Back to Long Tests report for BioC 3.21

This page was generated on 2025-04-05 23:55 -0400 (Sat, 05 Apr 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.1 LTS)x86_64R Under development (unstable) (2025-03-13 r87965) -- "Unsuffered Consequences" 4807
palomino7Windows Server 2022 Datacenterx64R Under development (unstable) (2025-03-01 r87860 ucrt) -- "Unsuffered Consequences" 4576
lconwaymacOS 12.7.1 Montereyx86_64R Under development (unstable) (2025-03-02 r87868) -- "Unsuffered Consequences" 4605
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 7/30HostnameOS / ArchCHECK
biodbHmdb 1.13.0  (landing page)
Pierrick Roger
Snapshot Date: 2025-04-05 09:55 -0400 (Sat, 05 Apr 2025)
git_url: https://git.bioconductor.org/packages/biodbHmdb
git_branch: devel
git_last_commit: d2b9830
git_last_commit_date: 2024-10-29 11:06:39 -0400 (Tue, 29 Oct 2024)
nebbiolo1Linux (Ubuntu 24.04.1 LTS) / x86_64  WARNINGS  
palomino7Windows Server 2022 Datacenter / x64  WARNINGS  
lconwaymacOS 12.7.1 Monterey / x86_64  WARNINGS  

CHECK results for biodbHmdb on palomino7

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: 1.13.0
Command: E:\biocbuild\bbs-3.21-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_1.13.0.tar.gz
StartedAt: 2025-04-05 16:02:50 -0400 (Sat, 05 Apr 2025)
EndedAt: 2025-04-05 16:05:18 -0400 (Sat, 05 Apr 2025)
EllapsedTime: 147.7 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: biodbHmdb.Rcheck
Warnings: 2

Tests output

biodbHmdb.Rcheck/tests/testthat.Rout


R Under development (unstable) (2025-03-01 r87860 ucrt) -- "Unsuffered Consequences"
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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 [2025-04-05 16:04:20.902][biodb::testContext]
biodb.INFO [2025-04-05 16:04:20.905][biodb::testContext] ********************************************************************************
biodb.INFO [2025-04-05 16:04:20.907][biodb::testContext] Test context - Generic long tests
biodb.INFO [2025-04-05 16:04:20.908][biodb::testContext] ********************************************************************************
biodb.INFO [2025-04-05 16:04:20.909][biodb::testContext]
biodb.INFO [2025-04-05 16:04:20.915][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.15.0.
biodb.DEBUG[2025-04-05 16:04:20.918][self$loadDefinitions] Load definitions from file "E:/biocbuild/bbs-3.21-bioc/R/library/biodb/definitions.yml".
biodb.DEBUG[2025-04-05 16:04:20.925][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-04-05 16:04:20.927][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-04-05 16:04:20.928][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-04-05 16:04:20.929][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-05 16:04:20.930][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-05 16:04:20.931][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-05 16:04:20.932][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-04-05 16:04:20.948][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-04-05 16:04:20.949][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-05 16:04:20.950][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-05 16:04:20.951][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-05 16:04:20.953][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-04-05 16:04:20.954][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-04-05 16:04:20.955][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-05 16:04:20.956][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-05 16:04:20.957][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-05 16:04:20.958][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-04-05 16:04:20.959][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-04-05 16:04:20.960][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-04-05 16:04:20.961][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-05 16:04:20.962][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-05 16:04:20.963][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-05 16:04:20.965][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-04-05 16:04:20.966][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-04-05 16:04:20.967][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-04-05 16:04:20.968][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-05 16:04:20.969][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-05 16:04:20.970][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-05 16:04:20.971][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-04-05 16:04:20.972][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-04-05 16:04:20.973][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-05 16:04:20.974][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-05 16:04:20.975][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-05 16:04:20.977][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-04-05 16:04:20.978][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-04-05 16:04:20.979][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-04-05 16:04:20.980][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-05 16:04:20.981][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-05 16:04:20.982][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-05 16:04:20.983][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-04-05 16:04:20.984][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-04-05 16:04:20.985][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-05 16:04:20.986][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-05 16:04:20.987][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-05 16:04:20.988][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-04-05 16:04:20.990][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-04-05 16:04:20.991][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-04-05 16:04:20.992][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-05 16:04:20.993][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-05 16:04:20.994][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-05 16:04:20.995][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-04-05 16:04:20.996][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-04-05 16:04:20.997][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-04-05 16:04:20.998][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-04-05 16:04:21.000][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-04-05 16:04:21.001][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-04-05 16:04:21.002][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-05 16:04:21.003][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-05 16:04:21.004][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-05 16:04:21.005][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-04-05 16:04:21.006][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-04-05 16:04:21.007][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-05 16:04:21.008][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-05 16:04:21.009][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-05 16:04:21.010][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-04-05 16:04:21.012][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-04-05 16:04:21.013][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-05 16:04:21.014][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-05 16:04:21.015][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-05 16:04:21.016][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-04-05 16:04:21.017][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-04-05 16:04:21.018][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-05 16:04:21.019][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-05 16:04:21.020][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-05 16:04:21.021][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-04-05 16:04:21.022][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2025-04-05 16:04:21.023][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-05 16:04:21.024][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-05 16:04:21.025][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-05 16:04:21.027][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-04-05 16:04:21.028][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-04-05 16:04:21.029][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-05 16:04:21.030][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-05 16:04:21.031][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-05 16:04:21.032][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-04-05 16:04:21.033][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-04-05 16:04:21.036][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-04-05 16:04:21.037][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-05 16:04:21.038][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-05 16:04:21.039][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-05 16:04:21.041][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-04-05 16:04:21.042][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-04-05 16:04:21.043][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-04-05 16:04:21.044][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-05 16:04:21.045][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-05 16:04:21.046][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-05 16:04:21.049][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-04-05 16:04:21.076][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-04-05 16:04:21.097][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2025-04-05 16:04:21.098][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-04-05 16:04:21.099][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-04-05 16:04:21.100][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-04-05 16:04:21.101][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-04-05 16:04:21.103][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-04-05 16:04:21.104][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-04-05 16:04:21.105][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-04-05 16:04:21.106][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-04-05 16:04:21.107][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-04-05 16:04:21.108][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-04-05 16:04:21.110][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-04-05 16:04:21.111][self$setPropertyValue]
biodb.DEBUG[2025-04-05 16:04:21.112][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-04-05 16:04:21.113][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-04-05 16:04:21.113][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-04-05 16:04:21.113][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-04-05 16:04:21.113][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-04-05 16:04:21.113][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-04-05 16:04:21.114][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-04-05 16:04:21.116][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-05 16:04:21.117][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-05 16:04:21.118][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-04-05 16:04:21.119][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-05 16:04:21.120][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-05 16:04:21.121][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-04-05 16:04:21.122][self$setPropertyValue]
biodb.DEBUG[2025-04-05 16:04:21.123][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-04-05 16:04:21.124][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-04-05 16:04:21.125][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-04-05 16:04:21.127][self$setPropertyValue]
biodb.DEBUG[2025-04-05 16:04:21.128][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-04-05 16:04:21.130][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-04-05 16:04:21.131][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-04-05 16:04:21.132][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-04-05 16:04:21.133][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-04-05 16:04:21.135][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-04-05 16:04:21.136][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-04-05 16:04:21.137][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-04-05 16:04:21.138][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-04-05 16:04:21.139][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-04-05 16:04:21.140][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-04-05 16:04:21.142][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-04-05 16:04:21.143][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-04-05 16:04:21.144][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-04-05 16:04:21.145][self$setPropertyValue]
biodb.DEBUG[2025-04-05 16:04:21.146][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-04-05 16:04:21.147][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-04-05 16:04:21.147][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-04-05 16:04:21.147][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-04-05 16:04:21.147][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-04-05 16:04:21.147][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-04-05 16:04:21.149][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-04-05 16:04:21.150][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-05 16:04:21.151][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-05 16:04:21.152][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-04-05 16:04:21.153][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-05 16:04:21.154][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-05 16:04:21.155][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-04-05 16:04:21.156][self$setPropertyValue]
biodb.DEBUG[2025-04-05 16:04:21.157][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-04-05 16:04:21.158][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-04-05 16:04:21.160][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-04-05 16:04:21.161][self$setPropertyValue]
biodb.DEBUG[2025-04-05 16:04:21.162][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-04-05 16:04:21.164][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-04-05 16:04:21.165][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2025-04-05 16:04:21.166][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-04-05 16:04:21.167][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-04-05 16:04:21.169][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-04-05 16:04:21.170][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-04-05 16:04:21.171][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-04-05 16:04:21.172][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-04-05 16:04:21.173][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-04-05 16:04:21.174][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-04-05 16:04:21.176][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-04-05 16:04:21.177][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-04-05 16:04:21.178][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-04-05 16:04:21.179][self$setPropertyValue]
biodb.DEBUG[2025-04-05 16:04:21.180][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-04-05 16:04:21.181][self$setPropertyValue]
biodb.DEBUG[2025-04-05 16:04:21.182][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-04-05 16:04:21.184][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-05 16:04:21.185][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-05 16:04:21.186][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-04-05 16:04:21.187][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-05 16:04:21.188][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-05 16:04:21.189][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-04-05 16:04:21.190][self$setPropertyValue]
biodb.DEBUG[2025-04-05 16:04:21.191][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-04-05 16:04:21.192][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-04-05 16:04:21.194][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-04-05 16:04:21.195][self$setPropertyValue]
biodb.DEBUG[2025-04-05 16:04:21.196][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-04-05 16:04:21.198][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-04-05 16:04:21.199][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-04-05 16:04:21.200][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-04-05 16:04:21.201][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-04-05 16:04:21.203][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-04-05 16:04:21.204][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-04-05 16:04:21.205][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-04-05 16:04:21.206][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-04-05 16:04:21.207][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-04-05 16:04:21.208][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-04-05 16:04:21.210][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-04-05 16:04:21.211][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-04-05 16:04:21.212][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-04-05 16:04:21.213][self$setPropertyValue]
biodb.DEBUG[2025-04-05 16:04:21.214][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-04-05 16:04:21.215][self$setPropertyValue]
biodb.DEBUG[2025-04-05 16:04:21.216][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-04-05 16:04:21.218][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-05 16:04:21.219][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-05 16:04:21.220][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-04-05 16:04:21.221][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-05 16:04:21.222][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-05 16:04:21.223][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-04-05 16:04:21.224][self$setPropertyValue]
biodb.DEBUG[2025-04-05 16:04:21.225][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-04-05 16:04:21.227][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-04-05 16:04:21.228][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-04-05 16:04:21.229][self$setPropertyValue]
