.055][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:49:25.057][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-02 16:49:25.058][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-02 16:49:25.059][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:49:25.061][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:49:25.062][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2024-11-02 16:49:25.064][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2024-11-02 16:49:25.065][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:49:25.066][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:49:25.068][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2024-11-02 16:49:25.069][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2024-11-02 16:49:25.070][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:49:25.071][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:49:25.073][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2024-11-02 16:49:25.074][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2024-11-02 16:49:25.076][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:49:25.077][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:49:25.078][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-11-02 16:49:25.080][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-11-02 16:49:25.081][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:49:25.082][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:49:25.084][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-11-02 16:49:25.085][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-11-02 16:49:25.086][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:49:25.088][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:49:25.089][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-11-02 16:49:25.090][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-11-02 16:49:25.092][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:49:25.093][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:49:25.094][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-11-02 16:49:25.096][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-11-02 16:49:25.097][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:49:25.098][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:49:25.100][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-11-02 16:49:25.101][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-11-02 16:49:25.102][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:49:25.104][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:49:25.105][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-11-02 16:49:25.106][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-11-02 16:49:25.108][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:49:25.109][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:49:25.110][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2024-11-02 16:49:25.112][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2024-11-02 16:49:25.113][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:49:25.114][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:49:25.116][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2024-11-02 16:49:25.117][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2024-11-02 16:49:25.118][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:49:25.120][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:49:25.121][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2024-11-02 16:49:25.122][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2024-11-02 16:49:25.124][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:49:25.125][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:49:25.126][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-11-02 16:49:25.128][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-11-02 16:49:25.129][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:49:25.130][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:49:25.132][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-11-02 16:49:25.133][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-11-02 16:49:25.134][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:49:25.136][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:49:25.137][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-11-02 16:49:25.138][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-11-02 16:49:25.140][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:49:25.141][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:49:25.142][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-11-02 16:49:25.144][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-02 16:49:25.145][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:49:25.146][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:49:25.148][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-11-02 16:49:25.149][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-02 16:49:25.151][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:49:25.152][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:49:25.153][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-11-02 16:49:25.155][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-02 16:49:25.156][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:49:25.157][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:49:25.158][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-11-02 16:49:25.160][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-02 16:49:25.161][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:49:25.162][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:49:25.164][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-11-02 16:49:25.165][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-02 16:49:25.166][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:49:25.168][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:49:25.169][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-11-02 16:49:25.171][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-02 16:49:25.172][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:49:25.173][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:49:25.174][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-02 16:49:25.176][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-02 16:49:25.177][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:49:25.178][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:49:25.180][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-02 16:49:25.181][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-02 16:49:25.183][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:49:25.184][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:49:25.185][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-02 16:49:25.187][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-02 16:49:25.188][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:49:25.189][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:49:25.191][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-02 16:49:25.192][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-02 16:49:25.193][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:49:25.195][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:49:25.196][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-02 16:49:25.197][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-02 16:49:25.199][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:49:25.200][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:49:25.201][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-02 16:49:25.203][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-02 16:49:25.204][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:49:25.205][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:49:25.207][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-02 16:49:25.208][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-02 16:49:25.209][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:49:25.211][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:49:25.212][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-02 16:49:25.213][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-02 16:49:25.215][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:49:25.216][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:49:25.217][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-02 16:49:25.219][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-02 16:49:25.220][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:49:25.221][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:49:25.223][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-02 16:49:25.224][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-02 16:49:25.225][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:49:25.227][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:49:25.228][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-02 16:49:25.293][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-02 16:49:25.295][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:49:25.296][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:49:25.297][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-02 16:49:25.298][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-02 16:49:25.299][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:49:25.300][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:49:25.302][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-11-02 16:49:25.303][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-11-02 16:49:25.304][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:49:25.305][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:49:25.306][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-11-02 16:49:25.308][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-11-02 16:49:25.309][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:49:25.310][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:49:25.311][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-11-02 16:49:25.312][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-11-02 16:49:25.313][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:49:25.314][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:49:25.316][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-11-02 16:49:25.317][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-11-02 16:49:25.318][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:49:25.319][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:49:25.320][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-11-02 16:49:25.322][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-11-02 16:49:25.323][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:49:25.324][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:49:25.325][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-11-02 16:49:25.326][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-11-02 16:49:25.327][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:49:25.328][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:49:25.330][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-11-02 16:49:25.331][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-02 16:49:25.332][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:49:25.333][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:49:25.334][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-11-02 16:49:25.335][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-02 16:49:25.336][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:49:25.338][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:49:25.339][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-11-02 16:49:25.340][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-02 16:49:25.341][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:49:25.342][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:49:25.343][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2024-11-02 16:49:25.345][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-02 16:49:25.346][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:49:25.347][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:49:25.348][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-02 16:49:25.349][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-02 16:49:25.350][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:49:25.351][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:49:25.353][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-02 16:49:25.354][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-02 16:49:25.355][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:49:25.356][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:49:25.357][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-02 16:49:25.358][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-02 16:49:25.359][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:49:25.361][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:49:25.362][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2024-11-02 16:49:25.363][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-02 16:49:25.364][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:49:25.365][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:49:25.367][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-02 16:49:25.369][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-02 16:49:25.370][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:49:25.371][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:49:25.372][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-02 16:49:25.373][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-02 16:49:25.374][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:49:25.375][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:49:25.377][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-02 16:49:25.378][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-02 16:49:25.379][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:49:25.380][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:49:25.381][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-02 16:49:25.382][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-02 16:49:25.383][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:49:25.385][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:49:25.386][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-02 16:49:25.387][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-02 16:49:25.388][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:49:25.389][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:49:25.391][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-11-02 16:49:25.392][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-11-02 16:49:25.393][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:49:25.394][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:49:25.395][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-11-02 16:49:25.397][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-11-02 16:49:25.398][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:49:25.399][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:49:25.400][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 16:49:25.401][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 16:49:25.402][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:49:25.403][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:49:25.404][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-11-02 16:49:25.406][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-11-02 16:49:25.407][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:49:25.408][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:49:25.409][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 16:49:25.410][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 16:49:25.411][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:49:25.413][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:49:25.414][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 16:49:25.415][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 16:49:25.416][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:49:25.417][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:49:25.418][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 16:49:25.420][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 16:49:25.421][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:49:25.422][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:49:25.423][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 16:49:25.424][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 16:49:25.426][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:49:25.427][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:49:25.428][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 16:49:25.429][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 16:49:25.430][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:49:25.431][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:49:25.433][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 16:49:25.434][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 16:49:25.435][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:49:25.436][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-02 16:49:25.437][self$createEntryFromContent] Accession numbers: HMDB0000001.
biodb.TRACE[2024-11-02 16:49:25.445][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-02 16:49:25.446][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-02 16:49:25.447][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:49:25.448][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:49:25.449][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-02 16:49:25.450][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-02 16:49:25.452][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:49:25.453][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:49:25.454][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-02 16:49:25.455][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-02 16:49:25.456][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:49:25.457][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-02 16:49:25.483][private$doSearchForEntries] fields NAMES = name
biodb.DEBUG[2024-11-02 16:49:25.484][private$doSearchForEntries] fields VALUES = 1-Methylhistidine
biodb.DEBUG[2024-11-02 16:49:25.485][private$doSearchForEntries] fields VALUES = 1-Methylhistidine
biodb.DEBUG[2024-11-02 16:49:25.487][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2024-11-02 16:49:25.489][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2024-11-02 16:49:25.491][private$doGetEntryIds] .doGetEntryIds 10
biodb.DEBUG[2024-11-02 16:49:25.493][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2024-11-02 16:49:25.494][private$doGetEntryIds] .doGetEntryIds 11
biodb.DEBUG[2024-11-02 16:49:25.495][private$doListFiles] List files in C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^.*\.xml$.
biodb.DEBUG[2024-11-02 16:49:27.066][cch$listFiles] Extracting accession number from file names associated with hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^(.*)\.xml$
biodb.DEBUG[2024-11-02 16:49:27.068][cch$listFiles] files = HMDB0000001.xml, HMDB0000002.xml, HMDB0000005.xml, HMDB0000008.xml, HMDB0000010.xml, HMDB0000011.xml
biodb.DEBUG[2024-11-02 16:49:27.251][private$doGetEntryIds] COUNT IDS = 217920
biodb.DEBUG[2024-11-02 16:49:27.302][private$doSearchForEntries] All IDs = [217920]: "HMDB0000001, HMDB0000002, HMDB0000005, HMDB0000008, HMDB0000010, HMDB0000011, HMDB0000012, HMDB0000014, HMDB0000015, HMDB0000016, ..."