biodb.DEBUG[2025-04-05 16:04:21.232][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-04-05 16:04:21.233][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-04-05 16:04:21.234][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-05 16:04:21.235][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-05 16:04:21.236][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-05 16:04:21.237][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-05 16:04:21.238][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-05 16:04:21.240][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-05 16:04:21.241][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-05 16:04:21.242][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-05 16:04:21.243][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-05 16:04:21.244][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-05 16:04:21.245][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-05 16:04:21.246][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-05 16:04:21.247][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-05 16:04:21.248][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-05 16:04:21.249][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-05 16:04:21.250][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-05 16:04:21.251][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-05 16:04:21.252][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-05 16:04:21.253][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-05 16:04:21.254][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-05 16:04:21.255][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-05 16:04:21.257][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-05 16:04:21.258][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-05 16:04:21.259][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-05 16:04:21.260][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-05 16:04:21.261][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-05 16:04:21.262][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-05 16:04:21.263][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-05 16:04:21.264][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-05 16:04:21.265][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-05 16:04:21.266][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-05 16:04:21.267][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-05 16:04:21.268][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-05 16:04:21.269][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-05 16:04:21.270][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-05 16:04:21.271][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-05 16:04:21.272][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-05 16:04:21.273][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-05 16:04:21.274][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-05 16:04:21.275][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-05 16:04:21.277][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-05 16:04:21.278][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-05 16:04:21.279][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-05 16:04:21.280][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-05 16:04:21.281][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-05 16:04:21.282][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-05 16:04:21.283][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-05 16:04:21.284][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-05 16:04:21.285][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-05 16:04:21.286][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-05 16:04:21.287][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-05 16:04:21.288][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-05 16:04:21.289][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-05 16:04:21.290][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-05 16:04:21.291][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-05 16:04:21.292][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-05 16:04:21.293][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-05 16:04:21.294][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-05 16:04:21.296][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-05 16:04:21.297][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-05 16:04:21.298][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-05 16:04:21.299][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-05 16:04:21.300][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-05 16:04:21.301][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-05 16:04:21.302][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-05 16:04:21.303][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-05 16:04:21.304][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-05 16:04:21.305][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-05 16:04:21.311][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-05 16:04:21.312][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-05 16:04:21.313][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-05 16:04:21.314][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-05 16:04:21.315][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-05 16:04:21.316][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-05 16:04:21.317][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-05 16:04:21.318][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-05 16:04:21.319][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-05 16:04:21.320][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-05 16:04:21.321][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-05 16:04:21.323][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-05 16:04:21.324][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-05 16:04:21.325][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-05 16:04:21.326][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-05 16:04:21.327][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-05 16:04:21.328][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-05 16:04:21.329][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-05 16:04:21.330][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-04-05 16:04:21.334][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-04-05 16:04:21.336][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-04-05 16:04:21.337][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-04-05 16:04:21.339][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-04-05 16:04:21.340][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-04-05 16:04:21.342][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-04-05 16:04:21.343][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-04-05 16:04:21.345][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-04-05 16:04:21.346][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-04-05 16:04:21.348][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-04-05 16:04:21.349][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-04-05 16:04:21.351][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-04-05 16:04:21.352][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-04-05 16:04:21.354][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-04-05 16:04:21.356][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-04-05 16:04:21.357][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-04-05 16:04:21.359][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-04-05 16:04:21.360][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-04-05 16:04:21.362][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-04-05 16:04:21.363][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-04-05 16:04:21.365][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-04-05 16:04:21.366][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-04-05 16:04:21.368][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-04-05 16:04:21.369][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-04-05 16:04:21.371][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-04-05 16:04:21.372][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-04-05 16:04:21.374][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-04-05 16:04:21.376][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-04-05 16:04:21.377][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-04-05 16:04:21.379][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-04-05 16:04:21.380][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-04-05 16:04:21.382][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-04-05 16:04:21.383][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-04-05 16:04:21.385][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-04-05 16:04:21.386][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-04-05 16:04:21.388][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-04-05 16:04:21.389][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-04-05 16:04:21.391][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-04-05 16:04:21.392][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-04-05 16:04:21.394][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-04-05 16:04:21.395][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-04-05 16:04:21.397][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-04-05 16:04:21.398][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-04-05 16:04:21.400][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-04-05 16:04:21.401][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-04-05 16:04:21.403][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-04-05 16:04:21.405][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-04-05 16:04:21.406][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-04-05 16:04:21.408][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-04-05 16:04:21.409][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-04-05 16:04:21.411][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-04-05 16:04:21.412][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-04-05 16:04:21.414][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-04-05 16:04:21.415][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-04-05 16:04:21.417][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-04-05 16:04:21.418][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-04-05 16:04:21.420][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-04-05 16:04:21.421][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-04-05 16:04:21.423][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-04-05 16:04:21.424][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-04-05 16:04:21.426][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-04-05 16:04:21.427][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-04-05 16:04:21.429][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-04-05 16:04:21.431][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-04-05 16:04:21.432][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-04-05 16:04:21.434][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-04-05 16:04:21.435][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-04-05 16:04:21.437][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-04-05 16:04:21.438][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-04-05 16:04:21.440][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-04-05 16:04:21.441][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-04-05 16:04:21.443][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-04-05 16:04:21.444][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-04-05 16:04:21.446][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-04-05 16:04:21.447][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-04-05 16:04:21.449][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-04-05 16:04:21.450][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-04-05 16:04:21.452][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-04-05 16:04:21.454][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-04-05 16:04:21.455][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-04-05 16:04:21.457][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-04-05 16:04:21.458][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-04-05 16:04:21.481][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-04-05 16:04:21.483][initialize] This is biodb version 1.15.0.
biodb.DEBUG[2025-04-05 16:04:21.487][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-04-05 16:04:21.488][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-04-05 16:04:21.489][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-05 16:04:21.490][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-04-05 16:04:21.491][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-05 16:04:21.495][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-05 16:04:21.496][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-05 16:04:21.497][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-05 16:04:21.498][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-05 16:04:21.500][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-05 16:04:21.501][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-05 16:04:21.502][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-05 16:04:21.503][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-05 16:04:21.504][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-05 16:04:21.505][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-05 16:04:21.506][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-05 16:04:21.507][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-05 16:04:21.508][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-05 16:04:21.509][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-05 16:04:21.510][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-05 16:04:21.511][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-05 16:04:21.512][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-05 16:04:21.513][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-05 16:04:21.514][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-05 16:04:21.516][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-05 16:04:21.517][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-05 16:04:21.518][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-05 16:04:21.519][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-05 16:04:21.520][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-05 16:04:21.521][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-05 16:04:21.522][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-05 16:04:21.523][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-05 16:04:21.551][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-05 16:04:21.552][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-05 16:04:21.553][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-05 16:04:21.554][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-05 16:04:21.555][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-05 16:04:21.556][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-05 16:04:21.557][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-05 16:04:21.559][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-05 16:04:21.560][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-05 16:04:21.561][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-05 16:04:21.562][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-05 16:04:21.563][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-05 16:04:21.564][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-05 16:04:21.565][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-05 16:04:21.566][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-05 16:04:21.567][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-05 16:04:21.568][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-05 16:04:21.569][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-05 16:04:21.570][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-05 16:04:21.571][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-05 16:04:21.572][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-05 16:04:21.573][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-05 16:04:21.574][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-05 16:04:21.575][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-05 16:04:21.576][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-05 16:04:21.578][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-05 16:04:21.579][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-05 16:04:21.581][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-05 16:04:21.582][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-05 16:04:21.583][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-05 16:04:21.584][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-05 16:04:21.585][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-05 16:04:21.586][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-05 16:04:21.587][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-05 16:04:21.588][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-05 16:04:21.589][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-05 16:04:21.590][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-05 16:04:21.591][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-05 16:04:21.592][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-05 16:04:21.593][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-05 16:04:21.594][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-05 16:04:21.595][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-05 16:04:21.597][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-05 16:04:21.598][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-05 16:04:21.599][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-05 16:04:21.600][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-05 16:04:21.601][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-05 16:04:21.602][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-05 16:04:21.603][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-05 16:04:21.604][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-05 16:04:21.605][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-05 16:04:21.606][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-05 16:04:21.607][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-05 16:04:21.608][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-05 16:04:21.609][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-05 16:04:21.610][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-05 16:04:21.611][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-05 16:04:21.612][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-05 16:04:21.613][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-05 16:04:21.615][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-05 16:04:21.616][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-05 16:04:21.617][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-05 16:04:21.618][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-05 16:04:21.619][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-05 16:04:21.620][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-05 16:04:21.621][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-05 16:04:21.622][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-05 16:04:21.623][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-05 16:04:21.624][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-05 16:04:21.625][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-05 16:04:21.626][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-05 16:04:21.627][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-05 16:04:21.628][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-05 16:04:21.629][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-05 16:04:21.630][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-05 16:04:21.631][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-05 16:04:21.632][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-05 16:04:21.633][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[2025-04-05 16:04:21.634][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-05 16:04:21.635][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-05 16:04:21.636][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-05 16:04:21.637][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-05 16:04:21.638][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-05 16:04:21.640][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-05 16:04:21.641][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-05 16:04:21.642][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-05 16:04:21.643][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-05 16:04:21.644][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-05 16:04:21.645][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-05 16:04:21.646][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-05 16:04:21.647][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-05 16:04:21.648][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[2025-04-05 16:04:21.649][biodb$getConfig()$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2025-04-05 16:04:21.650][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-05 16:04:21.651][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-05 16:04:21.652][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-05 16:04:21.653][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-05 16:04:21.654][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-05 16:04:21.655][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-05 16:04:21.656][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-05 16:04:21.659][biodb$loadDefinitions] Load definitions from file "E:/biocbuild/bbs-3.21-bioc-longtests/meat/biodbHmdb.Rcheck/biodbHmdb/definitions.yml".
biodb.DEBUG[2025-04-05 16:04:21.668][self$getDbsInfo()$define] Define connector hmdb.metabolites.
biodb.DEBUG[2025-04-05 16:04:21.670][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-04-05 16:04:21.671][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2025-04-05 16:04:21.675][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-04-05 16:04:21.676][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-04-05 16:04:21.677][self$setPropertyValue] Setting property "downloadable" to "TRUE".
biodb.DEBUG[2025-04-05 16:04:21.678][self$setPropertyValue] Setting property "dwnld.ext" to "zip".
biodb.DEBUG[2025-04-05 16:04:21.680][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-04-05 16:04:21.681][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-04-05 16:04:21.682][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-04-05 16:04:21.683][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-04-05 16:04:21.684][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-04-05 16:04:21.686][self$setPropertyValue] Setting property "name" to "HMDB Metabolites".
biodb.DEBUG[2025-04-05 16:04:21.687][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-04-05 16:04:21.688][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/accession".