biodb.DEBUG[2024-11-02 16:49:27.303][private$doSearchForEntries] Total number of IDs = 217920
biodb.TRACE[2024-11-02 16:49:27.305][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-02 16:49:27.307][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-02 16:49:27.308][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:49:27.309][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:49:27.310][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-02 16:49:27.312][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-02 16:49:27.313][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:49:27.314][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:49:27.315][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-02 16:49:27.317][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-02 16:49:27.318][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:49:27.319][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:49:27.320][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-02 16:49:27.322][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-02 16:49:27.323][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:49:27.324][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-02 16:49:27.325][private$doSearchForEntries] MATCHED = TRUE
biodb.DEBUG[2024-11-02 16:49:27.326][private$doSearchForEntries] COUNT IDS = 1
biodb.INFO [2024-11-02 16:49:27.350][biodb::testThat]
biodb.INFO [2024-11-02 16:49:27.351][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2024-11-02 16:49:27.352][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-11-02 16:49:27.353][biodb::testThat]
biodb.TRACE[2024-11-02 16:49:27.376][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-11-02 16:49:27.377][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-11-02 16:49:27.379][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:49:27.380][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:49:27.381][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-11-02 16:49:27.382][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-11-02 16:49:27.383][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:49:27.385][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:49:27.386][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-11-02 16:49:27.387][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-11-02 16:49:27.388][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:49:27.389][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:49:27.391][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-11-02 16:49:27.392][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-11-02 16:49:27.393][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:49:27.394][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:49:27.430][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-11-02 16:49:27.432][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-11-02 16:49:27.433][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:49:27.434][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:49:27.435][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-11-02 16:49:27.436][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-11-02 16:49:27.438][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:49:27.439][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:49:27.440][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-11-02 16:49:27.441][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-11-02 16:49:27.442][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:49:27.444][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:49:27.445][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-11-02 16:49:27.446][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-11-02 16:49:27.447][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:49:27.448][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-11-02 16:49:27.459][biodb::testThat]
biodb.INFO [2024-11-02 16:49:27.460][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2024-11-02 16:49:27.462][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-11-02 16:49:27.463][biodb::testThat]
biodb.INFO [2024-11-02 16:49:27.474][biodb::testThat]
biodb.INFO [2024-11-02 16:49:27.475][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2024-11-02 16:49:27.477][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-11-02 16:49:27.478][biodb::testThat]
biodb.INFO [2024-11-02 16:49:27.569][biodb::testThat]
biodb.INFO [2024-11-02 16:49:27.570][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2024-11-02 16:49:27.572][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-11-02 16:49:27.573][biodb::testThat]
biodb.DEBUG[2024-11-02 16:49:27.577][function(conn, opt)] Trying to download "http://www.hmdb.ca/metabolites/HMDB0000001".
biodb.DEBUG[2024-11-02 16:49:27.955][getUrlContent] Use base::url() for downloading content of URL http://www.hmdb.ca/metabolites/HMDB0000001.
biodb.INFO [2024-11-02 16:49:35.857][biodb::testThat]
biodb.INFO [2024-11-02 16:49:35.858][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2024-11-02 16:49:35.860][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-11-02 16:49:35.861][biodb::testThat]
biodb.DEBUG[2024-11-02 16:49:36.048][getUrlContent] Use base::url() for downloading content of URL http://www.hmdb.ca/structures/HMDB0000001/image.png.
biodb.TRACE[2024-11-02 16:49:40.008][ef$get] Asked field names are: name.
biodb.TRACE[2024-11-02 16:49:40.010][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-11-02 16:49:40.011][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:49:40.012][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:49:40.013][ef$get] Asked field names are: description.
biodb.TRACE[2024-11-02 16:49:40.014][ef$get] Realnames of fields are: description.