biodb.DEBUG[2025-04-05 16:04:21.688][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/secondary_accessions/accession".
biodb.DEBUG[2025-04-05 16:04:21.688][self$setPropertyValue] Setting property "parsing.expr" to "//average_molecular_weight".
biodb.DEBUG[2025-04-05 16:04:21.688][self$setPropertyValue] Setting property "parsing.expr" to "//cas_registry_number".
biodb.DEBUG[2025-04-05 16:04:21.688][self$setPropertyValue] Setting property "parsing.expr" to "//chebi_id".
biodb.DEBUG[2025-04-05 16:04:21.688][self$setPropertyValue] Setting property "parsing.expr" to "//chemspider_id".
biodb.DEBUG[2025-04-05 16:04:21.688][self$setPropertyValue] Setting property "parsing.expr" to "//kegg_id".
biodb.DEBUG[2025-04-05 16:04:21.688][self$setPropertyValue] Setting property "parsing.expr" to "//pubchem_compound_id".
biodb.DEBUG[2025-04-05 16:04:21.688][self$setPropertyValue] Setting property "parsing.expr" to "//iupac_name".
biodb.DEBUG[2025-04-05 16:04:21.688][self$setPropertyValue] Setting property "parsing.expr" to "//traditional_iupac".
biodb.DEBUG[2025-04-05 16:04:21.688][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/chemical_formula".
biodb.DEBUG[2025-04-05 16:04:21.688][self$setPropertyValue] Setting property "parsing.expr" to "//inchi".
biodb.DEBUG[2025-04-05 16:04:21.688][self$setPropertyValue] Setting property "parsing.expr" to "//inchikey".
biodb.DEBUG[2025-04-05 16:04:21.688][self$setPropertyValue] Setting property "parsing.expr" to "//monisotopic_molecular_weight".
biodb.DEBUG[2025-04-05 16:04:21.688][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/name".
biodb.DEBUG[2025-04-05 16:04:21.688][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/description".
biodb.DEBUG[2025-04-05 16:04:21.688][self$setPropertyValue] Setting property "parsing.expr" to "//smiles".
biodb.DEBUG[2025-04-05 16:04:21.688][self$setPropertyValue] Setting property "parsing.expr" to "//super_class".
biodb.DEBUG[2025-04-05 16:04:21.689][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-04-05 16:04:21.691][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-04-05 16:04:21.691][self$setPropertyValue] Setting property "searchable.fields" to "description".
biodb.DEBUG[2025-04-05 16:04:21.691][self$setPropertyValue] Setting property "searchable.fields" to "secondary.accessions".
biodb.DEBUG[2025-04-05 16:04:21.692][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-04-05 16:04:21.693][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-05 16:04:21.694][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-05 16:04:21.695][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-04-05 16:04:21.696][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-05 16:04:21.697][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-05 16:04:21.698][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-04-05 16:04:21.699][self$setPropertyValue] Setting property "urls" to "http://www.hmdb.ca/".
biodb.DEBUG[2025-04-05 16:04:21.699][self$setPropertyValue] Setting property "urls" to "http://www.hmdb.ca/system/downloads/current/hmdb_metabolites.zip".
biodb.DEBUG[2025-04-05 16:04:21.701][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-04-05 16:04:21.702][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-04-05 16:04:21.703][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-04-05 16:04:21.704][self$setPropertyValue]
biodb.DEBUG[2025-04-05 16:04:21.709][self$getEntryFields()$define] Define field secondary_accessions.
biodb.DEBUG[2025-04-05 16:04:21.711][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-04-05 16:04:21.713][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-04-05 16:04:21.714][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-04-05 16:04:21.716][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-04-05 16:04:21.736][initialize] Initialize connector hmdb.metabolites.
biodb.DEBUG[2025-04-05 16:04:21.738][initialize] Register connector hmdb.metabolites with the request scheduler
biodb.DEBUG[2025-04-05 16:04:21.741][private$bdb$getRequestScheduler()$re ...] Register connector hmdb.metabolites.
biodb.DEBUG[2025-04-05 16:04:21.745][private$addConnectorRules] Create new rule for URL "www.hmdb.ca" of connector "hmdb.metabolites".
biodb.DEBUG[2025-04-05 16:04:21.749][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-04-05 16:04:21.750][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-04-05 16:04:21.751][rule$addConnector] Connector "hmdb.metabolites" is already listed in rule "www.hmdb.ca".
biodb.DEBUG[2025-04-05 16:04:21.752][biodb$getFactory()$createConn] Creating new connector hmdb.metabolites for database class hmdb.metabolites .
biodb.INFO [2025-04-05 16:04:21.769][biodb::testThat]
biodb.INFO [2025-04-05 16:04:21.771][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2025-04-05 16:04:21.772][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-04-05 16:04:21.773][biodb::testThat]
biodb.TRACE[2025-04-05 16:04:21.779][loadFileContents] Loaded 1 files from cache: [1]: "E:/biocbuild/bbs-3.21-bioc-longtests/meat/biodbHmdb.Rcheck/biodbHmdb/testref/entry-hmdb.metabolites-HMDB0000001-content.xml".
biodb.DEBUG[2025-04-05 16:04:21.781][biodb$getFactory()$createEntryFromCo ...] Creating HMDB Metabolites entries from 1 content(s).
biodb.DEBUG[2025-04-05 16:04:21.784][biodb$getFactory()$createEntryFromCo ...] Parsing 1 HMDB Metabolites entries.
biodb.DEBUG[2025-04-05 16:04:21.791][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-05 16:04:21.792][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-05 16:04:21.793][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-05 16:04:21.809][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-05 16:04:21.810][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-05 16:04:21.811][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-05 16:04:21.812][FUN] Functions in observer BiodbConfig: [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[2025-04-05 16:04:21.822][ef$get] Asked field names are: accession.
biodb.TRACE[2025-04-05 16:04:21.824][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-05 16:04:21.825][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:21.826][ef$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:21.828][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-05 16:04:21.838][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-05 16:04:21.840][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:21.841][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:21.842][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-04-05 16:04:21.843][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-04-05 16:04:21.845][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:21.846][ef$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:21.867][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-04-05 16:04:21.869][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-04-05 16:04:21.870][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:21.871][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:21.872][ef$get] Asked field names are: average.mass.
biodb.TRACE[2025-04-05 16:04:21.873][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-04-05 16:04:21.875][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:21.876][ef$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:21.877][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-04-05 16:04:21.878][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-04-05 16:04:21.880][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:21.881][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:21.882][ef$get] Asked field names are: cas.id.
biodb.TRACE[2025-04-05 16:04:21.883][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-04-05 16:04:21.884][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:21.885][ef$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:21.887][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-04-05 16:04:21.888][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-04-05 16:04:21.889][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:21.890][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:21.892][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-05 16:04:21.893][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-05 16:04:21.894][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:21.895][ef$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:21.897][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-05 16:04:21.898][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-05 16:04:21.899][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:21.900][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:21.901][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-04-05 16:04:21.902][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-04-05 16:04:21.904][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:21.905][ef$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:21.906][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-04-05 16:04:21.907][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-04-05 16:04:21.909][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:21.910][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:21.911][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-04-05 16:04:21.912][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-04-05 16:04:21.913][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:21.914][ef$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:21.916][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-04-05 16:04:21.917][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-04-05 16:04:21.918][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:21.919][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:21.920][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-04-05 16:04:21.922][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-04-05 16:04:21.923][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:21.924][ef$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:21.925][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-04-05 16:04:21.927][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-04-05 16:04:21.928][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:21.929][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:21.930][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-04-05 16:04:21.931][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-04-05 16:04:21.933][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:21.934][ef$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:21.935][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-04-05 16:04:21.936][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-04-05 16:04:21.938][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:21.939][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:21.940][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-04-05 16:04:21.941][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-04-05 16:04:21.950][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:21.951][ef$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:21.952][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-04-05 16:04:21.954][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-04-05 16:04:21.955][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:21.956][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:21.957][ef$get] Asked field names are: formula.
biodb.TRACE[2025-04-05 16:04:21.958][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-05 16:04:21.960][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:21.961][ef$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:21.962][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-04-05 16:04:21.963][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-05 16:04:21.964][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:21.966][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:21.967][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-04-05 16:04:21.968][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-05 16:04:21.969][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:21.970][ef$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:21.972][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-04-05 16:04:21.973][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-05 16:04:21.974][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:21.975][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:21.977][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-05 16:04:21.978][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-05 16:04:21.979][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:21.980][ef$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:21.982][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-05 16:04:21.983][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-05 16:04:21.984][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:21.985][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:21.986][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-05 16:04:21.987][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-05 16:04:21.989][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:21.990][ef$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:21.991][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-05 16:04:21.992][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-05 16:04:21.994][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:21.995][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:21.996][ef$get] Asked field names are: name.
biodb.TRACE[2025-04-05 16:04:21.997][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-04-05 16:04:21.998][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:21.999][ef$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:22.001][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-05 16:04:22.002][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-05 16:04:22.003][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:22.004][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:22.006][ef$get] Asked field names are: description.
biodb.TRACE[2025-04-05 16:04:22.007][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-04-05 16:04:22.008][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:22.009][ef$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:22.010][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-04-05 16:04:22.011][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-04-05 16:04:22.013][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:22.014][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:22.015][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-04-05 16:04:22.016][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-05 16:04:22.017][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:22.018][ef$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:22.020][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-04-05 16:04:22.021][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-05 16:04:22.022][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:22.023][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:22.025][ef$get] Asked field names are: super.class.
biodb.TRACE[2025-04-05 16:04:22.026][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-04-05 16:04:22.027][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:22.028][ef$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:22.030][self$getBiodb()$getEntryFields()$get] Asked field names are: super.class.
biodb.TRACE[2025-04-05 16:04:22.031][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-04-05 16:04:22.032][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:22.033][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:22.035][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-05 16:04:22.036][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-05 16:04:22.037][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:22.038][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:22.039][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-05 16:04:22.040][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-05 16:04:22.042][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:22.043][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:22.044][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-05 16:04:22.045][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-05 16:04:22.046][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:22.047][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:22.075][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-04-05 16:04:22.077][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-04-05 16:04:22.078][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:22.079][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:22.080][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-04-05 16:04:22.081][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-04-05 16:04:22.083][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:22.084][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:22.085][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-04-05 16:04:22.086][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-04-05 16:04:22.087][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:22.088][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:22.090][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-04-05 16:04:22.091][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-04-05 16:04:22.092][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:22.093][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:22.094][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-04-05 16:04:22.096][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-04-05 16:04:22.097][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:22.098][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:22.099][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-04-05 16:04:22.104][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-04-05 16:04:22.106][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:22.107][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:22.108][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-05 16:04:22.109][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-05 16:04:22.110][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:22.111][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:22.113][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-05 16:04:22.114][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-05 16:04:22.115][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:22.116][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:22.117][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-05 16:04:22.118][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-05 16:04:22.119][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:22.121][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:22.122][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-04-05 16:04:22.123][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-04-05 16:04:22.124][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:22.125][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:22.126][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-04-05 16:04:22.128][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-04-05 16:04:22.129][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:22.130][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:22.131][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-04-05 16:04:22.132][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-04-05 16:04:22.133][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:22.135][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:22.136][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-04-05 16:04:22.137][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-04-05 16:04:22.138][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:22.139][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:22.140][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-04-05 16:04:22.142][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-04-05 16:04:22.143][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:22.144][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:22.145][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-04-05 16:04:22.146][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-04-05 16:04:22.147][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:22.148][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:22.150][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-04-05 16:04:22.151][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-04-05 16:04:22.152][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:22.153][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:22.154][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-04-05 16:04:22.156][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-04-05 16:04:22.157][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:22.158][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:22.159][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-04-05 16:04:22.160][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-04-05 16:04:22.161][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:22.162][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:22.164][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-04-05 16:04:22.165][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-04-05 16:04:22.166][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:22.167][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:22.168][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-04-05 16:04:22.169][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-04-05 16:04:22.171][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:22.172][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:22.173][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-04-05 16:04:22.174][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-04-05 16:04:22.175][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:22.176][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:22.178][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-04-05 16:04:22.179][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-04-05 16:04:22.180][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:22.181][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:22.182][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-04-05 16:04:22.183][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-04-05 16:04:22.185][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:22.186][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:22.187][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-04-05 16:04:22.188][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-04-05 16:04:22.189][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:22.190][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:22.191][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-04-05 16:04:22.193][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-05 16:04:22.194][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:22.195][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:22.196][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-04-05 16:04:22.197][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-05 16:04:22.198][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:22.200][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:22.201][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-04-05 16:04:22.202][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-05 16:04:22.203][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:22.204][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:22.205][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-04-05 16:04:22.207][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-05 16:04:22.208][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:22.209][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:22.210][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-04-05 16:04:22.211][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-05 16:04:22.212][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:22.213][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:22.215][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-04-05 16:04:22.216][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-05 16:04:22.217][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:22.218][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:22.219][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-05 16:04:22.221][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-05 16:04:22.222][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:22.223][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:22.224][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-05 16:04:22.225][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-05 16:04:22.226][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:22.227][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:22.229][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-05 16:04:22.230][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-05 16:04:22.231][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:22.232][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:22.233][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-04-05 16:04:22.234][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-04-05 16:04:22.235][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:22.237][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:22.238][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-04-05 16:04:22.239][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-04-05 16:04:22.240][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:22.241][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:22.242][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-04-05 16:04:22.244][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-04-05 16:04:22.245][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:22.246][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:22.247][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-05 16:04:22.248][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-05 16:04:22.249][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:22.250][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:22.252][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-05 16:04:22.253][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-05 16:04:22.254][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:22.255][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:22.256][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-05 16:04:22.257][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-05 16:04:22.259][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:22.260][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:22.261][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-05 16:04:22.262][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-05 16:04:22.263][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:22.264][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:22.265][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-05 16:04:22.267][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-05 16:04:22.268][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:22.269][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:22.270][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-05 16:04:22.271][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-05 16:04:22.272][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:22.273][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:22.275][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-04-05 16:04:22.280][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-04-05 16:04:22.281][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:22.282][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:22.283][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-04-05 16:04:22.285][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-04-05 16:04:22.286][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:22.287][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:22.288][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-04-05 16:04:22.289][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-04-05 16:04:22.290][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:22.291][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:22.293][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-04-05 16:04:22.294][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-04-05 16:04:22.295][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:22.296][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:22.297][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-04-05 16:04:22.299][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-04-05 16:04:22.300][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:22.301][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:22.302][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-04-05 16:04:22.303][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-04-05 16:04:22.304][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:22.306][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:22.307][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-04-05 16:04:22.308][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-05 16:04:22.309][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:22.310][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:22.312][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-04-05 16:04:22.313][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-05 16:04:22.314][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:22.315][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:22.316][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-04-05 16:04:22.317][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-05 16:04:22.318][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:22.320][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:22.321][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2025-04-05 16:04:22.322][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-05 16:04:22.323][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:22.324][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:22.325][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-05 16:04:22.327][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-05 16:04:22.328][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:22.329][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:22.330][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-05 16:04:22.331][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-05 16:04:22.332][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:22.334][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:22.335][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-05 16:04:22.336][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-05 16:04:22.337][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:22.338][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:22.340][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2025-04-05 16:04:22.341][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-05 16:04:22.342][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:22.343][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:22.359][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-05 16:04:22.361][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-05 16:04:22.362][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:22.363][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:22.364][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-05 16:04:22.365][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-05 16:04:22.366][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:22.367][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:22.369][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-05 16:04:22.370][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-05 16:04:22.371][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:22.372][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:22.373][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-05 16:04:22.375][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-05 16:04:22.376][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:22.377][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:22.378][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-05 16:04:22.379][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-05 16:04:22.380][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:22.381][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:22.383][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-04-05 16:04:22.384][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-04-05 16:04:22.385][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:22.386][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:22.388][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-04-05 16:04:22.389][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-04-05 16:04:22.390][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:22.391][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:22.392][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-05 16:04:22.393][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-05 16:04:22.394][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:22.396][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:22.397][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-04-05 16:04:22.398][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-04-05 16:04:22.399][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:22.400][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:22.401][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-05 16:04:22.403][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-05 16:04:22.404][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:22.405][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:22.406][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-05 16:04:22.407][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-05 16:04:22.408][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:22.409][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:22.411][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-05 16:04:22.412][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-05 16:04:22.413][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:22.414][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:22.415][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-05 16:04:22.417][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-05 16:04:22.418][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:22.419][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:22.420][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-05 16:04:22.421][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-05 16:04:22.422][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:22.424][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:22.425][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-05 16:04:22.426][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-05 16:04:22.427][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:22.428][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-05 16:04:22.429][biodb$getFactory()$createEntryFromCo ...] Accession numbers: HMDB0000001.
biodb.TRACE[2025-04-05 16:04:22.433][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-04-05 16:04:22.434][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-04-05 16:04:22.435][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:22.436][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:22.437][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-04-05 16:04:22.439][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-04-05 16:04:22.440][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:22.441][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:22.446][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-04-05 16:04:22.448][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-04-05 16:04:22.449][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:22.450][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:22.451][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-04-05 16:04:22.452][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-04-05 16:04:22.453][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:22.455][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:22.476][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-05 16:04:22.477][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-05 16:04:22.478][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:22.479][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:22.493][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-04-05 16:04:22.495][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-04-05 16:04:22.496][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:22.497][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:22.504][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-05 16:04:22.505][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-05 16:04:22.506][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:22.508][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:22.509][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-05 16:04:22.510][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-05 16:04:22.511][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:22.512][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:22.513][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-05 16:04:22.515][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-05 16:04:22.516][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:22.517][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:22.520][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-05 16:04:22.521][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-05 16:04:22.522][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:22.523][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:22.525][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-05 16:04:22.526][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-05 16:04:22.527][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:22.528][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:22.529][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-05 16:04:22.530][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-05 16:04:22.532][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:22.533][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:22.534][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-04-05 16:04:22.535][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-04-05 16:04:22.536][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:22.538][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:22.539][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-04-05 16:04:22.540][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-04-05 16:04:22.541][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:22.542][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:22.543][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-04-05 16:04:22.545][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-04-05 16:04:22.546][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:22.547][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:22.557][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-05 16:04:22.559][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-05 16:04:22.560][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:22.561][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:22.562][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-05 16:04:22.563][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-05 16:04:22.565][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:22.566][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:22.567][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-05 16:04:22.568][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-05 16:04:22.569][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:22.570][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:22.572][ef$get] Asked field names are: accession.
biodb.TRACE[2025-04-05 16:04:22.573][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-05 16:04:22.574][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:22.575][ef$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:22.576][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-05 16:04:22.578][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-05 16:04:22.579][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:22.581][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:22.592][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-04-05 16:04:22.593][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-04-05 16:04:22.594][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:22.596][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:22.597][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-04-05 16:04:22.598][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-04-05 16:04:22.599][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:22.600][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:22.601][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-04-05 16:04:22.603][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-04-05 16:04:22.604][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:22.605][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:22.606][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-04-05 16:04:22.607][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-04-05 16:04:22.608][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:22.609][ef$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:22.611][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-04-05 16:04:22.612][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-04-05 16:04:22.613][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:22.614][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:22.625][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-04-05 16:04:22.626][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-04-05 16:04:22.627][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:22.634][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:22.635][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-04-05 16:04:22.636][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-04-05 16:04:22.638][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:22.639][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:22.640][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-04-05 16:04:22.641][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-04-05 16:04:22.642][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:22.643][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:22.645][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-04-05 16:04:22.646][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-04-05 16:04:22.647][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:22.648][ef$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:22.649][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-04-05 16:04:22.651][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-04-05 16:04:22.652][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:22.653][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:22.664][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-04-05 16:04:22.665][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-04-05 16:04:22.666][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:22.667][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:22.668][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-04-05 16:04:22.670][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-04-05 16:04:22.671][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:22.672][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:22.673][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-04-05 16:04:22.674][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-04-05 16:04:22.676][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:22.677][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:22.678][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-04-05 16:04:22.679][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-04-05 16:04:22.680][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:22.681][ef$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:22.682][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-04-05 16:04:22.684][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-04-05 16:04:22.685][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:22.686][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:22.697][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-05 16:04:22.698][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-05 16:04:22.699][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:22.700][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:22.701][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-05 16:04:22.702][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-05 16:04:22.704][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:22.705][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:22.706][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-05 16:04:22.707][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-05 16:04:22.708][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:22.709][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:22.711][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-05 16:04:22.712][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-05 16:04:22.713][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:22.714][ef$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:22.715][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-05 16:04:22.716][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-05 16:04:22.717][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:22.719][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:22.729][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-04-05 16:04:22.731][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-04-05 16:04:22.732][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:22.733][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:22.734][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-04-05 16:04:22.735][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-04-05 16:04:22.736][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:22.738][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:22.739][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-04-05 16:04:22.740][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-04-05 16:04:22.741][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:22.742][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:22.743][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-04-05 16:04:22.745][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-04-05 16:04:22.746][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:22.747][ef$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:22.748][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-04-05 16:04:22.749][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-04-05 16:04:22.750][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:22.752][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:22.762][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-05 16:04:22.764][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-05 16:04:22.765][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:22.766][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:22.767][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-05 16:04:22.768][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-05 16:04:22.769][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:22.770][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:22.772][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-05 16:04:22.773][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-05 16:04:22.774][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:22.775][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:22.776][ef$get] Asked field names are: name.