biodb.TRACE[2024-11-02 16:49:40.016][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:49:40.017][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:49:40.018][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-11-02 16:49:40.019][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-11-02 16:49:40.020][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:49:40.022][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:49:40.023][ef$get] Asked field names are: name.
biodb.TRACE[2024-11-02 16:49:40.024][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-11-02 16:49:40.025][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:49:40.026][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:49:40.028][ef$get] Asked field names are: description.
biodb.TRACE[2024-11-02 16:49:40.029][ef$get] Realnames of fields are: description.
biodb.TRACE[2024-11-02 16:49:40.030][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:49:40.031][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:49:40.032][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-11-02 16:49:40.034][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-11-02 16:49:40.035][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:49:40.036][ef$get] fields variable is a list.
biodb.INFO [2024-11-02 16:49:40.037][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-11-02 16:49:40.039][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector hmdb.metabolites from the request scheduler
biodb.INFO [2024-11-02 16:49:40.040][self$deleteConn] Connector "hmdb.metabolites" deleted.
biodb.DEBUG[2024-11-02 16:49:40.041][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-11-02 16:49:40.042][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-02 16:49:40.043][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-02 16:49:40.044][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 16:49:40.045][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 16:49:40.046][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-11-02 16:49:40.047][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
[ FAIL 2 | WARN 4 | SKIP 0 | PASS 124 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test_long_100_generic.R:42:1'): RT unit is defined when there is an RT value. ──
Error in `utils::download.file(url = url, destfile = dest.file, mode = "wb", 
    method = "auto", cacheOK = FALSE, quiet = FALSE)`: download from 'http://www.hmdb.ca/system/downloads/current/hmdb_metabolites.zip' failed
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb (local) `<fn>`(conn = `<HmdbMtbC>`, opt = `<named list>`)
 3.   └─conn$getBiodb()$getFactory()$getEntry(...)
 4.     └─private$loadEntries(conn$getId(), missing.ids, drop = FALSE)
 5.       └─conn$getEntryContent(ids)
 6.         └─self$download()
 7.           └─private$doDownload()
 8.             └─sched$downloadFile(url = zip.url, dest.file = tmpFile)
 9.               └─utils::download.file(...)
── Error ('test_long_100_generic.R:42:1'): We can search for an entry by searchable field ──
Error in `utils::download.file(url = url, destfile = dest.file, mode = "wb", 
    method = "auto", cacheOK = FALSE, quiet = FALSE)`: download from 'http://www.hmdb.ca/system/downloads/current/hmdb_metabolites.zip' failed
Backtrace:
     ▆
  1. ├─base::do.call(fct, params)
  2. └─biodb (local) `<fn>`(conn = `<HmdbMtbC>`, opt = `<named list>`)
  3.   └─conn$getEntry(id, drop = TRUE)
  4.     └─private$bdb$getFactory()$getEntry(self$getId(), id = id, drop = drop)
  5.       └─private$loadEntries(conn$getId(), missing.ids, drop = FALSE)
  6.         └─conn$getEntryContent(ids)
  7.           └─self$download()
  8.             └─private$doDownload()
  9.               └─sched$downloadFile(url = zip.url, dest.file = tmpFile)
 10.                 └─utils::download.file(...)

[ FAIL 2 | WARN 4 | SKIP 0 | PASS 124 ]
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_1.12.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.20-bioc-longtests/meat/biodbHmdb.Rcheck'
* using R version 4.4.1 (2024-06-14 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 '1.12.0'
* 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:
       ▆
    1. ├─base::do.call(fct, params)
    2. └─biodb (local) `<fn>`(conn = `<HmdbMtbC>`, opt = `<named list>`)
    3.   └─conn$getEntry(id, drop = TRUE)
    4.     └─private$bdb$getFactory()$getEntry(self$getId(), id = id, drop = drop)
    5.       └─private$loadEntries(conn$getId(), missing.ids, drop = FALSE)
    6.         └─conn$getEntryContent(ids)
    7.           └─self$download()
    8.             └─private$doDownload()
    9.               └─sched$downloadFile(url = zip.url, dest.file = tmpFile)
   10.                 └─utils::download.file(...)
  
  [ FAIL 2 | WARN 4 | SKIP 0 | PASS 124 ]
  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)