biodb.TRACE[2025-04-05 16:04:22.778][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-04-05 16:04:22.779][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:22.780][ef$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:22.781][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-05 16:04:22.782][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-05 16:04:22.783][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:22.784][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:22.795][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-04-05 16:04:22.796][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-04-05 16:04:22.797][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:22.799][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:22.800][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-04-05 16:04:22.801][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-04-05 16:04:22.802][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:22.803][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:22.804][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-04-05 16:04:22.806][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-04-05 16:04:22.807][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:22.812][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:22.814][ef$get] Asked field names are: description.
biodb.TRACE[2025-04-05 16:04:22.815][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-04-05 16:04:22.816][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:22.817][ef$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:22.818][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-04-05 16:04:22.819][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-04-05 16:04:22.820][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:22.822][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:22.832][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-04-05 16:04:22.833][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-05 16:04:22.834][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:22.836][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:22.837][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-04-05 16:04:22.838][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-05 16:04:22.839][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:22.840][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:22.842][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-04-05 16:04:22.843][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-05 16:04:22.844][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:22.845][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:22.846][ef$get] Asked field names are: formula.
biodb.TRACE[2025-04-05 16:04:22.847][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-05 16:04:22.849][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:22.850][ef$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:22.851][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-04-05 16:04:22.852][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-05 16:04:22.853][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:22.854][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:22.865][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-04-05 16:04:22.866][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-04-05 16:04:22.867][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:22.868][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:22.870][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-04-05 16:04:22.871][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-04-05 16:04:22.872][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:22.873][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:22.874][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-04-05 16:04:22.875][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-04-05 16:04:22.877][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:22.878][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:22.879][ef$get] Asked field names are: average.mass.
biodb.TRACE[2025-04-05 16:04:22.880][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-04-05 16:04:22.881][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:22.882][ef$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:22.884][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-04-05 16:04:22.885][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-04-05 16:04:22.886][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:22.887][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:22.898][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-05 16:04:22.899][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-05 16:04:22.900][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:22.901][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:22.903][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-05 16:04:22.904][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-05 16:04:22.905][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:22.906][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:22.908][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-05 16:04:22.909][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-05 16:04:22.910][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:22.911][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:22.912][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-05 16:04:22.914][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-05 16:04:22.915][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:22.916][ef$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:22.917][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-05 16:04:22.918][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-05 16:04:22.919][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:22.920][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:22.931][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-04-05 16:04:22.933][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-04-05 16:04:22.934][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:22.935][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:22.936][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-04-05 16:04:22.938][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-04-05 16:04:22.939][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:22.940][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:22.941][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-04-05 16:04:22.942][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-04-05 16:04:22.943][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:22.945][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:22.946][ef$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-04-05 16:04:22.947][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-04-05 16:04:22.948][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:22.949][ef$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:22.950][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-04-05 16:04:22.952][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-04-05 16:04:22.953][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:22.954][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:22.965][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-04-05 16:04:22.966][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-04-05 16:04:22.967][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:22.968][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:22.970][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-04-05 16:04:22.971][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-04-05 16:04:22.972][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:22.973][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:22.974][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-04-05 16:04:22.975][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-04-05 16:04:22.977][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:22.978][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:22.979][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-04-05 16:04:22.980][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-04-05 16:04:22.981][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:22.982][ef$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:22.984][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-04-05 16:04:22.985][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-04-05 16:04:22.986][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:22.992][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:23.003][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-04-05 16:04:23.004][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-04-05 16:04:23.005][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:23.006][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:23.008][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-04-05 16:04:23.009][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-04-05 16:04:23.010][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:23.011][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:23.012][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-04-05 16:04:23.013][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-04-05 16:04:23.015][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:23.016][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:23.017][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-04-05 16:04:23.018][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-04-05 16:04:23.019][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:23.021][ef$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:23.022][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-04-05 16:04:23.023][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-04-05 16:04:23.024][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:23.025][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:23.036][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-04-05 16:04:23.038][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-05 16:04:23.039][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:23.040][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:23.041][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-04-05 16:04:23.042][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-05 16:04:23.043][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:23.045][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:23.046][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-04-05 16:04:23.047][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-05 16:04:23.048][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:23.049][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:23.050][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-04-05 16:04:23.052][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-05 16:04:23.053][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:23.054][ef$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:23.055][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-04-05 16:04:23.056][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-05 16:04:23.057][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:23.059][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:23.069][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-04-05 16:04:23.071][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-05 16:04:23.072][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:23.073][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:23.074][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-04-05 16:04:23.076][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-05 16:04:23.077][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:23.078][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:23.079][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-04-05 16:04:23.080][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-05 16:04:23.081][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:23.082][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:23.084][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-04-05 16:04:23.085][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-05 16:04:23.086][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:23.087][ef$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:23.088][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-04-05 16:04:23.090][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-05 16:04:23.091][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:23.092][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:23.103][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-05 16:04:23.104][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-05 16:04:23.105][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:23.107][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:23.108][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-05 16:04:23.109][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-05 16:04:23.110][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:23.111][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:23.113][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-05 16:04:23.114][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-05 16:04:23.115][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:23.116][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:23.117][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-05 16:04:23.119][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-05 16:04:23.120][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:23.121][ef$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:23.122][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-05 16:04:23.123][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-05 16:04:23.124][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:23.125][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:23.136][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-04-05 16:04:23.138][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-04-05 16:04:23.139][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:23.140][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:23.141][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-04-05 16:04:23.143][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-04-05 16:04:23.144][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:23.145][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:23.146][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-04-05 16:04:23.147][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-04-05 16:04:23.148][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:23.150][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:23.151][ef$get] Asked field names are: cas.id.
biodb.TRACE[2025-04-05 16:04:23.152][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-04-05 16:04:23.153][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:23.154][ef$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:23.156][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-04-05 16:04:23.157][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-04-05 16:04:23.158][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:23.159][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:23.175][ef$get] Asked field names are: accession.
biodb.TRACE[2025-04-05 16:04:23.176][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-05 16:04:23.177][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:23.179][ef$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:23.185][ef$get] Asked field names are: average.mass.
biodb.TRACE[2025-04-05 16:04:23.187][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-04-05 16:04:23.188][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:23.189][ef$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:23.196][ef$get] Asked field names are: cas.id.
biodb.TRACE[2025-04-05 16:04:23.197][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-04-05 16:04:23.198][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:23.200][ef$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:23.207][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-05 16:04:23.208][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-05 16:04:23.209][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:23.210][ef$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:23.217][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-04-05 16:04:23.219][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-04-05 16:04:23.220][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:23.221][ef$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:23.227][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-04-05 16:04:23.229][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-04-05 16:04:23.230][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:23.231][ef$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:23.237][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-04-05 16:04:23.239][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-04-05 16:04:23.240][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:23.241][ef$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:23.248][ef$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-04-05 16:04:23.249][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-04-05 16:04:23.250][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:23.251][ef$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:23.258][ef$get] Asked field names are: description.
biodb.TRACE[2025-04-05 16:04:23.259][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-04-05 16:04:23.260][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:23.261][ef$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:23.268][ef$get] Asked field names are: formula.
biodb.TRACE[2025-04-05 16:04:23.269][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-05 16:04:23.270][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:23.271][ef$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:23.278][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-04-05 16:04:23.279][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-05 16:04:23.280][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:23.282][ef$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:23.288][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-05 16:04:23.289][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-05 16:04:23.290][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:23.292][ef$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:23.298][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-04-05 16:04:23.299][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-04-05 16:04:23.300][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:23.302][ef$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:23.308][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-05 16:04:23.309][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-05 16:04:23.310][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:23.312][ef$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:23.318][ef$get] Asked field names are: name.
biodb.TRACE[2025-04-05 16:04:23.319][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-04-05 16:04:23.320][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:23.322][ef$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:23.328][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-04-05 16:04:23.329][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-04-05 16:04:23.330][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:23.331][ef$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:23.338][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-04-05 16:04:23.339][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-04-05 16:04:23.340][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:23.341][ef$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:23.348][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-04-05 16:04:23.349][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-05 16:04:23.350][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:23.351][ef$get] fields variable is a list.
biodb.INFO [2025-04-05 16:04:23.363][biodb::testThat]
biodb.INFO [2025-04-05 16:04:23.364][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2025-04-05 16:04:23.365][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-04-05 16:04:23.367][biodb::testThat]
biodb.DEBUG[2025-04-05 16:04:23.385][private$loadEntries] Creating entries from ids [1]: "HMDB0000001".
biodb.DEBUG[2025-04-05 16:04:23.391][conn$getEntryContent] Get HMDB Metabolites entry content(s) for 1 id(s)...
biodb.DEBUG[2025-04-05 16:04:23.397][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-04-05 16:04:23.399][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.TRACE[2025-04-05 16:04:23.402][cch$loadFileContent] Trying to load 1 files from cache: [1]: "HMDB0000001".
biodb.TRACE[2025-04-05 16:04:23.403][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-04-05 16:04:23.419][loadFileContents] Loaded 1 files from cache: [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/HMDB0000001.xml".
biodb.DEBUG[2025-04-05 16:04:23.421][conn$getEntryContent] 1 HMDB Metabolites entry content(s) loaded from cache.
biodb.DEBUG[2025-04-05 16:04:23.441][self$createEntryFromContent] Creating HMDB Metabolites entries from 1 content(s).
biodb.DEBUG[2025-04-05 16:04:23.442][self$createEntryFromContent] Parsing 1 HMDB Metabolites entries.
biodb.DEBUG[2025-04-05 16:04:23.444][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-05 16:04:23.445][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-05 16:04:23.446][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-05 16:04:23.453][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-05 16:04:23.454][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-05 16:04:23.455][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-05 16:04:23.456][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-05 16:04:23.461][ef$get] Asked field names are: accession.
biodb.TRACE[2025-04-05 16:04:23.462][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-05 16:04:23.463][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:23.464][ef$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:23.466][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-05 16:04:23.467][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-05 16:04:23.468][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:23.469][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:23.470][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-04-05 16:04:23.472][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-04-05 16:04:23.473][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:23.474][ef$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:23.475][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-04-05 16:04:23.477][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-04-05 16:04:23.478][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:23.479][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:23.480][ef$get] Asked field names are: average.mass.
biodb.TRACE[2025-04-05 16:04:23.481][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-04-05 16:04:23.482][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:23.484][ef$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:23.485][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-04-05 16:04:23.486][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-04-05 16:04:23.488][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:23.489][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:23.490][ef$get] Asked field names are: cas.id.
biodb.TRACE[2025-04-05 16:04:23.491][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-04-05 16:04:23.492][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:23.493][ef$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:23.495][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-04-05 16:04:23.496][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-04-05 16:04:23.497][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:23.498][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:23.500][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-05 16:04:23.501][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-05 16:04:23.502][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:23.503][ef$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:23.505][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-05 16:04:23.506][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-05 16:04:23.507][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:23.508][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:23.509][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-04-05 16:04:23.511][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-04-05 16:04:23.512][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:23.513][ef$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:23.514][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-04-05 16:04:23.516][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-04-05 16:04:23.517][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:23.518][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:23.519][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-04-05 16:04:23.520][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-04-05 16:04:23.521][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:23.523][ef$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:23.524][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-04-05 16:04:23.525][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-04-05 16:04:23.526][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:23.528][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:23.529][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-04-05 16:04:23.530][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-04-05 16:04:23.531][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:23.532][ef$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:23.534][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-04-05 16:04:23.535][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-04-05 16:04:23.536][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:23.537][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:23.539][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-04-05 16:04:23.540][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-04-05 16:04:23.541][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:23.542][ef$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:23.544][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-04-05 16:04:23.545][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-04-05 16:04:23.546][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:23.547][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:23.548][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-04-05 16:04:23.555][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-04-05 16:04:23.556][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:23.557][ef$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:23.559][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-04-05 16:04:23.560][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-04-05 16:04:23.561][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:23.562][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:23.563][ef$get] Asked field names are: formula.
biodb.TRACE[2025-04-05 16:04:23.565][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-05 16:04:23.566][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:23.567][ef$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:23.568][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-04-05 16:04:23.569][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-05 16:04:23.571][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:23.572][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:23.573][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-04-05 16:04:23.574][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-05 16:04:23.575][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:23.576][ef$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:23.578][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-04-05 16:04:23.580][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-05 16:04:23.582][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:23.583][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:23.584][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-05 16:04:23.586][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-05 16:04:23.587][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:23.588][ef$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:23.589][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-05 16:04:23.591][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-05 16:04:23.592][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:23.593][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:23.594][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-05 16:04:23.595][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-05 16:04:23.597][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:23.598][ef$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:23.599][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-05 16:04:23.600][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-05 16:04:23.602][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:23.603][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:23.604][ef$get] Asked field names are: name.
biodb.TRACE[2025-04-05 16:04:23.605][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-04-05 16:04:23.606][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:23.608][ef$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:23.609][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-05 16:04:23.610][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-05 16:04:23.611][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:23.612][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:23.614][ef$get] Asked field names are: description.
biodb.TRACE[2025-04-05 16:04:23.615][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-04-05 16:04:23.616][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:23.617][ef$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:23.619][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-04-05 16:04:23.620][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-04-05 16:04:23.621][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:23.622][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:23.623][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-04-05 16:04:23.625][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-05 16:04:23.626][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:23.627][ef$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:23.629][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-04-05 16:04:23.630][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-05 16:04:23.631][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:23.632][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:23.633][ef$get] Asked field names are: super.class.
biodb.TRACE[2025-04-05 16:04:23.635][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-04-05 16:04:23.636][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:23.637][ef$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:23.638][self$getBiodb()$getEntryFields()$get] Asked field names are: super.class.
biodb.TRACE[2025-04-05 16:04:23.640][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-04-05 16:04:23.641][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:23.642][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:23.643][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-05 16:04:23.645][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-05 16:04:23.646][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:23.647][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:23.648][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-05 16:04:23.649][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-05 16:04:23.650][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:23.652][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:23.653][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-05 16:04:23.654][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-05 16:04:23.655][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:23.656][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:23.660][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-04-05 16:04:23.661][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-04-05 16:04:23.662][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:23.663][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:23.665][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-04-05 16:04:23.666][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-04-05 16:04:23.667][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:23.668][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:23.669][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-04-05 16:04:23.671][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-04-05 16:04:23.672][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:23.673][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:23.674][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-04-05 16:04:23.675][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-04-05 16:04:23.677][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:23.678][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:23.679][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-04-05 16:04:23.680][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-04-05 16:04:23.681][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:23.682][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:23.684][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-04-05 16:04:23.685][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-04-05 16:04:23.686][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:23.687][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:23.688][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-05 16:04:23.690][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-05 16:04:23.691][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:23.692][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:23.693][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-05 16:04:23.694][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-05 16:04:23.695][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:23.696][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:23.698][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-05 16:04:23.699][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-05 16:04:23.700][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:23.701][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:23.702][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-04-05 16:04:23.704][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-04-05 16:04:23.705][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:23.706][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:23.707][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-04-05 16:04:23.708][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-04-05 16:04:23.709][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:23.710][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:23.712][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-04-05 16:04:23.713][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-04-05 16:04:23.714][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:23.715][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:23.716][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-04-05 16:04:23.718][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-04-05 16:04:23.719][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:23.720][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:23.721][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-04-05 16:04:23.722][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-04-05 16:04:23.723][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:23.729][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:23.730][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-04-05 16:04:23.731][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-04-05 16:04:23.732][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:23.733][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:23.735][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-04-05 16:04:23.736][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-04-05 16:04:23.737][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:23.738][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:23.739][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-04-05 16:04:23.741][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-04-05 16:04:23.742][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:23.743][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:23.744][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-04-05 16:04:23.745][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-04-05 16:04:23.746][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:23.747][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:23.749][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-04-05 16:04:23.750][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-04-05 16:04:23.751][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:23.752][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:23.753][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-04-05 16:04:23.755][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-04-05 16:04:23.756][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:23.757][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:23.758][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-04-05 16:04:23.759][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-04-05 16:04:23.760][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:23.761][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:23.763][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-04-05 16:04:23.764][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-04-05 16:04:23.765][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:23.766][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:23.767][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-04-05 16:04:23.769][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-04-05 16:04:23.770][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:23.771][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:23.772][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-04-05 16:04:23.773][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-04-05 16:04:23.774][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:23.775][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:23.777][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-04-05 16:04:23.778][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-05 16:04:23.779][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:23.780][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:23.781][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-04-05 16:04:23.782][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-05 16:04:23.784][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:23.785][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:23.786][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-04-05 16:04:23.787][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-05 16:04:23.788][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:23.789][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:23.791][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-04-05 16:04:23.792][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-05 16:04:23.793][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:23.794][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:23.795][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-04-05 16:04:23.796][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-05 16:04:23.797][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:23.799][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:23.800][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-04-05 16:04:23.801][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-05 16:04:23.802][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:23.803][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:23.804][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-05 16:04:23.806][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-05 16:04:23.807][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:23.808][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:23.809][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-05 16:04:23.810][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-05 16:04:23.811][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:23.812][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:23.814][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-05 16:04:23.815][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-05 16:04:23.816][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:23.817][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:23.818][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-04-05 16:04:23.820][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-04-05 16:04:23.821][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:23.822][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:23.823][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-04-05 16:04:23.824][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-04-05 16:04:23.825][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:23.826][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:23.828][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-04-05 16:04:23.829][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-04-05 16:04:23.830][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:23.831][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:23.832][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-05 16:04:23.834][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-05 16:04:23.835][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:23.836][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:23.837][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-05 16:04:23.838][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-05 16:04:23.839][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:23.840][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:23.842][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-05 16:04:23.843][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-05 16:04:23.844][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:23.845][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:23.846][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-05 16:04:23.848][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-05 16:04:23.849][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:23.850][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:23.851][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-05 16:04:23.852][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-05 16:04:23.853][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:23.854][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:23.856][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-05 16:04:23.857][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-05 16:04:23.858][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:23.859][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:23.860][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-04-05 16:04:23.862][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-04-05 16:04:23.863][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:23.864][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:23.865][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-04-05 16:04:23.866][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-04-05 16:04:23.867][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:23.868][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:23.869][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-04-05 16:04:23.871][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-04-05 16:04:23.872][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:23.873][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:23.874][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-04-05 16:04:23.875][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-04-05 16:04:23.877][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:23.878][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:23.879][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-04-05 16:04:23.880][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-04-05 16:04:23.881][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:23.882][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:23.884][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-04-05 16:04:23.885][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-04-05 16:04:23.886][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:23.887][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:23.888][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-04-05 16:04:23.890][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-05 16:04:23.895][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:23.896][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:23.897][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-04-05 16:04:23.899][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-05 16:04:23.900][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:23.901][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:23.902][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-04-05 16:04:23.903][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-05 16:04:23.904][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:23.905][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:23.907][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2025-04-05 16:04:23.908][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-05 16:04:23.909][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:23.910][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:23.911][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-05 16:04:23.913][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-05 16:04:23.914][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:23.915][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:23.916][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-05 16:04:23.917][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-05 16:04:23.919][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:23.920][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:23.921][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-05 16:04:23.922][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-05 16:04:23.923][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:23.924][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:23.926][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2025-04-05 16:04:23.927][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-05 16:04:23.928][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:23.929][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:23.931][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-05 16:04:23.932][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-05 16:04:23.934][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:23.935][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:23.936][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-05 16:04:23.937][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-05 16:04:23.938][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:23.939][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:23.941][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-05 16:04:23.942][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-05 16:04:23.943][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:23.944][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:23.945][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-05 16:04:23.946][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-05 16:04:23.948][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:23.949][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:23.950][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-05 16:04:23.951][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-05 16:04:23.952][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:23.953][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:23.955][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-04-05 16:04:23.956][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-04-05 16:04:23.957][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:23.958][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:23.959][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-04-05 16:04:23.960][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-04-05 16:04:23.962][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:23.963][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:23.964][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-05 16:04:23.965][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-05 16:04:23.966][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:23.967][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:23.968][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-04-05 16:04:23.970][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-04-05 16:04:23.971][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:23.972][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:23.973][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-05 16:04:23.974][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-05 16:04:23.975][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:23.977][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:23.978][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-05 16:04:23.979][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-05 16:04:23.980][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:23.981][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:23.982][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-05 16:04:23.984][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-05 16:04:23.985][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:23.986][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:23.987][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-05 16:04:23.988][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-05 16:04:23.989][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:23.991][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:23.992][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-05 16:04:23.993][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-05 16:04:23.994][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:23.995][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:23.996][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-05 16:04:23.998][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-05 16:04:23.999][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:24.000][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-05 16:04:24.001][self$createEntryFromContent] Accession numbers: HMDB0000001.
biodb.TRACE[2025-04-05 16:04:24.002][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2025-04-05 16:04:24.004][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2025-04-05 16:04:24.005][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:24.006][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:24.007][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2025-04-05 16:04:24.008][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2025-04-05 16:04:24.009][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:24.011][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:24.012][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2025-04-05 16:04:24.013][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2025-04-05 16:04:24.014][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:24.015][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2025-04-05 16:04:24.027][biodb::testThat]
biodb.INFO [2025-04-05 16:04:24.029][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2025-04-05 16:04:24.030][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-04-05 16:04:24.031][biodb::testThat]
biodb.TRACE[2025-04-05 16:04:24.034][ef$get] Asked field names are: name.
biodb.TRACE[2025-04-05 16:04:24.035][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-04-05 16:04:24.036][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:24.038][ef$get] fields variable is a list.
biodb.DEBUG[2025-04-05 16:04:24.039][function(conn, opt)] Testing searchForEntries() with entry "HMDB0000001" and field "name".
biodb.TRACE[2025-04-05 16:04:24.072][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-05 16:04:24.074][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-05 16:04:24.075][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:24.076][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:24.077][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-05 16:04:24.079][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-05 16:04:24.080][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:24.081][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:24.082][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-05 16:04:24.083][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-05 16:04:24.085][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:24.086][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-05 16:04:24.090][function(conn, opt)] With value "1-Methylhistidine".
biodb.DEBUG[2025-04-05 16:04:24.091][private$doSearchForEntries] fields NAMES = name
biodb.DEBUG[2025-04-05 16:04:24.092][private$doSearchForEntries] fields VALUES = 1-Methylhistidine
biodb.DEBUG[2025-04-05 16:04:24.093][private$doSearchForEntries] fields VALUES = 1-Methylhistidine
biodb.DEBUG[2025-04-05 16:04:24.095][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-04-05 16:04:24.097][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-04-05 16:04:24.099][private$doGetEntryIds] .doGetEntryIds 10
biodb.DEBUG[2025-04-05 16:04:24.101][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-04-05 16:04:24.102][private$doGetEntryIds] .doGetEntryIds 11
biodb.DEBUG[2025-04-05 16:04:24.103][private$doListFiles] List files in C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^.*\.xml$.
biodb.DEBUG[2025-04-05 16:04:24.105][cch$listFiles] Extracting accession number from file names associated with hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^(.*)\.xml$
biodb.DEBUG[2025-04-05 16:04:24.106][cch$listFiles] files = HMDB0000001.xml, HMDB0000002.xml
biodb.DEBUG[2025-04-05 16:04:24.107][private$doGetEntryIds] COUNT IDS = 2
biodb.DEBUG[2025-04-05 16:04:24.109][private$doSearchForEntries] All IDs = [2]: "HMDB0000001, HMDB0000002"
biodb.DEBUG[2025-04-05 16:04:24.110][private$doSearchForEntries] Total number of IDs = 2
biodb.TRACE[2025-04-05 16:04:24.112][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-05 16:04:24.113][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-05 16:04:24.114][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:24.115][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:24.116][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-05 16:04:24.118][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-05 16:04:24.119][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:24.120][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:24.121][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-05 16:04:24.122][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-05 16:04:24.124][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:24.125][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:24.126][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-05 16:04:24.127][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-05 16:04:24.128][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:24.129][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-05 16:04:24.131][private$doSearchForEntries] MATCHED = TRUE
biodb.DEBUG[2025-04-05 16:04:24.132][private$doSearchForEntries] COUNT IDS = 1
biodb.DEBUG[2025-04-05 16:04:24.133][function(conn, opt)] With found IDs [1]: "HMDB0000001".
biodb.TRACE[2025-04-05 16:04:24.150][ef$get] Asked field names are: description.
biodb.TRACE[2025-04-05 16:04:24.151][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-04-05 16:04:24.153][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:24.154][ef$get] fields variable is a list.
biodb.DEBUG[2025-04-05 16:04:24.155][function(conn, opt)] Testing searchForEntries() with entry "HMDB0000001" and field "description".
biodb.TRACE[2025-04-05 16:04:24.173][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-04-05 16:04:24.174][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-04-05 16:04:24.175][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:24.176][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:24.178][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-04-05 16:04:24.179][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-04-05 16:04:24.180][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:24.181][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:24.182][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-04-05 16:04:24.184][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-04-05 16:04:24.185][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:24.186][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-05 16:04:24.189][function(conn, opt)] With value "1-Methylhistidine, also known as 1-MHis, belongs to the class of organic compounds known as histidine and derivatives. Histidine and derivatives are compounds containing cysteine or a derivative thereof resulting from a reaction of cysteine at the amino group or the carboxy group, or from the replacement of any hydrogen of glycine by a heteroatom. 1-Methylhistidine is derived mainly from the anserine of dietary flesh sources, especially poultry. The enzyme, carnosinase, splits anserine into beta-alanine and 1-MHis. High levels of 1-MHis tend to inhibit the enzyme carnosinase and increase anserine levels. Conversely, genetic variants with deficient carnosinase activity in plasma show increased 1-MHis excretions when they consume a high meat diet. Reduced serum carnosinase activity is also found in patients with Parkinson's disease and multiple sclerosis and patients following a cerebrovascular accident. Vitamin E deficiency can lead to 1-methylhistidinuria from increased oxidative effects in skeletal muscle. 1-Methylhistidine is a biomarker for the consumption of meat, especially red meat.".
biodb.DEBUG[2025-04-05 16:04:24.238][private$doSearchForEntries] fields NAMES = description
biodb.DEBUG[2025-04-05 16:04:24.239][private$doSearchForEntries] fields VALUES = 1-Methylhistidine, also known as 1-MHis, belongs to the class of organic compounds known as histidine and derivatives. Histidine and derivatives are compounds containing cysteine or a derivative thereof resulting from a reaction of cysteine at the amino group or the carboxy group, or from the replacement of any hydrogen of glycine by a heteroatom. 1-Methylhistidine is derived mainly from the anserine of dietary flesh sources, especially poultry. The enzyme, carnosinase, splits anserine into beta-alanine and 1-MHis. High levels of 1-MHis tend to inhibit the enzyme carnosinase and increase anserine levels. Conversely, genetic variants with deficient carnosinase activity in plasma show increased 1-MHis excretions when they consume a high meat diet. Reduced serum carnosinase activity is also found in patients with Parkinson's disease and multiple sclerosis and patients following a cerebrovascular accident. Vitamin E deficiency can lead to 1-methylhistidinuria from increased oxidative effects in skeletal muscle. 1-Methylhistidine is a biomarker for the consumption of meat, especially red meat.
biodb.DEBUG[2025-04-05 16:04:24.240][private$doSearchForEntries] fields VALUES = 1-Methylhistidine, also known as 1-MHis, belongs to the class of organic compounds known as histidine and derivatives. Histidine and derivatives are compounds containing cysteine or a derivative thereof resulting from a reaction of cysteine at the amino group or the carboxy group, or from the replacement of any hydrogen of glycine by a heteroatom. 1-Methylhistidine is derived mainly from the anserine of dietary flesh sources, especially poultry. The enzyme, carnosinase, splits anserine into beta-alanine and 1-MHis. High levels of 1-MHis tend to inhibit the enzyme carnosinase and increase anserine levels. Conversely, genetic variants with deficient carnosinase activity in plasma show increased 1-MHis excretions when they consume a high meat diet. Reduced serum carnosinase activity is also found in patients with Parkinson's disease and multiple sclerosis and patients following a cerebrovascular accident. Vitamin E deficiency can lead to 1-methylhistidinuria from increased oxidative effects in skeletal muscle. 1-Methylhistidine is a biomarker for the consumption of meat, especially red meat.
biodb.DEBUG[2025-04-05 16:04:24.252][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-04-05 16:04:24.254][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-04-05 16:04:24.256][private$doGetEntryIds] .doGetEntryIds 10
biodb.DEBUG[2025-04-05 16:04:24.258][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-04-05 16:04:24.259][private$doGetEntryIds] .doGetEntryIds 11
biodb.DEBUG[2025-04-05 16:04:24.272][private$doListFiles] List files in C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^.*\.xml$.
biodb.DEBUG[2025-04-05 16:04:24.273][cch$listFiles] Extracting accession number from file names associated with hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^(.*)\.xml$
biodb.DEBUG[2025-04-05 16:04:24.275][cch$listFiles] files = HMDB0000001.xml, HMDB0000002.xml
biodb.DEBUG[2025-04-05 16:04:24.276][private$doGetEntryIds] COUNT IDS = 2
biodb.DEBUG[2025-04-05 16:04:24.277][private$doSearchForEntries] All IDs = [2]: "HMDB0000001, HMDB0000002"
biodb.DEBUG[2025-04-05 16:04:24.278][private$doSearchForEntries] Total number of IDs = 2
biodb.TRACE[2025-04-05 16:04:24.280][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-04-05 16:04:24.282][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-04-05 16:04:24.283][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:24.284][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:24.285][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-04-05 16:04:24.287][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-04-05 16:04:24.288][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:24.289][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:24.290][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-04-05 16:04:24.291][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-04-05 16:04:24.292][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:24.293][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:24.295][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-04-05 16:04:24.296][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-04-05 16:04:24.297][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:24.298][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-05 16:04:24.299][private$doSearchForEntries] MATCHED = TRUE
biodb.DEBUG[2025-04-05 16:04:24.301][private$doSearchForEntries] COUNT IDS = 1
biodb.DEBUG[2025-04-05 16:04:24.302][function(conn, opt)] With found IDs [1]: "HMDB0000001".
biodb.TRACE[2025-04-05 16:04:24.318][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-04-05 16:04:24.320][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-04-05 16:04:24.321][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:24.322][ef$get] fields variable is a list.
biodb.DEBUG[2025-04-05 16:04:24.324][function(conn, opt)] Testing searchForEntries() with entry "HMDB0000001" and field "secondary.accessions".
biodb.TRACE[2025-04-05 16:04:24.340][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-04-05 16:04:24.342][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-04-05 16:04:24.343][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:24.344][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:24.345][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-04-05 16:04:24.347][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-04-05 16:04:24.348][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:24.349][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:24.350][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-04-05 16:04:24.351][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-04-05 16:04:24.352][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:24.353][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-05 16:04:24.362][function(conn, opt)] With value "HMDB00001".
biodb.DEBUG[2025-04-05 16:04:24.363][private$doSearchForEntries] fields NAMES = secondary.accessions
biodb.DEBUG[2025-04-05 16:04:24.364][private$doSearchForEntries] fields VALUES = HMDB00001
biodb.DEBUG[2025-04-05 16:04:24.365][private$doSearchForEntries] fields VALUES = HMDB00001
biodb.DEBUG[2025-04-05 16:04:24.367][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-04-05 16:04:24.369][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-04-05 16:04:24.371][private$doGetEntryIds] .doGetEntryIds 10
biodb.DEBUG[2025-04-05 16:04:24.372][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-04-05 16:04:24.374][private$doGetEntryIds] .doGetEntryIds 11
biodb.DEBUG[2025-04-05 16:04:24.375][private$doListFiles] List files in C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^.*\.xml$.
biodb.DEBUG[2025-04-05 16:04:24.377][cch$listFiles] Extracting accession number from file names associated with hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^(.*)\.xml$
biodb.DEBUG[2025-04-05 16:04:24.378][cch$listFiles] files = HMDB0000001.xml, HMDB0000002.xml
biodb.DEBUG[2025-04-05 16:04:24.379][private$doGetEntryIds] COUNT IDS = 2
biodb.DEBUG[2025-04-05 16:04:24.380][private$doSearchForEntries] All IDs = [2]: "HMDB0000001, HMDB0000002"
biodb.DEBUG[2025-04-05 16:04:24.381][private$doSearchForEntries] Total number of IDs = 2
biodb.TRACE[2025-04-05 16:04:24.383][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-04-05 16:04:24.385][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-04-05 16:04:24.386][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:24.387][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:24.388][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-04-05 16:04:24.389][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-04-05 16:04:24.391][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:24.392][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:24.393][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-04-05 16:04:24.394][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-04-05 16:04:24.395][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:24.396][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:24.398][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-04-05 16:04:24.399][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-04-05 16:04:24.400][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:24.401][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-05 16:04:24.402][private$doSearchForEntries] MATCHED = TRUE
biodb.DEBUG[2025-04-05 16:04:24.403][private$doSearchForEntries] COUNT IDS = 1
biodb.DEBUG[2025-04-05 16:04:24.404][function(conn, opt)] With found IDs [1]: "HMDB0000001".
biodb.INFO [2025-04-05 16:04:24.427][biodb::testThat]
biodb.INFO [2025-04-05 16:04:24.428][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2025-04-05 16:04:24.429][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-04-05 16:04:24.430][biodb::testThat]
biodb.TRACE[2025-04-05 16:04:24.445][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-05 16:04:24.446][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-05 16:04:24.448][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:24.449][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:24.450][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-05 16:04:24.451][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-05 16:04:24.452][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:24.453][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:24.454][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-05 16:04:24.456][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-05 16:04:24.457][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:24.458][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-05 16:04:24.471][private$doSearchForEntries] fields NAMES = name
biodb.DEBUG[2025-04-05 16:04:24.472][private$doSearchForEntries] fields VALUES = 1-Methylhistidine
biodb.DEBUG[2025-04-05 16:04:24.473][private$doSearchForEntries] fields VALUES = 1-Methylhistidine
biodb.DEBUG[2025-04-05 16:04:24.475][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-04-05 16:04:24.477][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-04-05 16:04:24.479][private$doGetEntryIds] .doGetEntryIds 10
biodb.DEBUG[2025-04-05 16:04:24.481][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-04-05 16:04:24.482][private$doGetEntryIds] .doGetEntryIds 11
biodb.DEBUG[2025-04-05 16:04:24.483][private$doListFiles] List files in C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^.*\.xml$.
biodb.DEBUG[2025-04-05 16:04:24.485][cch$listFiles] Extracting accession number from file names associated with hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^(.*)\.xml$
biodb.DEBUG[2025-04-05 16:04:24.486][cch$listFiles] files = HMDB0000001.xml, HMDB0000002.xml
biodb.DEBUG[2025-04-05 16:04:24.487][private$doGetEntryIds] COUNT IDS = 2
biodb.DEBUG[2025-04-05 16:04:24.488][private$doSearchForEntries] All IDs = [2]: "HMDB0000001, HMDB0000002"
biodb.DEBUG[2025-04-05 16:04:24.489][private$doSearchForEntries] Total number of IDs = 2
biodb.TRACE[2025-04-05 16:04:24.492][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-05 16:04:24.493][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-05 16:04:24.494][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:24.495][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:24.496][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-05 16:04:24.498][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-05 16:04:24.499][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:24.500][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:24.501][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-05 16:04:24.502][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-05 16:04:24.503][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:24.505][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:24.506][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-05 16:04:24.507][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-05 16:04:24.508][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:24.509][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-05 16:04:24.511][private$doSearchForEntries] MATCHED = TRUE
biodb.DEBUG[2025-04-05 16:04:24.512][private$doSearchForEntries] COUNT IDS = 1
biodb.INFO [2025-04-05 16:04:24.534][biodb::testThat]
biodb.INFO [2025-04-05 16:04:24.535][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2025-04-05 16:04:24.536][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-04-05 16:04:24.537][biodb::testThat]
biodb.TRACE[2025-04-05 16:04:24.564][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-04-05 16:04:24.565][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-04-05 16:04:24.567][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:24.568][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:24.569][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-04-05 16:04:24.570][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-04-05 16:04:24.571][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:24.573][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:24.574][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-04-05 16:04:24.575][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-04-05 16:04:24.576][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:24.577][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:24.579][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-04-05 16:04:24.580][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-04-05 16:04:24.582][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:24.583][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:24.620][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-04-05 16:04:24.621][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-04-05 16:04:24.622][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:24.623][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:24.625][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-04-05 16:04:24.626][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-04-05 16:04:24.627][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:24.628][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:24.629][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-04-05 16:04:24.631][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-04-05 16:04:24.632][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:24.633][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:04:24.634][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-04-05 16:04:24.635][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-04-05 16:04:24.636][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:04:24.637][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2025-04-05 16:04:24.647][biodb::testThat]
biodb.INFO [2025-04-05 16:04:24.648][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2025-04-05 16:04:24.649][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-04-05 16:04:24.650][biodb::testThat]
biodb.INFO [2025-04-05 16:04:24.661][biodb::testThat]
biodb.INFO [2025-04-05 16:04:24.662][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2025-04-05 16:04:24.664][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-04-05 16:04:24.665][biodb::testThat]
biodb.INFO [2025-04-05 16:04:24.675][biodb::testThat]
biodb.INFO [2025-04-05 16:04:24.677][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2025-04-05 16:04:24.678][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-04-05 16:04:24.679][biodb::testThat]
biodb.DEBUG[2025-04-05 16:04:24.683][function(conn, opt)] Trying to download "http://www.hmdb.ca/metabolites/HMDB0000001".
biodb.DEBUG[2025-04-05 16:04:50.004][getUrlContent] Use RCurl for downloading content of URL http://www.hmdb.ca/metabolites/HMDB0000001.
biodb.INFO [2025-04-05 16:04:50.074][biodb::testThat]
biodb.INFO [2025-04-05 16:04:50.076][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2025-04-05 16:04:50.077][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-04-05 16:04:50.078][biodb::testThat]
biodb.DEBUG[2025-04-05 16:05:17.207][getUrlContent] Use RCurl for downloading content of URL http://www.hmdb.ca/structures/HMDB0000001/image.png.
biodb.TRACE[2025-04-05 16:05:17.272][ef$get] Asked field names are: name.
biodb.TRACE[2025-04-05 16:05:17.273][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-04-05 16:05:17.275][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:05:17.276][ef$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:05:17.288][ef$get] Asked field names are: description.
biodb.TRACE[2025-04-05 16:05:17.292][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-04-05 16:05:17.293][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:05:17.295][ef$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:05:17.296][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-04-05 16:05:17.298][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-04-05 16:05:17.299][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:05:17.300][ef$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:05:17.302][ef$get] Asked field names are: name.
biodb.TRACE[2025-04-05 16:05:17.303][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-04-05 16:05:17.304][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:05:17.305][ef$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:05:17.306][ef$get] Asked field names are: description.
biodb.TRACE[2025-04-05 16:05:17.307][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-04-05 16:05:17.309][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:05:17.310][ef$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:05:17.311][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-04-05 16:05:17.312][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-04-05 16:05:17.313][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:05:17.314][ef$get] fields variable is a list.
biodb.INFO [2025-04-05 16:05:17.315][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2025-04-05 16:05:17.317][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector hmdb.metabolites from the request scheduler
biodb.INFO [2025-04-05 16:05:17.318][self$deleteConn] Connector "hmdb.metabolites" deleted.
biodb.DEBUG[2025-04-05 16:05:17.319][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-04-05 16:05:17.320][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-05 16:05:17.321][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-05 16:05:17.322][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-05 16:05:17.323][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-05 16:05:17.324][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-04-05 16:05:17.325][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 147 ]
> 
> proc.time()
   user  system elapsed 
   5.39    0.48   58.17

'R CMD check' output

##############################################################################
##############################################################################
###
### Running command:
###
###   E:\biocbuild\bbs-3.21-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_1.13.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'E:/biocbuild/bbs-3.21-bioc-longtests/meat/biodbHmdb.Rcheck'
* using R Under development (unstable) (2025-03-01 r87860 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.3.0
    GNU Fortran (GCC) 13.3.0
* 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 '1.13.0'
* 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 'E:/biocbuild/bbs-3.21-bioc-longtests/meat/biodbHmdb.Rcheck/00install.out' for details.
* used C++ compiler: 'G__~1.EXE (GCC) 14.2.0'
* 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'
 OK
* DONE

Status: 2 WARNINGs, 1 NOTE
See
  'E:/biocbuild/bbs-3.21-bioc-longtests/meat/biodbHmdb.Rcheck/00check.log'
for details.

Installation output

biodbHmdb.Rcheck/00install.out

* installing *source* package 'biodbHmdb' ...
** this is package 'biodbHmdb' version '1.13.0'
** using staged installation
** libs
using C++ compiler: 'G__~1.EXE (GCC) 14.2.0'
g++ -std=gnu++17  -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rcpp/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/testthat/include'   -I"C:/rtools45/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"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rcpp/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/testthat/include'   -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign    -c FileEntryMaker.cpp -o FileEntryMaker.o
g++ -std=gnu++17  -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rcpp/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/testthat/include'   -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign    -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++17  -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rcpp/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/testthat/include'   -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign    -c StringEnrtryMaker.cpp -o StringEnrtryMaker.o
g++ -std=gnu++17  -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rcpp/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/testthat/include'   -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign    -c TagDetector.cpp -o TagDetector.o
g++ -std=gnu++17  -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rcpp/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/testthat/include'   -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign    -c XmlSplitter.cpp -o XmlSplitter.o
g++ -std=gnu++17  -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rcpp/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/testthat/include'   -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign    -c extractXmlEntries.cpp -o extractXmlEntries.o
g++ -std=gnu++17  -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rcpp/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/testthat/include'   -I"C:/rtools45/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"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rcpp/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/testthat/include'   -I"C:/rtools45/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"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rcpp/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/testthat/include'   -I"C:/rtools45/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"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rcpp/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/testthat/include'   -I"C:/rtools45/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:/rtools45/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools45/x86_64-w64-mingw32.static.posix/lib -LE:/biocbuild/bbs-3.21-bioc/R/bin/x64 -lR
installing to E:/biocbuild/bbs-3.21-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)